Transmission dynamics of Escherichia coli sequence type 131 in households – a “One Health” prospective cohort study

Transmission dynamics of Escherichia coli sequence type 131 in households – a “One Health” prospective cohort study | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Transmission dynamics of Escherichia coli sequence type 131 in households – a “One Health” prospective cohort study Yin Mo, Rebecca Perez, Hao Chung The, Kithalakshmi Vignesvaran, and 14 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5861827/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 26 Sep, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Escherichia coli sequence type 131 (ST131) is a major cause of community-onset, multidrug-resistant extraintestinal infections. The transmission and carriage dynamics associated with E. coli ST131’s global prevalence remain poorly understood. We collected up to twelve sequential stool samples from 135 human participants and six companion animals and environmental swabs from 34 households, sequencing up to twelve isolates per sample. Each household included an index patient with prior extraintestinal E. coli infection (17 with ST131, 17 with other sequence types) and their coresidents. While most participants carried E. coli ST131 intermittently, we identified a subset of participants that persistently carried E. coli ST131 in high densities (57·79% of E. coli isolates per sample) for a median carriage duration of 86·35 days (80% credible interval (CrI) 30·03 to 188·80). Coresiding with a persistent carrier was associated with an almost-doubled risk of acquiring E. coli ST131 (3·13% daily risk (80% CrI 1·22 to 10·14) versus 1·57% (80% CrI 0·65 to 5·19)). Persistent carriers and their coresidents carried genetically similar ST131 isolates (median single nucleotide polymorphism distance 2, interquartile range 2 to 7), but persistent carriers harboured greater diversity, suggesting that they were the source of inter-individual transmissions. Our results demonstrate that asymptomatic, persistent carriers represent potential reservoirs sustaining community E. coli ST131 transmissions. In identifying this subgroup, we highlight a potential target for public health interventions such as vaccination to limit the spread of multidrug resistance. Health sciences/Medical research/Epidemiology Health sciences/Pathogenesis/Infection Escherichia coli sequence type 131 antimicrobial resistance transmission dynamics Figures Figure 1 Figure 2 Figure 3 Figure 4 INTRODUCTION Escherichia coli sequence type 131 ( E. coli ST131) clone has disseminated rapidly worldwide since it was identified in 2008. 1 E. coli ST131 is an important cause of community-onset bloodstream and urinary tract infections, accounting for up to 30% of all E. coli infections globally. 1 The rising prevalence of this clone is associated with increasing multidrug resistance (MDR) observed in E. coli infections, particularly against fluoroquinolones and third generation cephalosporins, severely limiting antibiotic treatment options. Among E. coli ST131’s three sub-lineages, clades A, B and C, subclades H30R/C1 and H30Rx/C2 have dominated the spread of E. coli ST131. 2 These fluoroquinolone-resistant subclades possess the fimH30 allele and are the most frequently associated with CTX-M-class beta-lactamase alleles, especially blaCTX-M-15. These alleles are responsible for extended-spectrum beta-lactamase (ESBL) production and confer resistance to third-generation cephalosporins and carbapenems. CTX-M-type enzymes are currently recognised as the most common ESBL type globally. 2 The transmission dynamics of E. coli ST131 driving its global success remain poorly understood. 3 Cross-sectional epidemiological studies suggested that E. coli ST131 acquisition often occurs through person-to-person transmission, particularly within the community rather than healthcare settings. 4 – 6 However, there is limited understanding of the reservoirs and drivers of E. coli ST131 transmission in terms of demographic characteristics and community contact patterns. Delineating the transmission dynamics of E. coli ST131 is crucial in designing infection control and public health measures to curb its associated morbidity and mortality. In this prospective cohort study, we adopted a longitudinal, One Health sampling approach to identify the transmission pathways of E. coli ST131 as a gut colonising strain in households. We quantified the carriage duration and acquisition risks of E. coli ST131 via Markov models and mapped transmission events using both epidemiological and genomic data. The overall aim of this study was to clarify the transmission dynamics associated with asymptomatic E. coli ST131 carriage to identify key targets for control interventions. METHODS Participant enrolment and follow-up From February 2017 to November 2018, we screened and enrolled patients of all ages admitted to the National University Hospital, Singapore, whose urine or blood cultures performed for clinical indications were positive for E. coli . Patients and their household coresidents that provided consent were recruited into the longitudinal prospective study. Study participants completed a baseline questionnaire on demographics, lifestyle, familial relationships and interactions, dietary habits, medical history, and travel history. Home visits were conducted at two to six-weekly intervals over a 12-month period, during which participants and their companion animals (if applicable) provided stool samples. Environmental and food sampling was performed during the first home visit. Environmental samples included swabs of high-touch surfaces, such as kitchen counters, doorknobs, and toilet bowls using standard methods. 7 Food samples were taken from both raw and cooked meat and vegetables. Ethics approval was obtained from the National Healthcare Group Domain Specific Review Board (Reference: 2016/00998). Identification of E. coli ST131 from clinical, stool, food and environmental samples All samples were cultured on UriSelect™ 4 medium, a chromogenic medium used for E. coli detection and isolation. Up to 12 colonies per sample were randomly picked from the initial culture plates. Species identifications were confirmed using matrix-assisted laser desorption/ionisation and time-of-flight mass spectrometry (MALDI-TOF) spectrometry. E. coli isolates were tested for ST131 via polymerase chain reaction (qPCR) targeting the putative manganese transferase gene ( mntH ). 8 qPCR was performed using the CFX96 TouchTM Real-Time PCR Detection System, with the iTaq Universal SYBR Green Supermix (Bio-Rad Laboratories, Inc) and cycling conditions according to previously validated protocol. 8 All E. coli isolates identified as ST131 by qPCR were subjected to whole genome sequencing (WGS) and antibiotic susceptibility testing (appendix pp 11). Subsequently in this manuscript, E. coli ST131 isolates referred to are those confirmed with WGS. Statistical analysis and mathematical modelling Descriptive and statistical analyses were performed using the following definitions. A sample was considered positive for E. coli ST131 if at least one of the E. coli isolates recovered from the sample was confirmed to be E. coli ST131. The density of E. coli ST131 for each sample was calculated using the number of E. coli ST131 isolates divided by the total number of E. coli isolates recovered from the sample. A participant was considered a carrier of E. coli ST131 if any of their stool samples were positive for E. coli ST131. Participants with at least two sequential E. coli ST131 positive samples were considered “persistent carriers”. All other carriers, i.e. those who had one isolated positive sample or had more than one positive sample but interspersed between negative samples, were considered “intermittent carriers”. We performed sensitivity analysis by defining persistent carriers as those who carried E. coli ST131 for at least three sequential time points and intermittent carriers as those with no more than two sequential positive stool samples. To identify risk factors associated with E. coli ST131 carriage and with persistent carrier status, univariable and multivariable logistic regression analyses were conducted. Independent variables assessed in these regressions were selected following literature review, and included sex, age, time spent at home, comorbidities (including chronic metabolic conditions, major organ failures and cancer), urinary incontinence, use of medical devices, antibiotic use in the past six months, and hospital admittance within the past year. 9 – 13 We also included carriage status subgroups (persistent carriers, intermittent carriers who were coresident with a persistent carrier, all other intermittent carriers, non-carriers) as a categorical independent variable. A two-state Markov model was constructed to assess transition rates between non-carrier and carrier states for individual participants. We chose not to model carriage at the household level, given that household sizes in our study population ranged from two to eight members, and analysis would necessitate subsetting households by size, resulting in small sample sizes for each group with weak statistical power. In this model, the transition of individuals between non-carrier and carrier states was assumed to be a Markov process, in which the probability of a particular carrier status at the next time point depends only upon carrier status at the current time point and not on the status at earlier time points (appendix pp 7). The model was fit to each carriage status subgroup to explore differences in carriage and acquisition among these groups. The two-state Markov model was supplemented by a Hidden Markov Model, which incorporated the potential for false negative qPCR and culturing when screening for E. coli ST131. These false negatives would have resulted in E. coli ST131 isolates not being eventually sequenced and confirmed via WGS. In this model, we estimated carriage duration with underlying false negative rates of up to 20% (appendix pp 2). Phylogenetic analysis For all assemblies determined as E. coli ST131 by multilocus sequence typing (MLST), a maximum-likelihood phylogeny was constructed with RAxML-NG v1·2·2 with 100 bootstrap replicates using the single nucleotide polymorphism (SNP)-only core-genome alignment (alignment length: 7466 base pairs (bp)). 14 Pairwise SNP distance between isolates was calculated using the snp-dists programme (appendix pp 8). 15 For households which had persistent carriers and provided > 20 E. coli ST131 genomes, we further investigated the genomic variation of E. coli ST131 by mapping paired-end reads to an E. coli ST131 reference genome with bwa-mem v0.7.17. High-quality SNPs were identified using Freebayes v1.3.7 (appendix pp 8). Statistical analyses were conducted with R version 4.3.3, using RStan 16 (for the primary Markov model) and msm packages (for the Hidden Markov Model). 17 Visualisation of phylogenetic analysis was conducted in R version 4.3.1, using R packages ggplot2 and ggtree. 18 All analysis code is available publicly at https://github.com/rebeccalperez/ST131_Transmission_Dynamics_SG . RESULTS From February 2017 to November 2018, 135 participants from 34 households were enrolled (figure 1). The 34 index patients were initially identified from 355 consecutive hospitalised patients who had E. coli extraintestinalinfections. Seventeen of these index patients were previously infected with E. coli ST131 and the other 17 were previously infected with other E. coli STs (table 1). By end-of-study, 124 participants provided at least one stool sample. One index patient did not provide any stool samples, but their household coresidents did. The median age at enrolment was 38·16 years (IQR 23·88 to 62·03), with 16 participants (12·90%) under the age of two. Seventy-four participants (59·68%) were female. The median household size was four (interquartile range (IQR) 3 to 5). Fifty-one participants (41·13%) had chronic diseases, including cancer, diabetes, or heart diseases. Forty-eight (38·71%) took antibiotics within the six months prior to enrolment. The majority (87·10%) spent more than 30 hours at home per week. The participants provided stool samples over a median of 141·5 (IQR 86·5 to 220·0) days. In total, 601 human stool samples, 35 companion animal stool samples (from four cats and two birds), 127 environmental swabs and 73 food samples were collected. The median number of stool samples per human study participant was five (IQR 3 to 6), collected at a median of 28-day intervals (IQR 19 to 50). From these samples, 6559 E. coli isolates were recovered, of which 354 (5·15%) were confirmed E. coli ST131 by WGS. The majority of E. coli ST131 isolates were obtained from human samples (95·48%, 338/354). The remaining 16 E. coli ST131 isolates included three from domestic animals, two from food, and 11 from environmental sources. Out of the 338 human-source E. coli ST131 isolates, 135 (41·16%) were clade A, 23 (7·01%) were clade B, and 170 (51·83%) were clade C (including 122 in subclade C1-M27 (72·76%) and 48 in subclade C2 (28·24%). Coresidents were more likely to carry clade A than index patients (83% of E. coli ST131 isolates from coresidents were clade A, versus 53% of E. coli ST131 isolates from index patients (p < 0·001). Among 545 human-source E. coli isolates, resistance to more than two classes of antibiotics was greater among E. coli ST131 clades A (71·26%, 62/87) and C (75·93%, 82/108) in comparison to clade B (23·53%, 4/17) and non-ST131 E. coli (22·52%, 75/333). None were resistant to carbapenems (appendix pp 7). Asymptomatic E. coli ST131 carriage amongst index patients Amongst the 34 index patients, 22 had urinary tract infections while the other 12 had bloodstream infections. The proportion of E. coli ST131carriers amongst those infected with E. coli ST131and those infected with other E. coli STs were similar (6/16, 37·50% versus 6/17, 35·29%, respectively). However, E. coli ST131 carriers amongst index patients previously infected with E. coli ST131 had a longer carriage duration than those previously infected with other E. coli STs (median duration 59·71, 80% CrI 33·92 to 111·83 versus 16·97, 80% CrI 3·49 to 45·52 days, appendix pp 9). In addition, the density of E. coli ST131 in each stool sample was higher in index patients who were infected with E. coli ST131 (0·69 versus 0·27, p = 0·007, appendix pp 9) than those infected with other E. coli STs. Duration and density of E. coli ST131 carriage in the overall study population The majority of households (64·71%, 22/34) had at least one E. coli ST131 carrier (table 1). The overall prevalence of E. coli ST131 carriage in individuals was 33·06% (41/124). Similar proportions of E. coli ST131 carriers were found in households with an index patient previously infected with E. coli ST131 and those with an index patient previously infected with other E. coli STs . However, E. coli ST131 carriers living with an index patient with previous E. coli ST131 infection had more stool samples positive for E. coli ST131 during the study period and also carried E. coli ST131 at higher densities (table 1). Out of the E. coli ST131 carriers, the majority (78·05%, 32/41) carried E. coli ST131 intermittently. Nine E. coli ST131 carriers persistently carried E. coli ST131 for at least two consecutive time points. These persistent carriers had a median carriage duration of 86·35 days (80% CrI 30·03 to 187·80), whereas intermittent carriers had median carriage duration for 2·26 days (80% CrI 0·52 to 6·00) (figure 3A). The mean density of E. coli ST131 in positive stool samples collected from thepersistent carriers was 57·79%, compared with 36·06% among intermittent carriers (figure 2). When stratified by clade, median carriage duration for clade A, the most commonly isolated clade, was 35·33 days (80% CrI 23·81 to 52·47), longer than for clade C which was 21·55 days (80% CrI 14·14 to 33·28). Risk of E. coli ST131 carriage and acquisition None of the epidemiological risk factors, including age, sex, time spent at home per week, comorbidities, incontinence, medical devices including urinary catheter, antibiotic intake in the past six months, and hospital stay in the past year, were associated with E. coli ST131 carriage in both multivariable and univariable regression analyses (appendix pp 10). Similarly, there were no demographic or clinical risk factors associated with the status of being a persistent carrier (appendix pp 10). Daily probabilities of acquiring E. coli ST131 carriage amongst persistent carriers and coresidents of persistent carriers were 3·92% (80% CrI 2·01% to 11·11%) and 3·13% (80% CrI 1·22% to 10·14%), respectively. Amongst those who did not live with persistent carriers, daily acquisition probability was lower at 1·57% (80% CrI 0·65% to 5·19%). By clade, daily probability of acquisition was 0·16% (80% CrI 0·11% to 0·24%) and 0·26% (80% CrI 0·17% to 0·40%) for E. coli ST131 clades A and C, respectively. Sensitivity analyses found similar results when defining persistent carriers as detection of E. coli ST131 at three or more consecutive time points (appendix pp 3) and assuming a 20% false negative rate during screening for E. coli ST131 (appendix pp 5). Phylogenetic analysis for household transmissions of E. coli ST131 Phylogenetic grouping showed that each defined phylogenetic cluster (PC) consisted of genomes derived from single households (figure 4A). However, six households (households 3, 8, 9, 20, 21, 32 in figure 4A) had more than one PCs present across different clades including A, B, C1, and C2, highlighting the diverse E. coli ST131 populations in these households. Inter-individual genetic distance of E. coli ST131 was markedly different when comparing within-household and between-household. The median within-household pairwise SNP distance was 2 (IQR 1 to 7), while the between-household equivalent was 3777 (IQR 108 to 3794) (figure 4B). Focusing on the four households which included at least one persistent carrier and contributed at least 20 E. coli ST131 genomes (households 2, 8, 11, 34 in figure 4C), we performed high-resolution phylogenetic inferences (figure 4C). Notably, E. coli ST131 from persistent carriers had minimal SNP distances to sequenced ST131 isolates from within-household coresidents (figure 4C). In two households (households 11 and 34 in figure 6), persistent carriers (participants 11D and 34A in figure 4C) had higher E. coli ST131 genomic diversity than their coresident carriers. This evidence suggested that persistent carriers were the source of E. coli ST131 dissemination in their respective households. DISCUSSION In this prospective cohort study of asymptomatic E. coli ST131 carriage in households, we found two distinct patterns of carriage: persistent, high-density carriage and intermittent, low-density carriage. Individuals living with persistent, high-density carriers acquired E. coli ST131 at twice the rate of those who were not coresident with a persistent carrier. Genomic evidence showed that these persistent carriers shared genetically similar E. coli ST131 isolates with their household members and harboured greater E. coli ST131 diversity. This indicated that the persistent carriers were the likely source of E. coli ST131 in their respective households, with coresident colonisation resulting from transmissions of a single strain from the source persistent carriers. Our findings carry important implications for controlling the spread of E. coli ST131, identifying that a subset of individuals may carry E. coli ST131 asymptomatically for longer-than-average durations and act as a reservoir for spread to close contacts. These persistent carriers may be suitable candidates for infection prevention and control measures for E. coli ST131 in the community setting, such as the Extraintestinal Pathogenic E. coli 9-valent vaccine currently undergoing phase three clinical trial, 19 or decolonisation strategies. Given the infeasibility of finding these asymptomatic reservoirs in the community, individuals with a history of E. coli ST131 infection may be priority candidates for these prevention measures given that they were more likely to be persistent carriers. The importance of persistent asymptomatic carriers as drivers of pathogenic Gram-negative bacteria transmission has been well-described in Salmonella spp. 20 , 21 and Vibrio cholerae . However, unlike Salmonella spp. and V. cholerae , E. coli is a common gut commensal, and many serotypes can be carried concurrently, making it challenging to identify and trace its transmission. Our systematic and longitudinal approach, which included up to 12 time points at two- to six-week intervals, provided high-resolution data and allowed application of multistate Markov models to estimate carriage duration and inter-individual transmission rates. Furthermore, we obtained up to 12 individual colonies per sample, which allowed us to ascertain the density of carriage. This wealth of isolates per sample also permitted the assessment of genomic diversity within individuals and households, demonstrating the extent of strain sharing in some households with persistent carriers. We acknowledge several limitations in our study. Firstly, despite collecting up to 12 E. coli colonies per sample, microbiology cultures and qPCR may have missed E. coli ST131 isolates. This would have led to an underestimation of carriage duration, transmission rates, and number of persistent, high-density carriers. To assess the potential impact of these missed isolates, we fitted a Hidden Markov Model to our data, which found that estimates under assumptions of perfect observation fell within the credible intervals of estimates obtained assuming between 1 to 20% negative samples are true positives (appendix pp 3). Further, given that we only identified nine persistent carriers, our assessment of risk factors associated with persistent carrier status may have been underpowered due to small sample size. Secondly, the definition of at least two sequential E. coli ST131 positive samples for persistent carriage was arbitrary. The description of persistent carriage was meant to illustrate heterogeneity in carriage duration and risk of transmission to coresidents, and not to impose strict definitions on carrier types. Nonetheless, we performed sensitivity analyses using three sequential time points as the lower bound for defining persistent carriage, which produced similar estimates (appendix pp 2). Lastly, despite intense within-individual sampling, the limited genomic variation rendered transmission directionality inconclusive in many cases. In conclusion, asymptomatic persistent carriers are potential reservoirs for E. coli ST131 spread to household contacts in the community setting. Further investigation to identify the risk factors for these persistent carriers will be critical, as these groups represent a potential infection prevention and control target for mitigating the spread of E. coli ST131, a highly prevalent and antimicrobial resistant strain in the community. Declarations Supplementary information Supplementary Information is available for this paper. Competing interests The authors have no competing interests to declare. Author contributions MY, RB and PAT conceptualised and designed the study. MY and PAT obtained funding for the study. MY, KV, MCSH, TEY, PSY, ZL, WY and IS implemented the study and performed home visits. KV, MCSH, TEY, PSY, ZL, JT and WCT performed microbiology cultures and PCR testing. KTA performed antibiotic susceptibility testing. SRS, CYT, HCT and RTHO performed genomic analysis. RP, MY and BSC performed statistical analysis and mathematical modelling. RP, HCT and KV wrote the first draft of the manuscript. All authors contributed to the review and finalisation of the manuscript. Acknowledgements This study was funded by the Singapore Medical Research Council via the Master of Clinical Investigation course facilitated by the National University of Singapore (grant number: CG21APR2005) References Chen, S. L. et al. The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone. Sci. Rep. 9 , 13245 (2019). Doerr, N., Dietze, N., Lippmann, N. & Rodloff, A. C. Extended-spectrum beta-lactamases found in Escherichia coli isolates obtained from blood cultures and corresponding stool specimen. Sci. Rep. 13 , 8940 (2023). Kallonen, T. et al. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Res. 27 , 1437–1449 (2017). Johnson, J. R. et al. Intestinal Persistence of Colonizing Escherichia coli Strains, Especially ST131- H 30, in Relation to Bacterial and Host Factors. J. Infect. Dis. 225 , 2197–2207 (2022). Sarkar, S. et al. Intestinal Colonization Traits of Pandemic Multidrug-Resistant Escherichia coli ST131. J. Infect. Dis. 218 , 979–990 (2018). Mohamed, M. et al. Large Fecal Reservoir of Escherichia coli Sequence Type 131-H30 Subclone Strains That Are Shared Within Households and Resemble Clinical ST131-H30 Isolates. J. Infect. Dis. 221 , 1659–1668 (2020). Guo, S. et al. Prevalence and genomic analysis of ESBL-producing Escherichia coli in retail raw meats in Singapore. J. Antimicrob. Chemother. 76 , 601–605 (2021). Doumith, M. et al. Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections. J. Clin. Microbiol. 53 , 160–166 (2015). Rogers, B. A. et al. Prolonged carriage of resistant E. coli by returned travellers: clonality, risk factors and bacterial characteristics. Eur. J. Clin. Microbiol. Infect. Dis. 31 , 2413–2420 (2012). Brodrick, H. J. et al. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom. Genome Med. 9 , 70 (2017). Rodrigues, C., Machado, E., Fernandes, S., Peixe, L. & Novais, Â. Different Escherichia coli B2-ST131 clades (B and C) producing extended-spectrum β -lactamases (ESBL) colonizing residents of Portuguese nursing homes. Epidemiol. Infect. 145 , 3303–3306 (2017). Toombs-Ruane, L. J. et al. Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study. Int. J. Infect. Dis. 128 , 325–334 (2023). Van Der Putten, B. C. L. et al. Extraintestinal Pathogenic Escherichia Coli (ExPEC) Are Associated with Prolonged Carriage of Extended-Spectrum β-Lactamase-Producing E. Coli Acquired during Travel . http://biorxiv.org/lookup/doi/10.1101/2020.09.23.309856 (2020) doi:10.1101/2020.09.23.309856. Minh, B. Q. et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 37 , 1530–1534 (2020). Seemann, T. snp-dist. (2020). R Interface to Stan • rstan. https://mc-stan.org/rstan/. Jackson, C. Multi-State Models for Panel Data: The msm Package for R. J. Stat. Softw. 38 , 1–28 (2011). Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8 , 28–36 (2017). ClinicalTrials.gov. A Study of Vaccination With 9-Valent Extraintestinal Pathogenic Escherichia Coli Vaccine (ExPEC9V) in the Prevention of Invasive Extraintestinal Pathogenic Escherichia Coli Disease in Adults Aged 60 Years And Older With a History of Urinary Tract Infection in the Past 2 Years . https://clinicaltrials.gov/study/NCT04899336#more-information (2024). Devaraj, A. et al. Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi. PLOS Pathog. 17 , e1009209 (2021). Mbuyi-Kalonji, L. et al. Invasive non-typhoidal Salmonella from stool samples of healthy human carriers are genetically similar to blood culture isolates: a report from the Democratic Republic of the Congo. Front. Microbiol. 14 , 1282894 (2023). Table Table 1. Participant characteristics and E. coli ST131 carriage status. Participants with previous E. coli ST131 infection and their coresidents (n = 63) Participants with previous infection with other E. coli STs and their coresidents (n = 61) p-value Demographics Sex (%) Female 36 (57·14) 38 (62·30) 0·688 Male 27 (42·85) 23 (37·70) Mean age (SD) 41·68 (23·82) 41·52 (28·77) 0·973 Children under two years old (%) 7 (11·11) 9 (14.75) 0·549 Median household size (IQR) 5 (2·00) 4 (2·00) 0·068 Housing types (%) Public housing apartments 51 (80·95) 52 (85·25) 0·266 Condominium 8 (12·70) 3 (4·92) Landed property 4 (6·35) 6 (9·84) Vegetarian (%) 4 (6·35) 0 (0.00%) 0.046 International travel in the past year (%) 42 (66·67) 35 (57·38) 0·378 Spent more than 30 hours at home per week (%) 53 (84·13) 55 (90·16) 0·320 Chronic disease(s) # (%) 27 (42·86) 24 (39·34) 0·694 Incontinent (%) 12 (19·05) 11 (18·03) 1·000 Took antibiotics in the past six months (%) 27 (42·86) 21 (34·43) 0·436 E. coli ST131 carriage E. coli ST131 carriers (%) 24 (38·10) 17 (27·87) 0·230 Number of stool samples with at least one E. coli ST131 isolate (%) 46/289 (15·92) 24/312 (7·69) 0·001 Number of E. coli ST131 isolates recovered from stool samples (%) 249/2914 (8·54) 89/3359 (2·65) <0·001 Persistent E. coli ST131 carriers* (%) 7 (11·11) 2 (3·28) 0·094 # Chronic diseases included diabetes mellitus, hypertension, ischemic heart disease, cancer and other immunocompromising conditions. * Persistent carriage status was defined by the presence of at least one E. coli ST131 isolate in at least two consecutive stool samples. ST: sequence type; SD: standard deviation; IQR: interquartile range. Additional Declarations There is NO Competing Interest. Supplementary Files S1Supplementary3.pdf S1: Sensitivity analysis of persistent carrier status definition, defined by two or three sequential positive stool samples S2Supplementary.pdf S2: Hidden Markov model estimates of carriage duration with underlying assumption of false negative rates, the proportion of true positive samples that are falsely observed as negative samples, up to S3Supplementary1.pdf S3: Proportion of E. coli ST131, by sample and by isolate, derived from each source (human, domestic animal, environmental, and food) S4Supplementary.pdf S4: Antimicrobial susceptibility for all E. coli ST 131 isolates S5.docx S5: Clinical characteristics of persistent carriers and intermittent carriers S6Table2ST131.docx S6: E. coli sequence type (ST) 131 carriage characteristics for index patients infected with E. coli ST 131 and infected with other E. coli STs. S7RegressionAnalysisSubmission.pdf S7 SubmissionST131TransmissionDynamicsAppendixNatCommsJan10.docx Appendix Cite Share Download PDF Status: Published Journal Publication published 26 Sep, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5861827","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":408289824,"identity":"6db067e2-d0f3-4d25-becc-343a1a25974c","order_by":0,"name":"Yin Mo","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAv0lEQVRIiWNgGAWjYFCCBCCugDAlSNByhmQtjG2kaNFtT366mXfencT5DcwHb/Mw1Nk1ENJiduaZ2W3ebc8SNxxgS7bmYTicTFjLjRw2oJbDiRsYeMykeRgOJBN0GETLnMNAh/F/A2qpI1ZLw+HEhgM8bEAtzHaEtQD9cnPOscPGGw6zGVvOMTicQFjL8eRnN97UHJad39788Mabijp7glpAgIkHRDKDCAOGxAZitDD+QOIQZ8soGAWjYBSMKAAA9Iw+mNOMIDMAAAAASUVORK5CYII=","orcid":"","institution":"National University Hospital, Singapore","correspondingAuthor":true,"prefix":"","firstName":"Yin","middleName":"","lastName":"Mo","suffix":""},{"id":408289825,"identity":"def9e51c-f4a8-455f-a213-102ba66f3de4","order_by":1,"name":"Rebecca Perez","email":"","orcid":"https://orcid.org/0009-0006-8456-2749","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Rebecca","middleName":"","lastName":"Perez","suffix":""},{"id":408289826,"identity":"9514881f-db2b-4078-8444-51a47aeffe3b","order_by":2,"name":"Hao Chung The","email":"","orcid":"","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Hao","middleName":"Chung","lastName":"The","suffix":""},{"id":408289827,"identity":"e0b9ca9a-e5fe-4933-b6e9-2902efa85a6b","order_by":3,"name":"Kithalakshmi Vignesvaran","email":"","orcid":"","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Kithalakshmi","middleName":"","lastName":"Vignesvaran","suffix":""},{"id":408289828,"identity":"cff4e39f-1679-41e8-9472-3f626d46037b","order_by":4,"name":"Wei Cong Tan","email":"","orcid":"https://orcid.org/0009-0003-9648-2277","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Wei","middleName":"Cong","lastName":"Tan","suffix":""},{"id":408289829,"identity":"26483fb5-2664-4888-a7ed-fd8a87c101ef","order_by":5,"name":"Melissa Chua Sin Hui","email":"","orcid":"","institution":"National University Hospital, Singapore","correspondingAuthor":false,"prefix":"","firstName":"Melissa","middleName":"Chua Sin","lastName":"Hui","suffix":""},{"id":408289830,"identity":"8c189b80-23a5-430f-a8d0-5f59f01e76e8","order_by":6,"name":"En Ying Tan","email":"","orcid":"","institution":"National University Hospital, Singapore","correspondingAuthor":false,"prefix":"","firstName":"En","middleName":"Ying","lastName":"Tan","suffix":""},{"id":408289831,"identity":"de5e3823-3228-4768-9b9d-e33ae7d12865","order_by":7,"name":"Si Yu Peng","email":"","orcid":"","institution":"National University Hospital, Singapore","correspondingAuthor":false,"prefix":"","firstName":"Si","middleName":"Yu","lastName":"Peng","suffix":""},{"id":408289832,"identity":"6290e016-f0b4-48e7-bd83-c70ee68f112e","order_by":8,"name":"Lingyue Zhou","email":"","orcid":"","institution":"National University Hospital, Singapore","correspondingAuthor":false,"prefix":"","firstName":"Lingyue","middleName":"","lastName":"Zhou","suffix":""},{"id":408289833,"identity":"f1ee7bfe-73f5-4588-ac33-a79723652376","order_by":9,"name":"Shweta (R) Singh","email":"","orcid":"https://orcid.org/0000-0002-9182-8449","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Shweta","middleName":"(R)","lastName":"Singh","suffix":""},{"id":408289834,"identity":"6378afa3-a984-459e-8799-62b090e52521","order_by":10,"name":"Wesley Yeung","email":"","orcid":"","institution":"National University Hospital","correspondingAuthor":false,"prefix":"","firstName":"Wesley","middleName":"","lastName":"Yeung","suffix":""},{"id":408289835,"identity":"54c72010-a664-458a-8bf6-2e23f2dca0ec","order_by":11,"name":"Ivan Seah","email":"","orcid":"https://orcid.org/0000-0001-7843-1917","institution":"National University Hospital","correspondingAuthor":false,"prefix":"","firstName":"Ivan","middleName":"","lastName":"Seah","suffix":""},{"id":408289836,"identity":"6ab9c8a7-5949-42db-9978-97e4d4f272c9","order_by":12,"name":"Jeanette Teo","email":"","orcid":"","institution":"National University Hospital","correspondingAuthor":false,"prefix":"","firstName":"Jeanette","middleName":"","lastName":"Teo","suffix":""},{"id":408289837,"identity":"a6451c24-a191-41bc-ad16-1ef3bb738d99","order_by":13,"name":"Kyaw Thu Aung","email":"","orcid":"","institution":"Singapore Food Agency","correspondingAuthor":false,"prefix":"","firstName":"Kyaw","middleName":"Thu","lastName":"Aung","suffix":""},{"id":408289838,"identity":"b53950fc-2603-43cb-a1a0-01b29cc92047","order_by":14,"name":"Cheng Yee Tang","email":"","orcid":"","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Cheng","middleName":"Yee","lastName":"Tang","suffix":""},{"id":408289839,"identity":"2b25c956-fa06-4a2b-95e2-4bc59239db6b","order_by":15,"name":"Rick Ong","email":"","orcid":"","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Rick","middleName":"","lastName":"Ong","suffix":""},{"id":408289840,"identity":"06427fb8-b634-48d0-856e-adbcc8fbbd4f","order_by":16,"name":"Ben Cooper","email":"","orcid":"https://orcid.org/0000-0002-9445-7217","institution":"University of Oxford","correspondingAuthor":false,"prefix":"","firstName":"Ben","middleName":"","lastName":"Cooper","suffix":""},{"id":408289841,"identity":"1e526059-26a3-4d9f-ac37-d70247f8874c","order_by":17,"name":"Paul Tambyah","email":"","orcid":"","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Paul","middleName":"","lastName":"Tambyah","suffix":""}],"badges":[],"createdAt":"2025-01-20 01:55:06","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5861827/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5861827/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-025-63121-x","type":"published","date":"2025-09-26T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":75089365,"identity":"860f75f9-6c5c-4c8c-8fd5-654f8fd5d9fc","added_by":"auto","created_at":"2025-01-30 10:38:33","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":84091,"visible":true,"origin":"","legend":"\u003cp\u003eStudy enrolment flowchart.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/5883250fcab2ae560cb16194.png"},{"id":75087581,"identity":"896f5fa7-e5ef-493a-b57a-90b408f2964d","added_by":"auto","created_at":"2025-01-30 10:22:32","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":335868,"visible":true,"origin":"","legend":"\u003cp\u003eDensity of \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates identified per participant during follow-up. Persistent carriers, defined by having two or more consecutive stool samples which recovered \u003cem\u003eE. coli\u003c/em\u003e ST131, are highlighted in blue.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/3639577e8f199d5a7ff032d6.png"},{"id":75087582,"identity":"1a9c8a53-5632-4a85-b782-fbe75f4a8c0b","added_by":"auto","created_at":"2025-01-30 10:22:32","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":87653,"visible":true,"origin":"","legend":"\u003cp\u003eEstimates obtained for daily probability of acquisition and median duration of carriage of \u003cem\u003eE. coli \u003c/em\u003eST131. Estimates were calculated by: \u003cstrong\u003eFig 3A)\u003c/strong\u003e epidemiological participant subgroups, defined as i) persistent carriers, participants with at least two sequential samples positive for \u003cem\u003eE. coli \u003c/em\u003eST131 ii) intermittent carriers, those with no more than one sequential positive sample at a time, coresident with a persistent carrier and iii) all other intermittent carriers \u003cstrong\u003eFig 3B)\u003c/strong\u003e \u003cem\u003eE. coli \u003c/em\u003eST131 clades A and C, respectively (as identified by WGS). Clade B was not included in the analysis due to small sample size (\u0026lt;25 isolates obtained). All estimates were obtained using a two-state Markov model. Results are presented as median estimates with 80% credible intervals (CrI).\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/a96ba0d1b3e259f600a46ab0.png"},{"id":75087584,"identity":"6dacb4b1-b58d-4b28-b044-5777cdbedacd","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":461537,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogeny of \u003cem\u003eE. coli \u003c/em\u003eST131 isolates.\u003c/p\u003e\n\u003cp\u003e(A) Maximum likelihood phylogeny of 320 \u003cem\u003eE. coli \u003c/em\u003eST131 genomes sequenced for this study. \u003cem\u003eE. coli \u003c/em\u003eST131’s defined clade (A, B, C1, C2) was annotated to the phylogeny, based on \u003cem\u003eE. coli \u003c/em\u003eST131Typer output. The phylogeny is rooted using the basal clade A. Branches are coloured in accordance to bootstrap values, from low (light pink) to high (black). The rings present metadata associated with each taxon, in the following order (from inner to outermost): (1) household identity, (2) households with persistent carrier(s), and (3) presence of \u003cem\u003ebla\u003c/em\u003eCTX-M genes. Households with only one member yielding positive culture for \u003cem\u003eE. coli \u003c/em\u003eST131 (ID: 1, 4, 10, 12, 15, 23, 28) were masked and coloured grey.\u003c/p\u003e\n\u003cp\u003e(B) Inter-participant pairwise mutational SNP (single nucleotide polymorphism) distance of \u003cem\u003eE. coli\u003c/em\u003e ST131 genomes, classified by household membership of the examined pair (within and inter-household). The rectangular dashed box (lower panel) serves as a zoom-in subplot for part of the upper panel.\u003c/p\u003e\n\u003cp\u003e(C)\u003cstrong\u003e \u003c/strong\u003eGenomic variation of within-household \u003cem\u003eE. coli \u003c/em\u003eST131 in four households (2, 8, 11, 34) with persistent carriers. The upper panels detail the sampling schedule for each household (in days), with members named A to F. Stool samples positive and negative for \u003cem\u003eE. coli\u003c/em\u003e ST131 (via WGS results) are coloured in red and grey, respectively. Household members who have at least two consecutive \u003cem\u003eE. coli\u003c/em\u003e ST131 positive stool samples (persistent carriers) have names highlighted in orange, with positive duration denoted as red rectangular box. The lower panels provide the phylogenetic inferences of \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates recovered within each respective household. Phylogenies were constructed using a parsimony approach (see Methods), with branch lengths denoting estimated single nucleotide polymorphisms (SNPs; see scale bars). Tree tips are coloured according to the source of isolation (household members).\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/59fea914fde50f3e428caa80.png"},{"id":92304511,"identity":"745f5fe5-15df-487b-9869-3b3fd7d9399c","added_by":"auto","created_at":"2025-09-27 07:05:44","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1667165,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/4512c492-5634-46ed-9ddc-b59a27a6f526.pdf"},{"id":75087579,"identity":"50ba0830-211d-410c-aeea-5869eb42e052","added_by":"auto","created_at":"2025-01-30 10:22:32","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":412097,"visible":true,"origin":"","legend":"S1: Sensitivity analysis of persistent carrier status definition, defined by two or three sequential positive stool samples","description":"","filename":"S1Supplementary3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/c73d4ef6bae882c2f023389b.pdf"},{"id":75087587,"identity":"0e16506e-80fe-4a46-9cc6-c4f469e22a9f","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":577621,"visible":true,"origin":"","legend":"S2: Hidden Markov model estimates of carriage duration with underlying assumption of false negative rates, the proportion of true positive samples that are falsely observed as negative samples, up to","description":"","filename":"S2Supplementary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/b0ce1ff007922fb4e6ba55ff.pdf"},{"id":75087593,"identity":"7daf3c01-3f45-4c2d-8d14-45d813a60f1e","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":140793,"visible":true,"origin":"","legend":"S3: Proportion of E. coli ST131, by sample and by isolate, derived from each source (human, domestic animal, environmental, and food)","description":"","filename":"S3Supplementary1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/c5744ec1fec5b69b847ec2c4.pdf"},{"id":75087598,"identity":"413b2629-7ee0-419f-95c9-78f6d7611c92","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":401197,"visible":true,"origin":"","legend":"S4: Antimicrobial susceptibility for all E. coli ST 131 isolates","description":"","filename":"S4Supplementary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/f26ffb47ecf42cb95e3e21ed.pdf"},{"id":75088698,"identity":"9244f1bc-e97e-499e-8a69-86119a8aa84c","added_by":"auto","created_at":"2025-01-30 10:30:33","extension":"docx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":8271,"visible":true,"origin":"","legend":"S5: Clinical characteristics of persistent carriers and intermittent carriers","description":"","filename":"S5.docx","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/d50bfef77c6bd9e81aef46b7.docx"},{"id":75087590,"identity":"890f1e33-4d99-4d84-9373-7beb069d8847","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"docx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":13768,"visible":true,"origin":"","legend":"S6: E. coli sequence type (ST) 131 carriage characteristics for index patients infected with E. coli ST 131 and infected with other E. coli STs.","description":"","filename":"S6Table2ST131.docx","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/82079816986a284ca3e62d06.docx"},{"id":75087595,"identity":"38933f8a-ffa0-4d03-8655-d4ed7c2ea2d8","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"pdf","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":617276,"visible":true,"origin":"","legend":"\u003cp\u003eS7\u003c/p\u003e","description":"","filename":"S7RegressionAnalysisSubmission.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/f7c6bd5d1f4d0bacf0b52355.pdf"},{"id":75087597,"identity":"81b3a4ee-5cc8-4b09-b8b0-769e63b25e8e","added_by":"auto","created_at":"2025-01-30 10:22:33","extension":"docx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":1425645,"visible":true,"origin":"","legend":"\u003cp\u003eAppendix\u003c/p\u003e","description":"","filename":"SubmissionST131TransmissionDynamicsAppendixNatCommsJan10.docx","url":"https://assets-eu.researchsquare.com/files/rs-5861827/v1/1fbb4f375493a9bca29ea15c.docx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Transmission dynamics of Escherichia coli sequence type 131 in households – a “One Health” prospective cohort study","fulltext":[{"header":"INTRODUCTION","content":"\u003cp\u003e \u003cem\u003eEscherichia coli\u003c/em\u003e sequence type 131 (\u003cem\u003eE. coli\u003c/em\u003e ST131) clone has disseminated rapidly worldwide since it was identified in 2008.\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e \u003cem\u003eE. coli\u003c/em\u003e ST131 is an important cause of community-onset bloodstream and urinary tract infections, accounting for up to 30% of all \u003cem\u003eE. coli\u003c/em\u003e infections globally.\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e The rising prevalence of this clone is associated with increasing multidrug resistance (MDR) observed in \u003cem\u003eE. coli\u003c/em\u003e infections, particularly against fluoroquinolones and third generation cephalosporins, severely limiting antibiotic treatment options. Among \u003cem\u003eE. coli\u003c/em\u003e ST131\u0026rsquo;s three sub-lineages, clades A, B and C, subclades H30R/C1 and H30Rx/C2 have dominated the spread of \u003cem\u003eE. coli\u003c/em\u003e ST131.\u003csup\u003e\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e These fluoroquinolone-resistant subclades possess the fimH30 allele and are the most frequently associated with CTX-M-class beta-lactamase alleles, especially blaCTX-M-15. These alleles are responsible for extended-spectrum beta-lactamase (ESBL) production and confer resistance to third-generation cephalosporins and carbapenems. CTX-M-type enzymes are currently recognised as the most common ESBL type globally.\u003csup\u003e\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e\u003c/p\u003e \u003cp\u003eThe transmission dynamics of \u003cem\u003eE. coli\u003c/em\u003e ST131 driving its global success remain poorly understood. \u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u003c/sup\u003e Cross-sectional epidemiological studies suggested that \u003cem\u003eE. coli\u003c/em\u003e ST131 acquisition often occurs through person-to-person transmission, particularly within the community rather than healthcare settings.\u003csup\u003e\u003cspan additionalcitationids=\"CR5\" citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e However, there is limited understanding of the reservoirs and drivers of \u003cem\u003eE. coli\u003c/em\u003e ST131 transmission in terms of demographic characteristics and community contact patterns. Delineating the transmission dynamics of \u003cem\u003eE. coli\u003c/em\u003e ST131 is crucial in designing infection control and public health measures to curb its associated morbidity and mortality.\u003c/p\u003e \u003cp\u003eIn this prospective cohort study, we adopted a longitudinal, One Health sampling approach to identify the transmission pathways of \u003cem\u003eE. coli\u003c/em\u003e ST131 as a gut colonising strain in households. We quantified the carriage duration and acquisition risks of \u003cem\u003eE. coli\u003c/em\u003e ST131 via Markov models and mapped transmission events using both epidemiological and genomic data. The overall aim of this study was to clarify the transmission dynamics associated with asymptomatic \u003cem\u003eE. coli\u003c/em\u003e ST131 carriage to identify key targets for control interventions.\u003c/p\u003e"},{"header":"METHODS","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eParticipant enrolment and follow-up\u003c/h2\u003e \u003cp\u003eFrom February 2017 to November 2018, we screened and enrolled patients of all ages admitted to the National University Hospital, Singapore, whose urine or blood cultures performed for clinical indications were positive for \u003cem\u003eE. coli\u003c/em\u003e. Patients and their household coresidents that provided consent were recruited into the longitudinal prospective study. Study participants completed a baseline questionnaire on demographics, lifestyle, familial relationships and interactions, dietary habits, medical history, and travel history. Home visits were conducted at two to six-weekly intervals over a 12-month period, during which participants and their companion animals (if applicable) provided stool samples. Environmental and food sampling was performed during the first home visit. Environmental samples included swabs of high-touch surfaces, such as kitchen counters, doorknobs, and toilet bowls using standard methods. \u003csup\u003e\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e Food samples were taken from both raw and cooked meat and vegetables. Ethics approval was obtained from the National Healthcare Group Domain Specific Review Board (Reference: 2016/00998).\u003c/p\u003e \u003cp\u003e \u003cb\u003eIdentification of\u003c/b\u003e \u003cb\u003eE. coli\u003c/b\u003e \u003cb\u003eST131 from clinical, stool, food and environmental samples\u003c/b\u003e\u003c/p\u003e \u003cp\u003eAll samples were cultured on UriSelect\u0026trade; 4 medium, a chromogenic medium used for \u003cem\u003eE. coli\u003c/em\u003e detection and isolation. Up to 12 colonies per sample were randomly picked from the initial culture plates. Species identifications were confirmed using matrix-assisted laser desorption/ionisation and time-of-flight mass spectrometry (MALDI-TOF) spectrometry.\u003c/p\u003e \u003cp\u003e \u003cem\u003eE. coli\u003c/em\u003e isolates were tested for ST131 via polymerase chain reaction (qPCR) targeting the putative manganese transferase gene (\u003cem\u003emntH\u003c/em\u003e).\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e qPCR was performed using the CFX96 TouchTM Real-Time PCR Detection System, with the iTaq Universal SYBR Green Supermix (Bio-Rad Laboratories, Inc) and cycling conditions according to previously validated protocol.\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e All \u003cem\u003eE. coli\u003c/em\u003e isolates identified as ST131 by qPCR were subjected to whole genome sequencing (WGS) and antibiotic susceptibility testing (appendix pp 11). Subsequently in this manuscript, \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates referred to are those confirmed with WGS.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eStatistical analysis and mathematical modelling\u003c/h3\u003e\n\u003cp\u003eDescriptive and statistical analyses were performed using the following definitions. A sample was considered positive for \u003cem\u003eE. coli\u003c/em\u003e ST131 if at least one of the \u003cem\u003eE. coli\u003c/em\u003e isolates recovered from the sample was confirmed to be \u003cem\u003eE. coli\u003c/em\u003e ST131. The density of \u003cem\u003eE. coli\u003c/em\u003e ST131 for each sample was calculated using the number of \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates divided by the total number of \u003cem\u003eE. coli\u003c/em\u003e isolates recovered from the sample. A participant was considered a carrier of \u003cem\u003eE. coli\u003c/em\u003e ST131 if any of their stool samples were positive for \u003cem\u003eE. coli\u003c/em\u003e ST131. Participants with at least two sequential \u003cem\u003eE. coli\u003c/em\u003e ST131 positive samples were considered \u0026ldquo;persistent carriers\u0026rdquo;. All other carriers, i.e. those who had one isolated positive sample or had more than one positive sample but interspersed between negative samples, were considered \u0026ldquo;intermittent carriers\u0026rdquo;. We performed sensitivity analysis by defining persistent carriers as those who carried \u003cem\u003eE. coli\u003c/em\u003e ST131 for at least three sequential time points and intermittent carriers as those with no more than two sequential positive stool samples.\u003c/p\u003e \u003cp\u003eTo identify risk factors associated with \u003cem\u003eE. coli\u003c/em\u003e ST131 carriage and with persistent carrier status, univariable and multivariable logistic regression analyses were conducted. Independent variables assessed in these regressions were selected following literature review, and included sex, age, time spent at home, comorbidities (including chronic metabolic conditions, major organ failures and cancer), urinary incontinence, use of medical devices, antibiotic use in the past six months, and hospital admittance within the past year. \u003csup\u003e\u003cspan additionalcitationids=\"CR10 CR11 CR12\" citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e We also included carriage status subgroups (persistent carriers, intermittent carriers who were coresident with a persistent carrier, all other intermittent carriers, non-carriers) as a categorical independent variable.\u003c/p\u003e \u003cp\u003eA two-state Markov model was constructed to assess transition rates between non-carrier and carrier states for individual participants. We chose not to model carriage at the household level, given that household sizes in our study population ranged from two to eight members, and analysis would necessitate subsetting households by size, resulting in small sample sizes for each group with weak statistical power. In this model, the transition of individuals between non-carrier and carrier states was assumed to be a Markov process, in which the probability of a particular carrier status at the next time point depends only upon carrier status at the current time point and not on the status at earlier time points (appendix pp 7). The model was fit to each carriage status subgroup to explore differences in carriage and acquisition among these groups.\u003c/p\u003e \u003cp\u003eThe two-state Markov model was supplemented by a Hidden Markov Model, which incorporated the potential for false negative qPCR and culturing when screening for \u003cem\u003eE. coli\u003c/em\u003e ST131. These false negatives would have resulted in \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates not being eventually sequenced and confirmed via WGS. In this model, we estimated carriage duration with underlying false negative rates of up to 20% (appendix pp 2).\u003c/p\u003e\n\u003ch3\u003ePhylogenetic analysis\u003c/h3\u003e\n\u003cp\u003eFor all assemblies determined as \u003cem\u003eE. coli\u003c/em\u003e ST131 by multilocus sequence typing (MLST), a maximum-likelihood phylogeny was constructed with RAxML-NG v1\u0026middot;2\u0026middot;2 with 100 bootstrap replicates using the single nucleotide polymorphism (SNP)-only core-genome alignment (alignment length: 7466 base pairs (bp)).\u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e Pairwise SNP distance between isolates was calculated using the snp-dists programme (appendix pp 8).\u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e For households which had persistent carriers and provided \u0026gt;\u0026thinsp;20 \u003cem\u003eE. coli\u003c/em\u003e ST131 genomes, we further investigated the genomic variation of \u003cem\u003eE. coli\u003c/em\u003e ST131 by mapping paired-end reads to an \u003cem\u003eE. coli\u003c/em\u003e ST131 reference genome with bwa-mem v0.7.17. High-quality SNPs were identified using Freebayes v1.3.7 (appendix pp 8).\u003c/p\u003e \u003cp\u003eStatistical analyses were conducted with R version 4.3.3, using RStan\u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e (for the primary Markov model) and \u003cem\u003emsm\u003c/em\u003e packages (for the Hidden Markov Model).\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e Visualisation of phylogenetic analysis was conducted in R version 4.3.1, using R packages ggplot2 and ggtree.\u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e All analysis code is available publicly at \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/rebeccalperez/ST131_Transmission_Dynamics_SG\u003c/span\u003e\u003cspan address=\"https://github.com/rebeccalperez/ST131_Transmission_Dynamics_SG\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/p\u003e"},{"header":"RESULTS","content":"\u003cp\u003eFrom February 2017 to November 2018, 135 participants from 34 households were enrolled (figure 1). The 34 index patients were initially identified from 355 consecutive hospitalised patients who had \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eextraintestinalinfections. Seventeen of these index patients were previously infected with \u003cem\u003eE. coli\u003c/em\u003e ST131 and the other 17 were previously infected with other \u003cem\u003eE. coli\u003c/em\u003e STs (table 1). By end-of-study, 124 participants provided at least one stool sample. One index patient did not provide any stool samples, but their household coresidents did.\u003c/p\u003e\n\u003cp\u003eThe median age at enrolment was 38·16 years (IQR 23·88 to 62·03), with 16 participants (12·90%) under the age of two. Seventy-four participants (59·68%) were female. The median household size was four (interquartile range (IQR) 3 to 5). Fifty-one participants (41·13%) had chronic diseases, including cancer, diabetes, or heart diseases. Forty-eight (38·71%) took antibiotics within the six months prior to enrolment. The majority (87·10%) spent more than 30 hours at home per week.\u003c/p\u003e\n\u003cp\u003eThe participants provided stool samples over a median of 141·5 (IQR 86·5 to 220·0) days. In total, 601 human stool samples, 35 companion animal stool samples (from four cats and two birds), 127 environmental swabs and 73 food samples were collected. The median number of stool samples per human study participant was five (IQR 3 to 6), collected at a median of 28-day intervals (IQR 19 to 50).\u003c/p\u003e\n\u003cp\u003eFrom these samples, 6559 \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eisolates were recovered, of which 354 (5·15%) were confirmed \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 by WGS. The majority of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolates were obtained from human samples (95·48%, 338/354). The remaining 16 \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolates included three from domestic animals, two from food, and 11 from environmental sources. Out of the 338 human-source \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolates, 135 (41·16%) were clade A, 23 (7·01%) were clade B, and 170 (51·83%) were clade C (including 122 in subclade C1-M27 (72·76%) and 48 in subclade C2 (28·24%). Coresidents were more likely to carry clade A than index patients (83% of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolates from coresidents were clade A, versus 53% of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolates from index patients (p \u0026lt; 0·001).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAmong 545 human-source \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eisolates, resistance to more than two classes of antibiotics was greater among \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 clades A (71·26%, 62/87) and C (75·93%, 82/108) in comparison to clade B (23·53%, 4/17) and non-ST131 \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003e(22·52%, 75/333). None were resistant to carbapenems (appendix pp 7).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAsymptomatic \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage amongst index patients\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAmongst the 34 index patients, 22 had urinary tract infections while the other 12 had bloodstream infections. The proportion of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131carriers amongst those infected with \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131and those infected with other \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eSTs were similar (6/16, 37·50% versus 6/17, 35·29%, respectively). However, \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers amongst index patients previously infected with \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 had a longer carriage duration than those previously infected with other \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eSTs (median duration 59·71, 80% CrI 33·92 to 111·83 versus 16·97, 80% CrI 3·49 to 45·52 days, appendix pp 9). In addition, the density of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 in each stool sample was higher in index patients who were infected with \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 (0·69 versus 0·27, p = 0·007, appendix pp 9) than those infected with other \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eSTs.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDuration and density of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage in the overall study population\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe majority of households (64·71%, 22/34) had at least one \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carrier (table 1). The overall prevalence of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage in individuals was 33·06% (41/124). Similar proportions of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers were found in households with an index patient previously infected with \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 and those with an index patient previously infected with other \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eSTs\u003cem\u003e.\u003c/em\u003e However, \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers living with an index patient with previous \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 infection had more stool samples positive for \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 during the study period and also carried \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 at higher densities (table 1).\u003c/p\u003e\n\u003cp\u003eOut of the \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers, the majority (78·05%, 32/41) carried \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 intermittently. Nine \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers persistently carried \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 for at least two consecutive time points. These persistent carriers had a median carriage duration of 86·35 days (80% CrI 30·03 to 187·80), whereas intermittent carriers had median carriage duration for 2·26 days (80% CrI 0·52 to 6·00)\u0026nbsp;(figure 3A). The mean density of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 in positive stool samples collected from thepersistent carriers was 57·79%, compared with 36·06% among intermittent carriers (figure 2).\u0026nbsp;\u0026nbsp;When stratified by clade, median carriage duration for clade A, the most commonly isolated clade, was 35·33 days (80% CrI 23·81 to 52·47), longer than for clade C which was 21·55 days (80% CrI 14·14 to 33·28).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eRisk of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage and acquisition\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNone of the epidemiological risk factors, including age, sex, time spent at home per week, comorbidities, incontinence, medical devices including urinary catheter, antibiotic intake in the past six months, and hospital stay in the past year, were associated with \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage in both multivariable and univariable regression analyses (appendix pp 10). Similarly, there were no demographic or clinical risk factors associated with the status of being a persistent carrier (appendix pp 10).\u003c/p\u003e\n\u003cp\u003eDaily probabilities of acquiring \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage amongst persistent carriers and coresidents of persistent carriers were 3·92% (80% CrI 2·01% to 11·11%) and 3·13% (80% CrI 1·22% to 10·14%), respectively. Amongst those who did not live with persistent carriers, daily acquisition probability was lower at 1·57% (80% CrI 0·65% to 5·19%). By clade, daily probability of acquisition was 0·16% (80% CrI 0·11% to 0·24%) and 0·26% (80% CrI 0·17% to 0·40%) for \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 clades A and C, respectively. Sensitivity analyses found similar results when defining persistent carriers as detection of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 at three or more consecutive time points (appendix pp 3) and assuming a 20% false negative rate during screening for \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 (appendix pp 5).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePhylogenetic analysis for household transmissions of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePhylogenetic grouping showed that each defined phylogenetic cluster (PC) consisted of genomes derived from single households (figure 4A). However, six households (households 3, 8, 9, 20, 21, 32 in figure 4A) had more than one PCs present across different clades including A, B, C1, and C2, highlighting the diverse \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 populations in these households. Inter-individual genetic distance of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 was markedly different when comparing within-household and between-household. The median within-household pairwise SNP distance was 2 (IQR 1 to 7), while the between-household equivalent was 3777 (IQR 108 to 3794) (figure 4B).\u003c/p\u003e\n\u003cp\u003eFocusing on the four households which included at least one persistent carrier and contributed at least 20 \u003cem\u003eE. coli\u003c/em\u003e ST131 genomes (households 2, 8, 11, 34 in figure 4C), we performed high-resolution phylogenetic inferences (figure 4C). Notably, \u003cem\u003eE. coli\u003c/em\u003e ST131 from persistent carriers had minimal SNP distances to sequenced ST131 isolates from within-household coresidents (figure 4C). In two households (households 11 and 34 in figure 6), persistent carriers (participants 11D and 34A in figure 4C) had higher \u003cem\u003eE. coli\u003c/em\u003e ST131 genomic diversity than their coresident carriers. This evidence suggested that persistent carriers were the source of \u003cem\u003eE. coli\u003c/em\u003e ST131 dissemination in their respective households.\u003c/p\u003e"},{"header":"DISCUSSION","content":"\u003cp\u003eIn this prospective cohort study of asymptomatic \u003cem\u003eE. coli\u003c/em\u003e ST131 carriage in households, we found two distinct patterns of carriage: persistent, high-density carriage and intermittent, low-density carriage. Individuals living with persistent, high-density carriers acquired \u003cem\u003eE. coli\u003c/em\u003e ST131 at twice the rate of those who were not coresident with a persistent carrier. Genomic evidence showed that these persistent carriers shared genetically similar \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates with their household members and harboured greater \u003cem\u003eE. coli\u003c/em\u003e ST131 diversity. This indicated that the persistent carriers were the likely source of \u003cem\u003eE. coli\u003c/em\u003e ST131 in their respective households, with coresident colonisation resulting from transmissions of a single strain from the source persistent carriers.\u003c/p\u003e \u003cp\u003eOur findings carry important implications for controlling the spread of \u003cem\u003eE. coli\u003c/em\u003e ST131, identifying that a subset of individuals may carry \u003cem\u003eE. coli\u003c/em\u003e ST131 asymptomatically for longer-than-average durations and act as a reservoir for spread to close contacts. These persistent carriers may be suitable candidates for infection prevention and control measures for \u003cem\u003eE. coli\u003c/em\u003e ST131 in the community setting, such as the Extraintestinal Pathogenic \u003cem\u003eE. coli\u003c/em\u003e 9-valent vaccine currently undergoing phase three clinical trial,\u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e or decolonisation strategies. Given the infeasibility of finding these asymptomatic reservoirs in the community, individuals with a history of \u003cem\u003eE. coli\u003c/em\u003e ST131 infection may be priority candidates for these prevention measures given that they were more likely to be persistent carriers.\u003c/p\u003e \u003cp\u003eThe importance of persistent asymptomatic carriers as drivers of pathogenic Gram-negative bacteria transmission has been well-described in \u003cem\u003eSalmonella\u003c/em\u003e spp.\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e,\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e and \u003cem\u003eVibrio cholerae\u003c/em\u003e. However, unlike \u003cem\u003eSalmonella\u003c/em\u003e spp. and \u003cem\u003eV. cholerae\u003c/em\u003e, \u003cem\u003eE. coli\u003c/em\u003e is a common gut commensal, and many serotypes can be carried concurrently, making it challenging to identify and trace its transmission. Our systematic and longitudinal approach, which included up to 12 time points at two- to six-week intervals, provided high-resolution data and allowed application of multistate Markov models to estimate carriage duration and inter-individual transmission rates. Furthermore, we obtained up to 12 individual colonies per sample, which allowed us to ascertain the density of carriage. This wealth of isolates per sample also permitted the assessment of genomic diversity within individuals and households, demonstrating the extent of strain sharing in some households with persistent carriers.\u003c/p\u003e \u003cp\u003eWe acknowledge several limitations in our study. Firstly, despite collecting up to 12 \u003cem\u003eE. coli\u003c/em\u003e colonies per sample, microbiology cultures and qPCR may have missed \u003cem\u003eE. coli\u003c/em\u003e ST131 isolates. This would have led to an underestimation of carriage duration, transmission rates, and number of persistent, high-density carriers. To assess the potential impact of these missed isolates, we fitted a Hidden Markov Model to our data, which found that estimates under assumptions of perfect observation fell within the credible intervals of estimates obtained assuming between 1 to 20% negative samples are true positives (appendix pp 3). Further, given that we only identified nine persistent carriers, our assessment of risk factors associated with persistent carrier status may have been underpowered due to small sample size. Secondly, the definition of at least two sequential \u003cem\u003eE. coli\u003c/em\u003e ST131 positive samples for persistent carriage was arbitrary. The description of persistent carriage was meant to illustrate heterogeneity in carriage duration and risk of transmission to coresidents, and not to impose strict definitions on carrier types. Nonetheless, we performed sensitivity analyses using three sequential time points as the lower bound for defining persistent carriage, which produced similar estimates (appendix pp 2). Lastly, despite intense within-individual sampling, the limited genomic variation rendered transmission directionality inconclusive in many cases.\u003c/p\u003e \u003cp\u003eIn conclusion, asymptomatic persistent carriers are potential reservoirs for \u003cem\u003eE. coli\u003c/em\u003e ST131 spread to household contacts in the community setting. Further investigation to identify the risk factors for these persistent carriers will be critical, as these groups represent a potential infection prevention and control target for mitigating the spread of \u003cem\u003eE. coli\u003c/em\u003e ST131, a highly prevalent and antimicrobial resistant strain in the community.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eSupplementary information\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSupplementary Information is available for this paper.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors have no competing interests to declare.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eMY, RB and PAT conceptualised and designed the study. MY and PAT obtained funding for the study. MY, KV, MCSH, TEY, PSY, ZL, WY and IS implemented the study and performed home visits. KV, MCSH, TEY, PSY, ZL, JT and WCT performed microbiology cultures and PCR testing. KTA performed antibiotic susceptibility testing. SRS, CYT, HCT and RTHO performed genomic analysis. RP, MY and BSC performed statistical analysis and mathematical modelling. RP, HCT and KV wrote the first draft of the manuscript. All authors contributed to the review and finalisation of the manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was funded by the Singapore Medical Research Council via the Master of Clinical Investigation course facilitated by the National University of Singapore (grant number: CG21APR2005)\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eChen, S. L. \u003cem\u003eet al.\u003c/em\u003e The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone. \u003cem\u003eSci. Rep.\u003c/em\u003e \u003cstrong\u003e9\u003c/strong\u003e, 13245 (2019).\u003c/li\u003e\n \u003cli\u003eDoerr, N., Dietze, N., Lippmann, N. \u0026amp; Rodloff, A. C. Extended-spectrum beta-lactamases found in Escherichia coli isolates obtained from blood cultures and corresponding stool specimen. \u003cem\u003eSci. Rep.\u003c/em\u003e \u003cstrong\u003e13\u003c/strong\u003e, 8940 (2023).\u003c/li\u003e\n \u003cli\u003eKallonen, T. \u003cem\u003eet al.\u003c/em\u003e Systematic longitudinal survey of invasive \u003cem\u003eEscherichia coli\u003c/em\u003e in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. \u003cem\u003eGenome Res.\u003c/em\u003e \u003cstrong\u003e27\u003c/strong\u003e, 1437\u0026ndash;1449 (2017).\u003c/li\u003e\n \u003cli\u003eJohnson, J. R. \u003cem\u003eet al.\u003c/em\u003e Intestinal Persistence of Colonizing \u003cem\u003eEscherichia coli\u003c/em\u003e Strains, Especially ST131- \u003cem\u003eH\u003c/em\u003e 30, in Relation to Bacterial and Host Factors. \u003cem\u003eJ. Infect. Dis.\u003c/em\u003e \u003cstrong\u003e225\u003c/strong\u003e, 2197\u0026ndash;2207 (2022).\u003c/li\u003e\n \u003cli\u003eSarkar, S. \u003cem\u003eet al.\u003c/em\u003e Intestinal Colonization Traits of Pandemic Multidrug-Resistant Escherichia coli ST131. \u003cem\u003eJ. Infect. Dis.\u003c/em\u003e \u003cstrong\u003e218\u003c/strong\u003e, 979\u0026ndash;990 (2018).\u003c/li\u003e\n \u003cli\u003eMohamed, M. \u003cem\u003eet al.\u003c/em\u003e Large Fecal Reservoir of Escherichia coli Sequence Type 131-H30 Subclone Strains That Are Shared Within Households and Resemble Clinical ST131-H30 Isolates. \u003cem\u003eJ. Infect. Dis.\u003c/em\u003e \u003cstrong\u003e221\u003c/strong\u003e, 1659\u0026ndash;1668 (2020).\u003c/li\u003e\n \u003cli\u003eGuo, S. \u003cem\u003eet al.\u003c/em\u003e Prevalence and genomic analysis of ESBL-producing \u003cem\u003eEscherichia coli\u003c/em\u003e in retail raw meats in Singapore. \u003cem\u003eJ. Antimicrob. Chemother.\u003c/em\u003e \u003cstrong\u003e76\u003c/strong\u003e, 601\u0026ndash;605 (2021).\u003c/li\u003e\n \u003cli\u003eDoumith, M. \u003cem\u003eet al.\u003c/em\u003e Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections. \u003cem\u003eJ. Clin. Microbiol.\u003c/em\u003e \u003cstrong\u003e53\u003c/strong\u003e, 160\u0026ndash;166 (2015).\u003c/li\u003e\n \u003cli\u003eRogers, B. A. \u003cem\u003eet al.\u003c/em\u003e Prolonged carriage of resistant E. coli by returned travellers: clonality, risk factors and bacterial characteristics. \u003cem\u003eEur. J. Clin. Microbiol. Infect. Dis.\u003c/em\u003e \u003cstrong\u003e31\u003c/strong\u003e, 2413\u0026ndash;2420 (2012).\u003c/li\u003e\n \u003cli\u003eBrodrick, H. J. \u003cem\u003eet al.\u003c/em\u003e Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom. \u003cem\u003eGenome Med.\u003c/em\u003e \u003cstrong\u003e9\u003c/strong\u003e, 70 (2017).\u003c/li\u003e\n \u003cli\u003eRodrigues, C., Machado, E., Fernandes, S., Peixe, L. \u0026amp; Novais, \u0026Acirc;. Different \u003cem\u003eEscherichia coli\u003c/em\u003e B2-ST131 clades (B and C) producing extended-spectrum \u003cem\u003e\u0026beta;\u003c/em\u003e -lactamases (ESBL) colonizing residents of Portuguese nursing homes. \u003cem\u003eEpidemiol. Infect.\u003c/em\u003e \u003cstrong\u003e145\u003c/strong\u003e, 3303\u0026ndash;3306 (2017).\u003c/li\u003e\n \u003cli\u003eToombs-Ruane, L. J. \u003cem\u003eet al.\u003c/em\u003e Extended-spectrum \u0026beta;-lactamase- and AmpC \u0026beta;-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study. \u003cem\u003eInt. J. Infect. Dis.\u003c/em\u003e \u003cstrong\u003e128\u003c/strong\u003e, 325\u0026ndash;334 (2023).\u003c/li\u003e\n \u003cli\u003eVan Der Putten, B. C. L. \u003cem\u003eet al.\u003c/em\u003e \u003cem\u003eExtraintestinal Pathogenic\u0026nbsp;\u003c/em\u003eEscherichia Coli\u003cem\u003e\u0026nbsp;(ExPEC) Are Associated with Prolonged Carriage of Extended-Spectrum \u0026beta;-Lactamase-Producing\u0026nbsp;\u003c/em\u003eE. Coli\u003cem\u003e\u0026nbsp;Acquired during Travel\u003c/em\u003e. http://biorxiv.org/lookup/doi/10.1101/2020.09.23.309856 (2020) doi:10.1101/2020.09.23.309856.\u003c/li\u003e\n \u003cli\u003eMinh, B. Q. \u003cem\u003eet al.\u003c/em\u003e IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. \u003cem\u003eMol. Biol. Evol.\u003c/em\u003e \u003cstrong\u003e37\u003c/strong\u003e, 1530\u0026ndash;1534 (2020).\u003c/li\u003e\n \u003cli\u003eSeemann, T. snp-dist. (2020).\u003c/li\u003e\n \u003cli\u003eR Interface to Stan \u0026bull; rstan. https://mc-stan.org/rstan/.\u003c/li\u003e\n \u003cli\u003eJackson, C. Multi-State Models for Panel Data: The msm Package for R. \u003cem\u003eJ. Stat. Softw.\u003c/em\u003e \u003cstrong\u003e38\u003c/strong\u003e, 1\u0026ndash;28 (2011).\u003c/li\u003e\n \u003cli\u003eYu, G., Smith, D. K., Zhu, H., Guan, Y. \u0026amp; Lam, T. T. ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \u003cem\u003eMethods Ecol. Evol.\u003c/em\u003e \u003cstrong\u003e8\u003c/strong\u003e, 28\u0026ndash;36 (2017).\u003c/li\u003e\n \u003cli\u003eClinicalTrials.gov. \u003cem\u003eA Study of Vaccination With 9-Valent Extraintestinal Pathogenic Escherichia Coli Vaccine (ExPEC9V) in the Prevention of Invasive Extraintestinal Pathogenic Escherichia Coli Disease in Adults Aged 60 Years And Older With a History of Urinary Tract Infection in the Past 2 Years\u003c/em\u003e. https://clinicaltrials.gov/study/NCT04899336#more-information (2024).\u003c/li\u003e\n \u003cli\u003eDevaraj, A. \u003cem\u003eet al.\u003c/em\u003e Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi. \u003cem\u003ePLOS Pathog.\u003c/em\u003e \u003cstrong\u003e17\u003c/strong\u003e, e1009209 (2021).\u003c/li\u003e\n \u003cli\u003eMbuyi-Kalonji, L. \u003cem\u003eet al.\u003c/em\u003e Invasive non-typhoidal Salmonella from stool samples of healthy human carriers are genetically similar to blood culture isolates: a report from the Democratic Republic of the Congo. \u003cem\u003eFront. Microbiol.\u003c/em\u003e \u003cstrong\u003e14\u003c/strong\u003e, 1282894 (2023).\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Table","content":"\u003cp\u003e\u003cstrong\u003eTable 1.\u0026nbsp;\u003c/strong\u003eParticipant characteristics and\u003cem\u003e\u0026nbsp;E. coli\u003c/em\u003e ST131 carriage status.\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"601\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003eParticipants with previous \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 infection and their coresidents (n = 63)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003eParticipants with previous infection with other \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eSTs and their coresidents\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e(n = 61)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003ep-value\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eDemographics\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eSex (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eFemale\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e36 (57\u0026middot;14)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e38 (62\u0026middot;30)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;688\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eMale\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e27 (42\u0026middot;85)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e23 (37\u0026middot;70)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eMean age (SD)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e41\u0026middot;68 (23\u0026middot;82)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e41\u0026middot;52 (28\u0026middot;77)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;973\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eChildren under two years old (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e7 (11\u0026middot;11)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e9 (14.75)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;549\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eMedian household size (IQR)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e5 (2\u0026middot;00)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e4 (2\u0026middot;00)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;068\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eHousing types (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003ePublic housing apartments\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e51 (80\u0026middot;95)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e52 (85\u0026middot;25)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;266\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eCondominium\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e8 (12\u0026middot;70)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e3 (4\u0026middot;92)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003eLanded property\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e4 (6\u0026middot;35)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e6 (9\u0026middot;84)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eVegetarian (%)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e4 (6\u0026middot;35)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e0 (0.00%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0.046\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eInternational travel in the past year (%)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e42 (66\u0026middot;67)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e35 (57\u0026middot;38)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;378\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eSpent more than 30 hours at home per week (%)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e53 (84\u0026middot;13)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e55 (90\u0026middot;16)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;320\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eChronic disease(s)\u003csup\u003e#\u003c/sup\u003e(%)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e27 (42\u0026middot;86)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e24 (39\u0026middot;34)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;694\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eIncontinent (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e12 (19\u0026middot;05)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e11 (18\u0026middot;03)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e1\u0026middot;000\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eTook antibiotics in the past six months (%)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e27 (42\u0026middot;86)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e21 (34\u0026middot;43)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;436\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003e\u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriage\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003e\u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers \u0026nbsp;(%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e24 (38\u0026middot;10)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e17 (27\u0026middot;87)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;230\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eNumber of stool samples with at least one \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolate (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e46/289 (15\u0026middot;92)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e24/312 (7\u0026middot;69)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;001\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003eNumber of \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolates recovered from stool samples (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e249/2914 (8\u0026middot;54)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e89/3359 (2\u0026middot;65)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e\u0026lt;0\u0026middot;001\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 149px;\"\u003e\n \u003cp\u003ePersistent \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 carriers* (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 115px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e7 (11\u0026middot;11)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 139px;\"\u003e\n \u003cp\u003e2 (3\u0026middot;28)\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0\u0026middot;094\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e# Chronic diseases included diabetes mellitus, hypertension, ischemic heart disease, cancer and other immunocompromising conditions.\u003c/p\u003e\n\u003cp\u003e* Persistent carriage status was defined by the presence of at least one \u003cem\u003eE. coli\u0026nbsp;\u003c/em\u003eST131 isolate in at least two consecutive stool samples.\u003c/p\u003e\n\u003cp\u003eST: sequence type; SD: standard deviation; IQR: interquartile range.\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Escherichia coli sequence type 131, antimicrobial resistance, transmission dynamics","lastPublishedDoi":"10.21203/rs.3.rs-5861827/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5861827/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003eEscherichia coli \u003c/em\u003esequence type 131 (ST131) is a major cause of community-onset, multidrug-resistant extraintestinal infections. The transmission and carriage dynamics associated with \u003cem\u003eE. coli \u003c/em\u003eST131’s global prevalence remain poorly understood. \u0026nbsp;We collected up to twelve sequential stool samples from 135 human participants and six companion animals and environmental swabs from 34 households, sequencing up to twelve isolates per sample. \u0026nbsp;Each household included an index patient with prior extraintestinal \u003cem\u003eE. coli \u003c/em\u003einfection (17 with ST131, 17 with other sequence types) and their coresidents. While most participants carried \u003cem\u003eE. coli \u003c/em\u003eST131 intermittently, we identified a subset of participants that persistently carried \u003cem\u003eE. coli \u003c/em\u003eST131 in high densities (57·79% of \u003cem\u003eE. coli \u003c/em\u003eisolates per sample) for a median carriage duration of 86·35 days (80% credible interval (CrI) 30·03 to 188·80). Coresiding with a persistent carrier was associated with an almost-doubled risk of acquiring \u003cem\u003eE. coli \u003c/em\u003eST131 (3·13% daily risk (80% CrI 1·22 to 10·14) versus 1·57% (80% CrI 0·65 to 5·19)). Persistent carriers and their coresidents carried genetically similar ST131 isolates (median single nucleotide polymorphism distance 2, interquartile range 2 to 7), but persistent carriers harboured greater diversity, suggesting that they were the source of inter-individual transmissions. Our results demonstrate that asymptomatic, persistent carriers represent potential reservoirs sustaining community \u003cem\u003eE. coli \u003c/em\u003eST131 transmissions. \u0026nbsp;In identifying this subgroup, we highlight a potential target for public health interventions such as vaccination to limit the spread of multidrug resistance.\u003c/p\u003e","manuscriptTitle":"Transmission dynamics of Escherichia coli sequence type 131 in households – a “One Health” prospective cohort study","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-01-30 10:22:28","doi":"10.21203/rs.3.rs-5861827/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"c8a2e6e9-4e55-49c3-aef1-76f6d92c11f5","owner":[],"postedDate":"January 30th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":43532953,"name":"Health sciences/Medical research/Epidemiology"},{"id":43532954,"name":"Health sciences/Pathogenesis/Infection"}],"tags":[],"updatedAt":"2025-09-27T07:05:39+00:00","versionOfRecord":{"articleIdentity":"rs-5861827","link":"https://doi.org/10.1038/s41467-025-63121-x","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2025-09-26 04:00:00","publishedOnDateReadable":"September 26th, 2025"},"versionCreatedAt":"2025-01-30 10:22:28","video":"","vorDoi":"10.1038/s41467-025-63121-x","vorDoiUrl":"https://doi.org/10.1038/s41467-025-63121-x","workflowStages":[]},"version":"v1","identity":"rs-5861827","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5861827","identity":"rs-5861827","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}