Biofilm formation on endotracheal and tracheostomy tubing: A systematic review and meta-analysis of culture data and sampling method.

Biofilm formation on endotracheal and tracheostomy tubing: A systematic review and meta-analysis of culture data and sampling method. | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL MicrobiologyOpen This is a preprint and has not been peer reviewed. Data may be preliminary. 25 February 2025 V1 Latest version Share on Biofilm formation on endotracheal and tracheostomy tubing: A systematic review and meta-analysis of culture data and sampling method. Authors : Ed Deshmukh-Reeves 0009-0004-0511-7854 [email protected] , Campbell Gourlay 0000-0002-2373-6788 , Matthew Shaw , and Charlotte Bilsby Authors Info & Affiliations https://doi.org/10.22541/au.174048689.91496251/v1 Published MicrobiologyOpen Version of record Peer review timeline 479 views 289 downloads Contents Abstract Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Objectives: Biofilm formation on tracheal tubing is a key risk factor for ventilator-associated pneumonia. The microbiology of endotracheal tubing has been reviewed systematically but the profile of tracheostomy tubing has not. Analysis of the tube-associated microbiome is not standardised, and sampling methods are varied. We seek to compare the microbiome of patients intubated by endotracheal or tracheostomy tubes and observe the impact of sampling by tracheal aspiration or direct culture. Methods: Eligible clinical microbiology studies were retrieved from PubMed, SCOPUS and Web of Knowledge from 2000-2024, and a data extraction performed to record tubing and sampling type, and the most prevalent genera. Genera were compared by Spearman’s rank correlation and pairwise analyses by Šidák’s multiple comparisons test. Results: Data from 49 studies identified 30 genera. Pseudomonas were the most prevalent in all conditions, followed by Klebsiella , Staphylococcus, and Acinetobacter. 25 studies performed tracheal aspiration, and 22, direct culture. 2 studies used both methods. Correlation was observed between endotracheal and tracheostomy tubes, and aspirates and direct cultures. (Spearman’s rho=0.69; 0.59) Pseudomonas were more prevalent in tracheostomy tubes. (p<0.0001) Coagulase positive Staphylococci were more common in tracheal aspirates, and coagulase-negative Staphylococci in direct culture. Conclusions: The microbial profiles of endotracheal and tracheostomy tubes are comparable, with Pseudomonas being the most common coloniser. Our analyses suggest that tracheal aspiration can effectively identify the constituents of biofilms without requiring tube removal, making it a valuable tool for clinical researchers to analyse or monitor biofilms before extubation or device failure using existing microbiology procedures. Biofilm formation on endotracheal and tracheostomy tubing: A systematic review and meta-analysis of culture data and sampling method. Authors: Ed Deshmukh-Reeves 1 (Author for correspondence) ORCID: https://orcid.org/0009-0004-0511-7854 Campbell Gourlay 1 ORCID: https://orcid.org/0000-0002-2373-6788 Matthew Shaw 1 , ORCID: https://orcid.org/0009-0009-2721-5435 Charlotte Bilsby 1 , ORCID: https://orcid.org/0009-0005-3585-2996 1 Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ Telephone: +447311254361 Email: [email protected] Objectives: Biofilm formation on tracheal tubing is a key risk factor for ventilator-associated pneumonia. The microbiology of endotracheal tubing has been reviewed systematically but the profile of tracheostomy tubing has not. Analysis of the tube-associated microbiome is not standardised, and sampling methods are varied. We seek to compare the microbiome of patients intubated by endotracheal or tracheostomy tubes and observe the impact of sampling by tracheal aspiration or direct culture. Methods: Eligible clinical microbiology studies were retrieved from PubMed, SCOPUS and Web of Knowledge from 2000-2024, and a data extraction performed to record tubing and sampling type, and the most prevalent genera. Genera were compared by Spearman’s rank correlation and pairwise analyses by Šidák’s multiple comparisons test. Results: Data from 49 studies identified 30 genera. Pseudomonas were the most prevalent in all conditions, followed by Klebsiella , Staphylococcus, and Acinetobacter. 25 studies performed tracheal aspiration, and 22, direct culture. 2 studies used both methods. Correlation was observed between endotracheal and tracheostomy tubes, and aspirates and direct cultures. (Spearman’s rho=0.69; 0.59) Pseudomonas were more prevalent in tracheostomy tubes. (p<0.0001) Coagulase positive Staphylococci were more common in tracheal aspirates, and coagulase-negative Staphylococci in direct culture. Conclusions: The microbial profiles of endotracheal and tracheostomy tubes are comparable, with Pseudomonas being the most common coloniser. Our analyses suggest that tracheal aspiration can effectively identify the constituents of biofilms without requiring tube removal, making it a valuable tool for clinical researchers to analyse or monitor biofilms before extubation or device failure using existing microbiology procedures. Introduction Nosocomial infections particularly those caused by ESKAPE pathogens ( E nterococcus faecium, S taphylococcus aureus, K lebsiella pneumoniae, A cinetobacter baumannii, P seudomonas aeruginosa, and E nterobacter spp. ), are associated with high morbidity and mortality. These pathogens are often resistant to multiple antibiotics, including last-resort treatments. (1,2) A key risk factor for these infections, is the presence of medical devices, which are linked to 60-70% of all nosocomial infections. (3) Indwelling devices such as urinary catheters and tracheal tubing, coated in bodily secretions, promote microbial proliferation and biofilm formation, offering enhanced protection from therapeutic interventions. (4,5) In clinical scenarios which the patient is unable to maintain a reliable passage of air, an artificial airway must be rapidly established. Intubation by endotracheal or tracheostomy tubing can secure the airway. Combined with mechanical ventilation, this system can maintain a patient’s respiratory system for extended periods of time (6). Biofilm formation on tracheal tubing is a major risk factor for ventilator associated pneumonia (VAP), which affects up to 40% of ventilated patients and has a direct attributable mortality of approximately 10%. (7) Biofilms are complex, often polymicrobial communities of microorganisms adhered to a surface, and encased in an extracellular matrix of polysaccharides, nucleic acids and other biological material. This matrix enhances the biofilm’s resistance to antimicrobial treatments, with the minimum inhibitory concentrations to treat biofilms, often hundreds of times higher than that for planktonic cells (8–10). Biofilm formation begins with planktonic cells adhering to a surface through weak physical forces, followed by receptor-adhesin interactions (5). Surface-attached cells proliferate and secrete substances that form the extracellular matrix. As the biofilm matures, it develops into 3D structures of cells and polymers, sharing resources to support the survival of the community (11). Planktonic cells or whole aggregates originating from the biofilm can also dissociate, travelling to secondary locations, while retaining the antimicrobial tolerance traits observed in the surface attached biofilm (12). In tracheal tubing, the dissociation of cells and aggregates into tracheal secretions is crucial in the development of VAP (7). The key distinction between endotracheal tubes and tracheostomy tubes is their insertion route and resulting exposure to differing microbiomes. The endotracheal tube is inserted orally and therefore exposed to the oral microbiome while the tracheostomy bypasses the oral microbiome by insertion through a stoma in the neck. Studies have explored the oral microbiome’s impact on VAP, some indicating mouth disinfection as an effective prophylactic. However, clinical trials report mixed efficacy, with a systematic review concluding that oral hygiene care only “probably reduces the incidence of VAP”. A separate review and meta-analysis then concluded that disinfection with chlorhexidine was ineffective at all concentrations (13). Complete characterisation of the microbiology associated with tracheal tubing is limited, and generally restricted to a single tubing type, with sampling methods often diverse. Commonly, clinicians will obtain microbial profiles upon extubation, cutting the distal tip of the tracheal tubing and performing microbiology assessments downstream. Often this includes some form of disruption such as sonication or vortexing (14,15). Another common method is by tracheal aspiration, in which tracheal secretions are suctioned using either the tracheal tubing itself, or by a secondary catheter inserted through the artificial airway. While this technique does not retrieve a sample directly from the biofilm itself, it is easier to collect, as this suctioning is typically performed regularly to prevent accumulation and therefore does not require extubation (16). To date, two systematic reviews, (17,18) have investigated biofilm formation on tracheal tubing, focusing exclusively on endotracheal tubes. While microbial characterisation was included in both, it was not the primary objective. Codru et al. summarised biofilm detection rates and their influence on microbiology, whereas Mishra et al. analysed strain-specific biofilm formation rates and antibiotic resistance profiles. This review aims to examine and compare the microbial profiles of endotracheal and tracheostomy tubing and analyse the differences between samples collected via tracheal aspiration and those directly from the biofilm. As no such systematic review has been published to date, this review aims to guide strategies against biofilm formation on tracheal tubing by characterising the microbiology and evaluating whether direct culture or aspiration sampling are suitable/comparable for identifying the constituents of tracheal tube biofilms and the potential causes of VAP. Methods Definitions “Tracheal aspirates :” Samples gathered by the suctioning of tracheal secretions performed using the tracheal tubing itself, or an additional catheter. “Direct biofilm culture” The process of sampling from the surface of the tubing directly, generally requiring extubation and excision of a portion of tubing. This is followed by any microbiology process to dislodge a portion of the biofilm including swabbing, vortexing or sonicating and plate-rolling. Study design This systematic review was designed following the “Preferred Reporting Items for Systematic Reviews and Meta-Analyses” (PRISMA) guidelines (19). Search strategy. PubMed, SCOPUS and WebOfKnowledge were searched for articles published between 1 st January 2000 and 30 th October 2024. The searches were performed using the Medical Subject Headings (MeSH) terms “tracheostomy”, “tracheotomy”, “biofilms”, “biofouling”, “isolation and purification”, “microbiology”, “pathogenicity”, “bacteria”, “fungi”, and “culture”, in addition to other relevant keywords. Keywords were connected using Boolean operators “AND” and “OR”. Full details of the search are provided in the supplementary material. From each database, the retrieved record’s titles and digital object identifier (DOI)(when available) was exported to a .CSV file, and duplicate records were removed. An initial screen of title and abstracts was performed by E.D.R to remove irrelevant records. Records that passed the initial title/abstract screen were then exported to Mendeley Reference Manager (online version) for full text screening. Full text screening was performed independently by E.D.R, M.S and C.B in accordance with the defined eligibility criteria. Discordance was resolved by combined discussion until a consensus was reached. Eligibility criteria For inclusion, studies were required to meet the following eligibility criteria: (1) Study included at least genus-level culture data from patients intubated by endotracheal or tracheostomy tubing; (2) Culture data was grouped by the presence of either tracheostomy or endotracheal tubing; (3) Sample was collected by either tracheal aspiration, or direct culture from the tracheal tubing. Direct culture was defined as any form of swabbing/isolating from the tubing surface while still inserted, or removal of the tubing and any downstream culture based microbiology analysis. Studies that met the following criteria were excluded: (1) studies that did not include genus level culture data from intubated patients; (2) studies that exclusively report culture data from specific, pre-defined organism(s); (3) studies that combine/pool culture data from tracheostomy and endotracheal tubing; (4) Studies that combine/pool culture data from samples gathered by multiple methods; (5) studies that do not specify or use a sampling method other than tracheal aspiration or direct culture; (6) studies that perform exclusively molecular analyses; (7) in vitro or animal model investigations; (8) review articles. In the full text screening process, the reason for exclusion was noted. Exclusion criteria (1) or (2) were marked as “Insufficient microbiology data”. Exclusion criteria (3) or (4) were marked as “Mixed sampling” Exclusion criteria (5) were marked as “Insufficient sampling practice” Quality assessment and risk of bias Quality assessment of the included studies was performed using an adapted Newcastle-Ottawa scale for cross sectional studies (20). Each study was scored 0-9, with 0 being the highest risk of bias. Each study was scored for its sample size, representativeness, non-response rate, ascertainment of exposure, control of confounding variables, assessment of outcome, and use of statistical analysis. For this review, the primary confounding variables were the use of antibiotics prior to or during the study and the presence of a pre-existing respiratory tract infection. Studies scoring 0-3 were deemed very high risk for bias, 4-6 as high risk for bias, and 7-9 as low risk for bias. Data extraction and ranking Data from eligible studies was extracted into a Microsoft Excel ® spreadsheet with the pre-defined headings of “Author”, “Date”, “Tubing Type”, “Organisms isolated”, “Number of organisms isolated”, and “Sampling method”. In the cases that a study had collected culture data from more than one point in time, the data associated with the final time point was extracted. Once data was extracted it was processed into a summary by pooling number of organisms isolated by genus level. Staphylococcus was separated by Coagulase positive Staphylococcus ( CoPS ) and Coagulase negative Staphylococcus ( CoNS ). Any data referring to “Other organisms”, “Commensal organisms” or a taxa higher than genus level were omitted from the analysis. From this data a list of total detected genera was compiled. Per study, the genera were then ranked by abundance. Genera that occurred in the top 5 most abundant were scored 1-5 (most abundant = 5) All other organisms were scored 0. Genera present on the list of total detected genera but not detected were also scored 0. In the cases of tied ranks, each tied genus was included in the summary. The mean rank for each organism was then calculated and compared across conditions. Results Study selection Study selection was performed in accordance with PRISMA guidelines. From the 3 databases searches performed 2489 records were identified, 2012 of which were unique. Following initial title/abstract screening 156 reports were sought for full text, of which 133 were accessed and screened against the eligibility criteria. 84 reports were excluded, with the most common cause for exclusion being “insufficient microbiology data”. While not specified in the eligibility criteria, 2 studies were excluded for the use of broncho-alveolar lavage for to collect samples, and 1 was excluded for reporting data already presented in another study included in the review. 49 studies aligned with the eligibility criteria and were progressed to data extraction. (4,14,15,21–66) The study selection process is summarised in Figure 1 and a list of the included studies and associated characteristics in Table 1. Figure 1: PRIMA Flow of Study Selection Process Akrami, 2023 Endotracheal Direct Klebsiella, Escherichia, Pseudomonas, Citrobacter, Serratia, Acinetobacter (21) Aly, 2012 Endotracheal Aspiration Klebsiella, Pseudomonas, CoPS, CoNS, Streptococcus (22) Bello, 2020 Endotracheal Aspiration Acinetobacter, CoPS, Pseudomonas, Klebsiella Escherichia (23) Cader, 2020 Tracheostomy Direct Pseudomonas, Acinetobacter, Klebsiella, CoNS, Proteus, Escherichia, CoPS (14) Chan, 2024 Tracheostomy Direct Stenotrophomonas, Corynebacterium, Streptococcus, Pseudomonas, CoNS, Acinetobacter, Neisseria, Klebsiella, CoPS, Enterococcus, Providencia, Achromobacter, Proteus, Micrococcus, Candida, Elizabethkingia (24) van Charante, 2022 Endotracheal Direct Candida, CoNS, Streptococcus, Enterococcus, Klebsiella (25) Cifuentes, 2022 Endotracheal Direct Candida, Escherichia, Pseudomonas, Klebsiella, Nakaseomyces, Serratia, Stenotrophomonas, Moraxella, Raoultella, Citrobacter, Proteus, CoPS (26) Danin, 2015 Endotracheal Direct Pseudomonas, Streptococcus, CoNS, CoPS, Enterococcus, Candida (27) Dargahi, 2022 Endotracheal Aspiration Streptococcus, Klebsiella, Pseudomonas, Acinetobacter, CoPS (28) Duran, 2021 Endotracheal Aspiration Acinetobacter, Pseudomonas, Klebsiella, Escherichia, CoPS (29) El Cheikh, 2017 Tracheostomy Aspiration Pseudomonas, Staphylococcus, Morganella, Klebsiella, Stenotrophomonas, Proteus (4) Fengling Yu, 2022 Endotracheal Aspiration Klebsiella, Pseudomonas, Acinetobacter, CoPS, Candida, Stenotrophomonas, Enterococcus (30) Ferreira, 2016 Endotracheal Aspiration Pseudomonas, Streptococcus, Acinetobacter, CoNS, Klebsiella, Candida (15) Friedland, 2001 Endotracheal Direct CoNS, Klebsiella, CoPS, Pseudomonas, Escherichia (31) García-Boyano, 2023 Tracheostomy Aspiration Pseudomonas, CoPS, Serratia, Escherichia, Klebsiella (32) Gil-Perotin, 2012 Endotracheal Aspiration Candida, Acinetobacter, Pseudomonas, Staphylococcus (33) Golli, 2019 Endotracheal Aspiration Klebsiella, CoPS, CoNS, Acinetobacter, Pseudomonas (34) Gupta, 2014 Endotracheal Direct CoPS, Klebsiella, CoNS, Citrobacter, Micrococcus (35) Hotterbeekx, 2016 Endotracheal Direct Candida, CoNS, Nakaseomyces, Pseudomonas, Enterococcus, Escherichia (36) Ismail, 2016 Endotracheal Aspiration Klebsiella, Pseudomonas, CoNS, Candida, Enterobacter, Acinetobacter, Escherichia, CoPS, Serratia (37) Jadhav & Deokar, 2020 Endotracheal Aspiration Acinetobacter, Klebsiella, Pseudomonas, CoPS, Escherichia (38) Khatri, 2023 Endotracheal Direct Acinetobacter, Klebsiella, Pseudomonas, Escherichia, CoPS (39) Khosravi, 2012 Endotracheal Direct Enterobacter, Pseudomonas, CoNS, CoPS, Escherichia, Proteus (40) Lee, 2012 Endotracheal Aspiration Pseudomonas, CoPS, Acinetobacter (41) Maldiney, 2022 Endotracheal Direct CoNS, Enterococcus, Candida, CoPS, Escherichia, Streptococcus (42) McCaleb, 2016 Tracheostomy Aspiration CoPS, Pseudomonas, Stenotrophomonas, Serratia, Streptococcus (43) Mclaren, 2021 Tracheostomy Aspiration CoPS, Pseudomonas, Haemophilus, Streptococcus, Klebsiella (44) Mulla & Revdiwala, 2011 Both Direct ETT: Pseudomonas, Acinetobacter, Klebsiella, Escherichia, Enterobacter TT: Pseudomonas, Acinetobacter, Klebsiella (45) Naderifar, 2024 Endotracheal Aspiration Klebsiella, Escherichia, Salmonella, Proteus (46) Nagmoti, 2022 Tracheostomy Aspiration Pseudomonas, Klebsiella, Citrobacter, Enterococcus, CoPS (47) Phuaksaman, 2022 Tracheostomy Aspiration Pseudomonas, Moraxella, Acinetobacter, Klebsiella, CoPS (48) Pinheiro, 2021 Endotracheal Aspiration Klebsiella, Candida, Acinetobacter, Enterobacter, CoPS, Chryseobacterium, Escherichia, Raoultella, Pseudomonas, Citrobacter (49) Pons-Tomàs, 2024 Tracheostomy Aspiration Pseudomonas, CoPS, Moraxella, Streptococcus, Haemophilus (50) Raveendra, 2022 Tracheostomy Direct Klebsiella, Acinetobacter, Pseudomonas, CoPS, Escherichia (51) Sahoo, 2024 Tracheostomy Aspiration Candida, Acinetobacter, Pseudomonas, Aspergillus, CoPS (52) Saravanam, 2022 Tracheostomy Direct Pseudomonas, CoNS, Streptococcus, Escherichia, Klebsiella (53) Ścibik, 2022 Tracheostomy Direct CoPS, Klebsiella, CoNS, Candida, Streptococcus, Escherichia, Enterobacter, Pseudomonas (54) Shen, 2019 Endotracheal Both Direct: Acinetobacter, Pseudomonas, CoPS, Klebsiella, Enterococcus Aspiration: Acinetobacter, Pseudomonas, Klebsiella, CoPS, Morganella, Proteus, Xanthomonas (55) Shin, 2011 Endotracheal Aspiration Stenotrophomonas, CoPS, Pseudomonas, Acinetobacter (56) Singhai, 2012 Endotracheal Direct Klebsiella, CoNS (57) Solomon, 2009 Tracheostomy Direct CoPS, CoNS, Escherichia, Pseudomonas, Streptococcus, Serratia, Stenotrophomonas, Proteus, Candida, Enterococcus (58) Taj, 2018 Endotracheal Direct Acinetobacter, Escherichia, Pseudomonas, Klebsiella (59) Thorarinsdottir, 2020 Endotracheal Both Direct: Candida, Enterococcus, CoPS, Pseudomonas, Stenotrophomonas, Klebsiella, Chryseobacterium Aspirates: Candida, Enterococcus, CoPS, Stenotrophomonas, Pseudomonas, Haemophilus, Klebsiella (60) Tsukahara, 2022 Both Aspiration ETT: Pseudomonas, Haemophilus, CoPS, Pandoraea, Escherichia, Aspergillus, Streptococcus TT: Pseudomonas, CoPS (61) Tuteja, 2022 Endotracheal Aspiration Acinetobacter, Klebsiella, Stenotrophomonas, Escherichia, Enterobacter, Elizabethkingia, Pseudomonas, CoNS, Achromobacter, Serratia (62) Vandecandelaere, 2012 Endotracheal Direct CoNS, Micrococcus, Candida, CoPS, Klebsiella (63) Vandecandelaere, 2013 Endotracheal Direct CoNS, Micrococcus, CoPS, Candida, Klebsiella, Escherichia, Pseudomonas (64) Vasconcellos Severo, 2023 Tracheostomy Aspiration Pseudomonas, CoPS, Stenotrophomonas, Klebsiella, Morganella, Serratia, Proteus, Streptococcus, Acinetobacter, Citrobacter, Haemophilus (65) Zorgani, 2015 Both Direct ETT: Klebsiella, Acinetobacter, Pseudomonas, Enterobacter, Serratia, Proteus TT: Klebsiella, Pseudomonas (66) Table 1: Summary of included studies and associated characteristics Quality assessment. Across the 49 assessed studies, the mean scoring based on the Newcastle-Ottawa scale was 6.9. Primarily, studies were deducted points based on the control of confounding variables, in which 39 studies scored 0. The absence of statistical analysis led to a 1 point deduction in 11 studies, and a small sample size was recorded in 5 studies. In summary, 38 studies were scored as low risk for bias, and 11 as high risk of bias. Of the studies scored as high risk for bias, 6 would be scored as low risk, if not considering the use of statistical analysis, which, in the context of our review, is not essential for the unbiased extraction and analysis of raw data. The complete scoring is available in the supplementary material. Study characteristics Data was extracted and processed from 49 studies, 31 of which were analyses of endotracheal and 15 for tracheostomy. Three studies independently analysed and compared both endotracheal and tracheostomy tubing. Of the endotracheal studies, 16 included samples collected by tracheal aspirates, while 16 reported cultures directly from the tubing. Two studies independently collected samples by both tracheal aspirates and direct culture. Of the tracheostomy studies, 10 included samples collected by tracheal aspirates, while 8 performed cultures directly from the tubing. Tables ranking the prevalence of each genus by tubing type and sampling method are summarised in complete data extraction, included in the supplementary material. 25 genera were identified across the 49 studies. In all groups, Pseudomonas was the most commonly identified genus, with a combination of Klebsiella, Staphylococcus and Acinetobacter forming the majority of detected isolates. Candida spp. were the most abundant fungal pathogen and the most prevalent genus after the 4 most common bacteria. (Figure 2) Figure 2: Prevalence of genera in endotracheal and tracheostomy tubing when sampled by tracheal aspiration or direct culture. Proportions of most prevalent isolates identified by all sampling methods from (upper-left) endotracheal tubes or (upper-right) tracheostomy tubes. Summary of most prevalent isolates identified on both tracheostomy and endotracheal tubes samples by (lower-left) tracheal aspiration or (lower-right) direct culture. A breakdown of prevalence of “Other Genera” is available in the supplementary material (CoPS: Coagulase positive Staphylococcus , “CoNS”: Coagulase negative Staphylococcus ) Good correlation was observed between both endotracheal and tracheostomy samples, as well as samples collected by either direct sampling, or tracheal aspiration. (Spearman’s rho = 0.69 and 0.59 respectively). To calculate variance of individual genera, we performed pairwise comparisons of each genus’ mean score. Our analysis showed that Pseudomonas was significantly more prevalent in tracheostomy tubes than in endotracheal tubes (p<0.0001). For sampling method, the only significant difference was between CoPS and CoNS , with more CoNS found in direct cultures (p<0.0001) and more CoPS in aspirate samples (p<0.01). (Figure 3) Figure 3 Meta-Analysis of Extracted Data . Genera were ranked by prevalence within each study and then scored based on their mean rank. Spearman’s rank correlation of (a) endotracheal vs tracheostomy tubes, (Spearman’s rho=0.61, p<0.0001) and (b) aspirate vs direct samples (Spearman’s rho = 0.59, p<0.001). Pairwise comparisons of mean score of (c) endotracheal vs tracheostomy tubes, and (d) aspirate vs direct samples. “CoPS”: Coagulase positive Staphylococcus, “CoNS”: Coagulase negative Staphylococcus (Statistical significance calculated by way of Šidák’s multiple comparisons test ((****)=p<0.0001, (**)=p<0.01)) Our review included 3 studies that sampled both tracheostomy and endotracheal tubing, and two that compared tracheal aspiration with direct culture, enabling comparisons while controlling for extraneous variables. Of the studies comparing tubing types, only Tsukahara et al. addressed concordance, finding good agreement but limited conclusions due to a small sample size. Both studies comparing aspiration and direct culture found concordance, with Thorarinsdottir et al. noting that early surveillance cultures often predicting extubation cultures. A summary of these studies is provided in Table 2. Mulla % Revdiwala (249) Endotracheal vs Tracheostomy Not addressed by authors. Higher genus diversity in endotracheal samples. Concordance between most prevalent genera. Tsukahara (259) Endotracheal vs Tracheostomy Sample size of tracheostomy tubes too small for viable comparison. Greater proportion of Pseudomonas in tracheostomy samples. Zorgani (264) Endotracheal vs Tracheostomy Not directly addressed by authors. Some concordance, with higher prevalence of Pseudomonas in tracheostomy samples. Shen (256) Aspiration vs Direct Strong correlation between samples collected by aspiration and direct culture. Thorarinsdottir (126) Aspiration vs Direct Endotracheal aspirate surveillance cultures were often predictive of direct culture on extubation. Concordance between most prevalent genera. Table 2: Summary of independent comparisons. Studies including both endotracheal and tracheostomy tubes, or aspiration and direct culture samples. Discussion This review analyses clinical microbiology data on biofilm formation on endotracheal and tracheostomy tubes. Consistent with previous systematic reviews on endotracheal tubes, Pseudomonas was the most common genus on both tubing types, followed by Klebsiella, Staphylococcus and Acinetobacter. A slight increase in prevalence of Pseudomonas was observed on tracheostomy tubes. This is possibly due to their use in long-term intubation, which may allow Pseudomonas to outcompete other biofilm contributors, in line with current literature trends (67,68). The microbial profiles of both tube types otherwise showed good concordance with only minor changes in ranks. Tracheal aspiration samples also correlated well with direct biofilm cultures. The only significant difference was within the Staphylococcus genus, in which CoPS were more common in aspirates and CoNS were more common in biofilms. This may indicate increased dissociation of CoPS or enhanced adhesion of CoNS. There may also be a bias in studies collecting aspirate samples for patients diagnosed or suspected of pneumonia, therefore skewing the data towards pathogenic organisms and causes of VAP such as Staphylococcus aureus. ESKAPE pathogens were highly prevalent among tracheal tube isolates, representing the four most commonly detected. This indicates that tracheal tube biofilms are likely to contain multidrug resistant strains (1,2). Candida spp. were also frequently identified. This is of interest as there are numerous studies reporting synergism between the Candida spp. and each of the 4 most common bacterial pathogens identified in this study (69–72). We acknowledge this review has some limitations, notably the inclusion of studies with variable inclusion criteria. Some studies collected data from all intubated patients, while others focused only on those with a pneumonia diagnosis, which, as mentioned above, may skew our results towards common causes of VAP. The timing of collection also varied, with some studies sampling at extubation, and others using routine aspirate cultures. Controlling for these variables during study design was deemed too restrictive, limiting the number of studies included and preventing a comprehensive comparison. Our analysis at the genus level limited the distinction between some common pathogens and commensals of the same genus. However, this was done to provide a clearer representation of more prevalent genera, like Streptococcus and Candida, which were split across less prevalent species. This review shows good concordance between the microbial profiles of endotracheal and tracheostomy tubing. Recent research highlights a possible role of the oral microbiome in tubing colonisation, particularly Pseudomonas, Klebsiella, and Staphylococcus which are associated with oral dysbiosis and disease (73,74). Our analysis, comparing both orally and inter-tracheally inserted tubing, finds minimal differences in the microorganisms colonising the devices. This suggests that the oral cavity may not be the main source of biofilm-forming pathogens, supported by the inefficacy of oral disinfection in preventing the onset of VAP (13). Our analysis concludes that tracheal aspiration may be sufficient for obtaining the microbial profile of the tracheal tube-associated biofilm. The microbial profiles from aspiration were generally equivalent to those directly sampled from the biofilm besides an increased prevalence of CoPS in aspirates, and CoNS in the biofilm. Despite this, biofilm-forming pathogens and VAP causes were equally represented in both methods indicating that routine tracheal aspiration cultures are sufficient for detecting potential VAP pathogens. Additionally, as tracheal aspiration is already a standard care practice, it offers a practical tool for clinical research. Aspiration allows for continuous monitoring of biofilm colonisation without requiring extubation, saving time and costs by leveraging existing microbiological workflows. Funding Statement This work was funded by a University of Kent Industrial case PhD studentship to EDR that was part funded by ICU Medical. Conflict of Interest Statement The authors declare that funding to EDR to support his PhD studentship as part of an industry CASE studentship was provided by ICU Medical Inc. However, no member of ICU Medical played any part in the research that contributed to this publication or in its writing or editing prior to submission. This article was not commissioned nor conceived by ICU Medical. References 1. Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens—A Review on Proteomic Perspective. Diagnostics. 2023 Mar 7;13(6):1014. 2. De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, et al. 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Information & Authors Information Version history V1 Version 1 25 February 2025 Peer review timeline Published MicrobiologyOpen Version of Record 7 Jul 2025 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Collection MicrobiologyOpen Keywords biofilm microbiome pseudomonas respiratory infections Authors Affiliations Ed Deshmukh-Reeves 0009-0004-0511-7854 [email protected] University of Kent School of Biosciences View all articles by this author Campbell Gourlay 0000-0002-2373-6788 University of Kent School of Biosciences View all articles by this author Matthew Shaw University of Kent School of Biosciences View all articles by this author Charlotte Bilsby University of Kent School of Biosciences View all articles by this author Metrics & Citations Metrics Article Usage 479 views 289 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Ed Deshmukh-Reeves, Campbell Gourlay, Matthew Shaw, et al. 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