Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019

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In Kenya, incidences of Non-Tuberculous Mycobacteria (NTM) species have steadily been on the increase. Most NTMare resistant to first line treatment of tuberculosis and have a challenge in timely and accurate diagnosis. Misdiagnosis has led to prescribing anti-tuberculosis regimens to patients suffering from NTM. We aimed to determine the most prevalent Non-Tuberculous Mycobacterium in Kenya. Methods: We reviewed records from the National Tuberculosis Reference Laboratory(NTRL ) Laboratory information management system (LIMS) between January 2018 and December 2019 for the patients on surveillance. All isolates were cultured in Mycobacterial Growth Indicator Tubes (MGIT) and incubated for detection using BACTEC™ MGIT™ system. Those with negative acid-fast bacilli (AFB) growth and negative for Mycobacterium Tuberculosis Complex Species (MTBC) protein-MPT64 were suggestive of NTM infections, which were sub-cultured in MGIT and characterized using Line Probe Assay (LPA) GenoType® MTBDR CM/AS. Descriptive and bivariate analysis was done. Results: Of the total 24,549 records reviewed, 167(0.7%) were NTM isolates. Males comprised of 74.2% (124/167), and the mean age was 42 years (SD±16), age group 35-44 years had the highest NTM at 26.3% (44/167). Nairobi had 12.6% (21/167), Mombasa 10.8% (18/167), Kilifi and Meru each had 7.8% (13/167). Eleven isolated species comprised of Mycobacterium intracellulare 35.3% (65/167), M. fortuitum at 27% (48/167), and M. scrofulaceum at 10.2% (17/167). Previously treated patients had higher NTM [63.5% (106/167)] than Drug-resistant follow-up patients [26.9% (45/167)]. Coinfection with HIV was at 27.5% (46/167). Conclusion: Previously treated patients should have an additional screening of NTMS, and drug susceptibility testing should be done before initiation of treatment." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/12-1104", "name": "Non-tuberculous mycobacterium isolations from tuberculosis presumptive..." } } ] } Home Browse Non-tuberculous mycobacterium isolations from tuberculosis presumptive... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Kamau G, Mwangi Z, Bargul J et al. Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.12688/f1000research.135106.2 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Research Article Revised Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] George Kamau https://orcid.org/0000-0003-1556-4434 1-3 , Zakayo Mwangi https://orcid.org/0000-0002-3608-6892 4 , Joel Bargul 3 , [...] Maurice owiny 2 , Nellie Mukiri 5 , Immaculate Kathure 6 , Beatrice Khamala 5 , Nassoro Mwanyalu 2 , Richard Kiplimo 7 , Raphael Lihana 1 George Kamau https://orcid.org/0000-0003-1556-4434 1-3 , Zakayo Mwangi https://orcid.org/0000-0002-3608-6892 4 , [...] Joel Bargul 3 , Maurice owiny 2 , Nellie Mukiri 5 , Immaculate Kathure 6 , Beatrice Khamala 5 , Nassoro Mwanyalu 2 , Richard Kiplimo 7 , Raphael Lihana 1 PUBLISHED 09 Jul 2024 Author details Author details 1 Biomedical, Kenya Medical Research Institute (KEMRI), Nairobi, Nairobi, Kenya 2 Department of Preventive and Promotive Health (DPPH), Field Epidemiology Laboratory Training Program (FELTP), Nairobi, Nairobi, Kenya 3 Biochemistry Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Nairobi County, Kenya 4 Medical Laboratory Sciences, Meru University of Science and Technology, Meru, Kenya 5 Laboratory services, National Tuberculosis Reference Laboratory, Kenya ( NTRL), Nairobi, Nairobi, Kenya 6 National Strategic Public Health Programs,, 2. National Tuberculosis and Lung Diseases, Kenya (NTLD-P), Nairobi, Nairobi, Kenya 7 Statistics, African Medical Research and Education Foundation, Nairobi, Nairobi, Kenya George Kamau Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Zakayo Mwangi Roles: Data Curation, Writing – Review & Editing Joel Bargul Roles: Conceptualization, Data Curation, Methodology, Visualization, Writing – Review & Editing Maurice owiny Roles: Conceptualization, Data Curation, Methodology, Supervision, Validation, Visualization, Writing – Review & Editing Nellie Mukiri Roles: Investigation, Resources Immaculate Kathure Roles: Supervision, Writing – Review & Editing Beatrice Khamala Roles: Investigation, Validation, Writing – Review & Editing Nassoro Mwanyalu Roles: Data Curation, Formal Analysis, Validation, Visualization, Writing – Review & Editing Richard Kiplimo Roles: Data Curation, Formal Analysis, Writing – Review & Editing Raphael Lihana Roles: Conceptualization, Data Curation, Formal Analysis, Methodology, Supervision, Validation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS Abstract Background: Mycobacterial pathogens are among the top causes of diseases in humans. In Kenya, incidences of Non-Tuberculous Mycobacteria (NTM) species have steadily been on the increase. Most NTMare resistant to first line treatment of tuberculosis and have a challenge in timely and accurate diagnosis. Misdiagnosis has led to prescribing anti-tuberculosis regimens to patients suffering from NTM. We aimed to determine the most prevalent Non-Tuberculous Mycobacterium in Kenya. Methods: We reviewed records from the National Tuberculosis Reference Laboratory(NTRL ) Laboratory information management system (LIMS) between January 2018 and December 2019 for the patients on surveillance. All isolates were cultured in Mycobacterial Growth Indicator Tubes (MGIT) and incubated for detection using BACTEC™ MGIT™ system. Those with negative acid-fast bacilli (AFB) growth and negative for Mycobacterium Tuberculosis Complex Species (MTBC) protein-MPT64 were suggestive of NTM infections, which were sub-cultured in MGIT and characterized using Line Probe Assay (LPA) GenoType® MTBDR CM/AS. Descriptive and bivariate analysis was done. Results: Of the total 24,549 records reviewed, 167(0.7%) were NTM isolates. Males comprised of 74.2% (124/167), and the mean age was 42 years (SD±16), age group 35-44 years had the highest NTM at 26.3% (44/167). Nairobi had 12.6% (21/167), Mombasa 10.8% (18/167), Kilifi and Meru each had 7.8% (13/167). Eleven isolated species comprised of Mycobacterium intracellulare 35.3% (65/167), M. fortuitum at 27% (48/167), and M. scrofulaceum at 10.2% (17/167). Previously treated patients had higher NTM [63.5% (106/167)] than Drug-resistant follow-up patients [26.9% (45/167)]. Coinfection with HIV was at 27.5% (46/167). Conclusion: Previously treated patients should have an additional screening of NTMS, and drug susceptibility testing should be done before initiation of treatment. READ ALL READ LESS Keywords Nontuberculous Mycobacteria, Kenya, Mycobacterium avium Complex, Mycobacterium tuberculosis, Prevalence Corresponding Author(s) George Kamau ( [email protected] ) Close Corresponding author: George Kamau Competing interests: No competing interests were disclosed. Grant information: The author(s) declared that no grants were involved in supporting this work. Copyright: © 2024 Kamau G et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Kamau G, Mwangi Z, Bargul J et al. Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.12688/f1000research.135106.2 ) First published: 04 Sep 2023, 12 :1104 ( https://doi.org/10.12688/f1000research.135106.1 ) Latest published: 09 Jul 2024, 12 :1104 ( https://doi.org/10.12688/f1000research.135106.2 ) Revised Amendments from Version 1 I have expounded on the inclusion criteria and exclusion criteria, added a table with the rapid and slow growers and refined the conclusion. I have expounded on the inclusion criteria and exclusion criteria, added a table with the rapid and slow growers and refined the conclusion. See the authors' detailed response to the review by Durga Shankar Meena READ REVIEWER RESPONSES Introduction Humans are often affected by Mycobacterium infections. In developing countries, non-tuberculous mycobacterial (NTM) infections have been overshadowed by high incidences of tuberculosis. This trend is, however, fast-changing. The number of new infections is increasing due to the growing number of immune-deficient patients ( Ferreira et al. , 2002 ) and nonsterile endoscopic medical devices ( Duarte et al. , 2009 ). Pulmonary diseases caused by NTM have been on the increase worldwide ( Hoefsloot et al., 2013 ). In 2014 estimated prevalence of pulmonary tuberculosis caused by NTM was estimated to be 33–65 per 100,000 persons ( Morimoto et al., 2014 ). Globally, positive acid-fast bacilli (AFB) specimens are assumed to develop Mycobacterium tuberculosis (MTBC) and are therefore managed by anti-tuberculosis agents whereas some are put under speculated areas ( Mertaniasih et al., 2017 ). The high prevalence of AFB leads to isolation of mycobacterial illness, meaning that more patients with AFB-positive samples have been administered unsuitable and, more so, unnecessary empirical anti-tuberculosis treatment ( Ngayo et al., 2015 ). As a result of this incorrect treatment and high treatment letdown, the mortality of patients with lung infections is increasing. Therefore, appropriate diagnosis and regular monitoring are crucial in monitoring and treating patients ( Aksamit et al., 2014 ). In Kenya, data regarding the burden of pulmonary illness is scanty, partly due to constraints in surveillance and diagnosis of mycobacterial species. Distribution of these species (NTM) contributes to the difficulties in interpreting positive culture results. Furthermore, it is not mandatory to report cases of disease to the database at the Ministry of Health; thus, data regarding the epidemiology and distribution of pulmonary disease’s causation is inadequate in Kenya ( Jacqueline et al. , 2015 ). The decision to initiate treatment should be influenced by the severity of disease, the risk of progressive NTM-pulmonary disease, the presence of comorbidity and the goals of treatment. Decision to treat remains individualized with consultations and individuals may require a period of longitudinal assessment (symptoms, radiological change and mycobacterial culture results) to inform NTM treatment decisions. To determine the clinical relevance of NTM positive cultures, it is essential to distinguish transient or persistent colonization (which is usually not treated) from true infection ( Daley et al. , 2020 ). It’s against this background that the current study was undertaken to characterize the NTM. Methods Ethical clearance This study was approved by Kenyatta National Hospital-University of Nairobi Ethics Review Committee (Ref:KNH-ERC/A/306) on September 14, 2020. Waiver for individual informed consent was granted as the study utilized remnant clinical samples and the research posed no greater than minimal risk to the study subjects. Inclusion criteria All AFB positive samples which are Mycobacterium tuberculosis complex (MTBC) negative by line probe assay are screened for NTM. After culture growth all AFB positive and MPT64 antigen test negative, are also screened for NTM. Exclusion criteria All AFB positive samples with MTBC confirmation are exclude and culture growths which are AFB negative also excluded. Samples, processing, mycobacterial culture, and growth identification Sputum samples were collected in a leak proof container with a volume of >3ml, which were labelled with client name, date of sample collection and client registration number. The samples were accompanied by a duly filled request form and transported in triple package which were received at the National Tuberculosis Reference Laboratory (NTRL)] underwent mycobacterial culture and identification procedures as described in NTRL standard operating procedures (SOP). Where sputum samples were decontaminated and digested using the N-acetyl-L-cysteine 2% NaOH (NALC-NaOH) procedure. Inoculation into mycobacteria growth indicator tube (MGIT) and Lowenstein-Jensen (LJ) media was done and incubated at 37°C. Growth monitoring for up to 6 and 8 weeks respectively, was done. At the same time, sputum smears were prepared, air dried, heat-fixed then fluorochrome stained with Auramine O. Appearance of mycobacteria as bright yellow fluorescent rods was definitive of correct diagnosis when viewed under a light-emitting diodes microscope. Upon thorough mixing, the tubes were centrifuged at 14,000g for five minutes. The supernatant was gathered in distinct 1.5ml tubes for onward processing. Culture growth in liquid and solid media went through MTB identification using Ag MPT64 assay (capilia), the positive ones were excluded in the study and the negative samples underwent ZN microscopy and presence of AFB indicating a possible NTM. Extraction of DNA Mycobacterial DNA was extracted from 500 μL of re-suspended colonies using GenoLyse (Hain Lifescience, Nehren,Germany) (106477), according to the manufacturer’s instructions. Briefly, 100ul of lysis buffer (A-LYS) was added to each cryovial containing the resuspended colonies and incubated for five minutes at 95°C after which 100ul neutralization buffer (A-NB) was added and centrifugation was done at 5000g for 10 minutes. The supernatant was transferred to a newly labeled cryovial awaiting PCR. A conventional PCR targeting the hsp65 gene was conducted using the GoTaq Green Master Mix (Promega, Madison, Wisconsin, USA) in a final reaction volume of 13 μl comprising 6.25 μl of 2X GoTaq Hot Start Green Master Mix, 2.5 μl DNA template, 0.25 μl of each of both F-(5′-ACCAACGATGGTGTGTCCAT-3′) and R-(5′-CTTGTCGAACCGCATACCCT-3′) primers at a final concentration of 10 pmoles, and 3.75 μl of nuclease-free water to make up the reaction volume. Thermal cycling conditions were 1 cycle of 94°C for 4 min, 35 cycles of 94°C for 1 min, 57°C for 1 min, 72°C for 1 min and a final extension for 10 min at 72°C. Amplified products were confirmed on a 1% Agarose gel stained with 4.6 μl SYBR safe DNA stain (Invitrogen, Carlsbad, California, USA), and bands at 441 bp were observed in an Ultra Violet gel viewer. The PCR products were enzymatically purified using ExoSAP IT (Applied Biosystems, Foster City, California, USA). Purification conditions were 37°c for 15 min followed by a second incubation at 80°c for 15 min and a final cooling step at 4°C for 5 min. Results A total 24,549 records were reviewed. Of these, 167 (0.7%) NTMs were isolated ( Kamau, 2023 ). The highest isolation was among individual aged 35-44 years, (46/167, 27.5%). Males comprised 74.2% (124). The mean age (SD) was 42(16) years. The NTM were isolated in 65% (31/47) of the counties; Most isolated NTM samples came from Nairobi County at 12.6% (21/167), then Mombasa 10.8% (18/167), and Kilifi and Meru counties at 7.8% (13/167). Most NTM were isolated from previously treated patients 63.5%(106/167), drug-resistant follow-up patients 26.9% (45/167) and New patients 9.6%(16/167) [ Table 1 ]. Coinfection with NTM and HIV was at 27.5% (46/167). Table 1. Sociodemographic characteristics of patients with nontuberculous mycobacteria, Kenya 2018-2019. Variables Participants (%)n χ 2 , p Age (years) ≤14 3.0(5) 11.31, 0.334 15-24 7.8(13) 25-34 22.8(38) 35-44 27.5(46) 45-54 18.0(30) 55-64 12.6(21) ≥65 8.4(14) Sub total 100(167) Gender Male 74.2(124) Female 25.8(43) Sub total 100(167) Hiv status Negative 56.3(94) 69.67, 0.184 Positive 27.5(46) Not reported 16.2(27) Sub total 100(167) Type of patient Previously treated 63.5(106) 80.87, 0.744 MDR/RR 26.9(45) New 9.6(16) Sub total 100(167) Counties Nairobi 12.6(21) 33.56, 0.299 Mombasa 10.8(18) Kilifi 7.8(13) Meru 7.8(13) Murang'a 6.0(10) Machakos 4.8(8) Kitui 4.8(8) Turkana 4.2(7) West Pokot 4.2(7) Kirinyaga 3.0(5) Nakuru 3.0(5) Kisumu 3.0(5) Makueni 3.0(5) Laikipia 2.4(4) Taita Taveta 2.4(4) Kakamega 2.4(4) Tharaka Nithi 2.4(4) Nyeri 1.8(3) Kajiado 1.8(3) Siaya 1.8(3) Embu 1.2(2) Nyandarua 1.2(2) Kiambu 1.2(2) Bomet 1.2(2) Nandi 1.2(2) Busia 1.2(2) Garissa 0.6(1) Narok 0.6(1) Baringo 0.6(1) Migori 0.6(1) Trans Nzoia 0.6(1) Sub total 100(167) A total of eleven NTM species were identified, with frequent ones being Mycobacterium intracellulare at 35.3% (59/167), M. fortuitum at 26.3% (44/167), and M. scrofulaceum at 10.2% (17/167). Majority of NTM had a Smear outcome of No AFB seen [59.3%(99)], Smear 1+ [11.4%(19)], and smear 2+ [10.2%(17)] [ Table 2 ]. Table 2. Types of non-tuberculous species isolated microscopy concentrate outcome, Kenya 2018-2019. NTM species No of species isolated %, n M.intracellulare 35.3(59) M.fortuitum 26.3(44) M.scrofulaceum 10.2(17) M.kansasii 9.6(16) M.simiae 4.2(7) M.gordonae 4.2(7) M.avium 3.0(5) M.szulgai 3.0(5) M.abscessus 3.0(5) M.asiaticum 0.6(1) M.lentiflavum 0.6(1) Sub total 100(167) Smear concentrate Smear Outcome %, n NEG 59.3(99) 1+ 11.4(19) 2+ 10.2(17) 3+ 9.6(16) SCANTY 29.6(16) Sub total 100(167) Table 3. Slow and Rapid growing NTM. No of species %, n Slow growing NTM M.abscessus 5.9(5) M.avium 5.9(5) M.intracellulare 69.4(59) M.kansasii 18.8(16) Sub total 50.9(85) Rapid growing NTM M.asiaticum 1.2(1) M.fortuitum 53.7(44) M.gordonae 8.5(7) M.lentiflavum 1.2(1) M.scrofulaceum 20.7(17) M.simiae 8.5(7) M.szulgai 6.1(5) Sub total 49.1(82) Table 4. MAC distribution in Counties. County No of species %, n Nairobi 12.5(8) Kilifi 9.4(6) Kisumu 7.8(5) Kitui 7.8(5) Machakos 7.8(5) Mombasa 7.8(5) Murang'a 7.8(5) Turkana 6.3(4) West Pokot 6.3(4) Meru 4.7(3) Kakamega 3.1(2) Laikipia 3.1(2) Makueni 3.1(2) Siaya 3.1(2) Busia 1.6(1) Embu 1.6(1) Kajiado 1.6(1) Nakuru 1.6(1) Nyandarua 1.6(1) Tharaka Nithi 1.6(1) Sub total 100(64) Discussion Our study found that the prevalence of NTM was low AT [0.7%(167/24,549)] and most of the cases were males which was similar to study done by ( Fatima & Nm, 2019 ) on prevalence of Nontuberculous Mycobacterial infection in Non-HIV subjects. The MAC complex is considered to be the most prevalent globally accounting for 86% ( Nishiuchi et al. , 2017 ). These findings are consistent with our study that isolated MAC species M.intracellulare [35.3 % (59/167), M.fortuitum 26.3% (44/167) M. scrofulaceum 10.2% (17/167), M.kansasii 9.6% (16/167)] [ Table 2 ]. MAC species are frequently isolated in different environmental sources like water and soil and there is frequent contact with this sources thus increasing its infection to human ( van Ingen et al. , 2009 ). Similar findings from other countries have described isolation of MAC species ( Namkoong et al. , 2016 ; Nishiuchi et al. , 2017 ). Similar finding found out that M. intracellulare was most prevalent ( Epola Dibamba Ndanga et al. , 2022 ). However, MAC was not reported as predominant in other settings i.e. South Pacifica where M.fortuitum complex fewer cases were isolated; in India M.fortuitum was predominant and MAC was not detected. The high infectivity rate of MAC species may be linked to their apparent abundance and distribution in many environmental sources such as water and soil, which increases the ease of dissemination and infection to people. MAC has been strongly linked to NTM Pulmonary Disease (NTMPD); nevertheless, it is unknown how its infectivity connects to NTMPD ( Mwangi et al. , 2021 , 2022 ). In our findings persons within the age group (35-44 years) were most affected. More males were affected suggesting that women could be having a protective effect due to the hormonal variation which triggers a response and clears the bacterial infection ( Namkoong et al. , 2016 ; Ji et al. , 2020 ). Pulmonary NTM were mostly found in patients who were previously treated for TB Most of the cases were HIV negative which was inconsistent with what has been reported previously ( Stepanyan et al. , 2019 ). In people with HIV/AIDS, NTM infections can occur in various parts of the body, including the lungs, lymph nodes, and skin. These infections can be severe and difficult to treat, especially if the immune system is severely compromised. Most NTM were isolated from of counties, leading county being Nairobi County with [12.6 %(21/167)], followed by Mombasa County and Kilifi and Meru County. These findings may be inconclusive on factors influencing the geographical distribution of NTM in the different geographical landscapes in Kenya, a more comprehensive study capturing both human and environmental particulars is required for a better understanding of environmental NTM species distribution. Differences in specific NTM species predominance in various environments may in part influence the frequency of pulmonary NTM disease in each geographical location. The presence of NTM among the presumptive cases poses a public health challenge and which potentially complicates TB diagnosis and management. The Division of National TB, Leprosy and Lung Diseases Program (DNTLD-P) should put NTM in planning the prevention and management of tuberculosis control, these findings are similar to a study done in Gabon ( Epola Dibamba Ndanga et al. , 2022 ). Conclusion Our study characterized the diversity of NTM and identified 11 different species. MAC was the most prevalent followed by M. fortuitum complex and M. scrofulaceum species. Slow growing NTM were majority 50.9% (85/167) while rapid growing NTM were 49.1% (82/167). Most of the previously treated patients had NTM, Males were the majority within (35-44) years. Limitation of the study The study lacked clinical data to correlate the NTM isolation. Despite the limitations the study was able to characterize the diversity of NTM. Data availability Underlying data figshare: Non-Tuberculous Mycobacterium isolations from Tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018 –2019. https://doi.org/10.6084/m9.figshare.23498426.v1 ( Kamau, 2023 ). Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0). Acknowledgments The authors wish to express their gratitude to all participants who took part in this study, grateful to National Public Health Laboratories- Kenya for granting the access to NTRL and conduct the research and appreciate the assistance accorded by the staffs in their technical support in preparation and analysis of samples in this study. References Aksamit TR, Philley JV, Griffith DE: Nontuberculous mycobacterial (NTM) lung disease: The top ten essentials. Respir. Med. 2014; 108 (3): 417–425. 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PubMed Abstract | Publisher Full Text Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 04 Sep 2023 ADD YOUR COMMENT Comment Author details Author details 1 Biomedical, Kenya Medical Research Institute (KEMRI), Nairobi, Nairobi, Kenya 2 Department of Preventive and Promotive Health (DPPH), Field Epidemiology Laboratory Training Program (FELTP), Nairobi, Nairobi, Kenya 3 Biochemistry Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Nairobi County, Kenya 4 Medical Laboratory Sciences, Meru University of Science and Technology, Meru, Kenya 5 Laboratory services, National Tuberculosis Reference Laboratory, Kenya ( NTRL), Nairobi, Nairobi, Kenya 6 National Strategic Public Health Programs,, 2. National Tuberculosis and Lung Diseases, Kenya (NTLD-P), Nairobi, Nairobi, Kenya 7 Statistics, African Medical Research and Education Foundation, Nairobi, Nairobi, Kenya George Kamau Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Zakayo Mwangi Roles: Data Curation, Writing – Review & Editing Joel Bargul Roles: Conceptualization, Data Curation, Methodology, Visualization, Writing – Review & Editing Maurice owiny Roles: Conceptualization, Data Curation, Methodology, Supervision, Validation, Visualization, Writing – Review & Editing Nellie Mukiri Roles: Investigation, Resources Immaculate Kathure Roles: Supervision, Writing – Review & Editing Beatrice Khamala Roles: Investigation, Validation, Writing – Review & Editing Nassoro Mwanyalu Roles: Data Curation, Formal Analysis, Validation, Visualization, Writing – Review & Editing Richard Kiplimo Roles: Data Curation, Formal Analysis, Writing – Review & Editing Raphael Lihana Roles: Conceptualization, Data Curation, Formal Analysis, Methodology, Supervision, Validation, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information The author(s) declared that no grants were involved in supporting this work. Article Versions (2) version 2 Revised Published: 09 Jul 2024, 12:1104 https://doi.org/10.12688/f1000research.135106.2 version 1 Published: 04 Sep 2023, 12:1104 https://doi.org/10.12688/f1000research.135106.1 Copyright © 2024 Kamau G et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Kamau G, Mwangi Z, Bargul J et al. Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.12688/f1000research.135106.2 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 2 VERSION 2 PUBLISHED 09 Jul 2024 Revised Views 0 Cite How to cite this report: Nishiuchi Y. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.168666.r312892 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v2#referee-response-312892 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 30 Aug 2024 Yukiko Nishiuchi , Hiroshima University, Higashi-Hiroshima, Japan Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.168666.r312892 Title: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018â2019 Review comments As the authors described, data on mycobacterial species in pulmonary infections are scarce and misdiagnosis is common in ... Continue reading READ ALL Title: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018â2019 Review comments As the authors described, data on mycobacterial species in pulmonary infections are scarce and misdiagnosis is common in Kenya, making it necessary and important to identify patient-derived strains and to properly diagnose and treat patients. However, the authors’ work seems to lack precision. First, it is unclear whether this study is a prospective or retrospective study. If it is a prospective study, the diagnosis should be confirmed by multiple positive cultures according to the diagnostic criteria. If it is a retrospective study, a diagnostic history should be provided to determine the false positive rate. In addition, information on the method of sputum sample collection and storage is required. Other information is also scarce. It is not known when the sample was provided, whether the patient was first diagnosed or not, nor the treatment and medical history. In the table of individual cases, abbreviations are not explained. If MDR is multidrug resistant, how did the authors know it was resistant? Did the authors check for drug susceptibility? It is also important to know if NTM patients were given anti-tuberculosis drugs. Including as much information as possible would provide a good basis for understanding the current situation in Kenya and developing effective countermeasures. Second, there are many typographical errors. In addition, some sentences do not make sense. Some of them are listed below: Title: 2018â2019 Abstract “Non-Tuberculous Mycobacteria” should be written as “nontuberculous mycobacteria”. “NTMare”: A space is missing. “Most NTM have a challenge in timely and accurate diagnosis.”: Is this statement true? “patients suffering from NTM” should be written as “patients suffering from NTM infections” “Those with negative acid-fast bacilli (AFB) growth and negative for Mycobacterium Tuberculosis Complex Species (MTBC) protein-MPT64 were suggestive of NTM infections“: If MGIT negative and MPT64 negative, is the strain NTM? Table 2 and 3, and text: The names of bacteria should be italicized with the initial letter of the genus name, a period, a space and the species name. The authors should carefully rewrite their manuscript as many other typographical errors can be seen. Discussion The readers would appreciate it if the authors could include a constructive description of the current situation and problems in Kenya. Are the authors trying to say that their results ( M. intracellulare 35.3%, M. fortuitum 26.3%, M. scrofulaceum 10.2%, M. kansasii 9.6%, total 81.4%) are consistent with previously reported values (86%)? However, M. fortuitum and M. kansasii are not included in the MAC complex, and in addition to this, the results for M. avium are not included. Therefore, I do not understand the intent of this statemen Is the work clearly and accurately presented and does it cite the current literature? No Is the study design appropriate and is the work technically sound? Partly Are sufficient details of methods and analysis provided to allow replication by others? No If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Partly Are the conclusions drawn adequately supported by the results? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: NTM research I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Nishiuchi Y. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.168666.r312892 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v2#referee-response-312892 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Odeyemi AO. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.168666.r300687 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v2#referee-response-300687 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 11 Jul 2024 Abiona Oluwadamilola Odeyemi , College of Health Sciences, Department of Medicine, Osun State University, Osogbo, Osun, Nigeria Approved VIEWS 0 https://doi.org/10.5256/f1000research.168666.r300687 I have no ... Continue reading READ ALL I have no further comment to make. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Lung infection and lung function in people with chronic illnesses. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Odeyemi AO. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.168666.r300687 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v2#referee-response-300687 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Version 1 VERSION 1 PUBLISHED 04 Sep 2023 Views 0 Cite How to cite this report: Odeyemi AO. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.148209.r276826 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v1#referee-response-276826 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 06 Jun 2024 Abiona Oluwadamilola Odeyemi , College of Health Sciences, Department of Medicine, Osun State University, Osogbo, Osun, Nigeria Approved VIEWS 0 https://doi.org/10.5256/f1000research.148209.r276826 Overall, it was a good research. It was technically sound and exhibited originality. It was also well structured and it gave adequate detail as to how the organisms were isolated. I would have attached the PDF file ... Continue reading READ ALL Overall, it was a good research. It was technically sound and exhibited originality. It was also well structured and it gave adequate detail as to how the organisms were isolated. I would have attached the PDF file of the manuscript with my comments so that my comments on some aspects of the manuscript can be seen here . Thank you Is the work clearly and accurately presented and does it cite the current literature? Yes Is the study design appropriate and is the work technically sound? Yes Are sufficient details of methods and analysis provided to allow replication by others? Yes If applicable, is the statistical analysis and its interpretation appropriate? Yes Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Lung infection and lung function in people with chronic illnesses. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Odeyemi AO. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.148209.r276826 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v1#referee-response-276826 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Meena DS. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.148209.r246327 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v1#referee-response-246327 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 20 Mar 2024 Durga Shankar Meena , All India Institute of Medical Sciences, Jodhpur, India Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.148209.r246327 1. In 'abstract' section, patient with negative AFB and MPT 64 ag were analysed? What about AFB +, gene Xpert negative patients? Many of such patients might belonged to NTM group. 2. Line "Nairobi had 12.6% (21/167), ... Continue reading READ ALL 1. In 'abstract' section, patient with negative AFB and MPT 64 ag were analysed? What about AFB +, gene Xpert negative patients? Many of such patients might belonged to NTM group. 2. Line "Nairobi had 12.6% (21/167), Mombasa 10.8% (18/167), Kilifi and Meru each had 7.8% (13/167)." Please complete the sentence. 3. Conclusion of the abstract is not corroborative with objectives of study. It should be revised. 4. 'Introduction' last line - it seems unclear. 5. Methodology - Authors should clearly mention what were the inclusion and exclusion criteria for this study? 6. Results - Number of patients with HIV positivity and HIV coinfection both sentences are the same. 7. MAC was commonest species isolated. What were the possible factors for this? It should also be compared with other geographical/national prevalence. 8. What was the proportion of MAC in HIV patients in this study? How many patients had previous tuberculosis? Any data on clinical profile of these patients? Mortality ? Outcomes? 9. Please mention the proportion of rapid growers and slow grower NTM in this study. The major limitation of this study is lack of clinical data correlating to NTM isolation. Methodology is also unclear, how were these samples were selected for NTM isolation? Is the work clearly and accurately presented and does it cite the current literature? Partly Is the study design appropriate and is the work technically sound? No Are sufficient details of methods and analysis provided to allow replication by others? No If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: Infectious Diseases I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Meena DS. Reviewer Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.148209.r246327 ) The direct URL for this report is: https://f1000research.com/articles/12-1104/v1#referee-response-246327 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 09 Jul 2024 George Kamau , Department of Preventive and Promotive Health (DPPH), Field Epidemiology Laboratory Training Program (FELTP), Nairobi, Kenya 09 Jul 2024 Author Response I addressed all the reviews and recommendations made and sent a revised version Competing Interests: I do not have any competing interests I addressed all the reviews and recommendations made and sent a revised version I addressed all the reviews and recommendations made and sent a revised version Competing Interests: I do not have any competing interests Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 09 Jul 2024 George Kamau , Department of Preventive and Promotive Health (DPPH), Field Epidemiology Laboratory Training Program (FELTP), Nairobi, Kenya 09 Jul 2024 Author Response I addressed all the reviews and recommendations made and sent a revised version Competing Interests: I do not have any competing interests I addressed all the reviews and recommendations made and sent a revised version I addressed all the reviews and recommendations made and sent a revised version Competing Interests: I do not have any competing interests Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 04 Sep 2023 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 3 Version 2 (revision) 09 Jul 24 read read Version 1 04 Sep 23 read read Durga Shankar Meena , All India Institute of Medical Sciences, Jodhpur, India Abiona Oluwadamilola Odeyemi , Osun State University, Osogbo, Nigeria Yukiko Nishiuchi , Hiroshima University, Higashi-Hiroshima, Japan Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Nishiuchi Y. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 30 Aug 2024 | for Version 2 Yukiko Nishiuchi , Hiroshima University, Higashi-Hiroshima, Japan 0 Views copyright © 2024 Nishiuchi Y. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Not Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Title: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018â2019 Review comments As the authors described, data on mycobacterial species in pulmonary infections are scarce and misdiagnosis is common in Kenya, making it necessary and important to identify patient-derived strains and to properly diagnose and treat patients. However, the authors’ work seems to lack precision. First, it is unclear whether this study is a prospective or retrospective study. If it is a prospective study, the diagnosis should be confirmed by multiple positive cultures according to the diagnostic criteria. If it is a retrospective study, a diagnostic history should be provided to determine the false positive rate. In addition, information on the method of sputum sample collection and storage is required. Other information is also scarce. It is not known when the sample was provided, whether the patient was first diagnosed or not, nor the treatment and medical history. In the table of individual cases, abbreviations are not explained. If MDR is multidrug resistant, how did the authors know it was resistant? Did the authors check for drug susceptibility? It is also important to know if NTM patients were given anti-tuberculosis drugs. Including as much information as possible would provide a good basis for understanding the current situation in Kenya and developing effective countermeasures. Second, there are many typographical errors. In addition, some sentences do not make sense. Some of them are listed below: Title: 2018â2019 Abstract “Non-Tuberculous Mycobacteria” should be written as “nontuberculous mycobacteria”. “NTMare”: A space is missing. “Most NTM have a challenge in timely and accurate diagnosis.”: Is this statement true? “patients suffering from NTM” should be written as “patients suffering from NTM infections” “Those with negative acid-fast bacilli (AFB) growth and negative for Mycobacterium Tuberculosis Complex Species (MTBC) protein-MPT64 were suggestive of NTM infections“: If MGIT negative and MPT64 negative, is the strain NTM? Table 2 and 3, and text: The names of bacteria should be italicized with the initial letter of the genus name, a period, a space and the species name. The authors should carefully rewrite their manuscript as many other typographical errors can be seen. Discussion The readers would appreciate it if the authors could include a constructive description of the current situation and problems in Kenya. Are the authors trying to say that their results ( M. intracellulare 35.3%, M. fortuitum 26.3%, M. scrofulaceum 10.2%, M. kansasii 9.6%, total 81.4%) are consistent with previously reported values (86%)? However, M. fortuitum and M. kansasii are not included in the MAC complex, and in addition to this, the results for M. avium are not included. Therefore, I do not understand the intent of this statemen Is the work clearly and accurately presented and does it cite the current literature? No Is the study design appropriate and is the work technically sound? Partly Are sufficient details of methods and analysis provided to allow replication by others? No If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Partly Are the conclusions drawn adequately supported by the results? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise NTM research I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) Nishiuchi Y. Peer Review Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.168666.r312892) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/12-1104/v2#referee-response-312892 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Odeyemi A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 11 Jul 2024 | for Version 2 Abiona Oluwadamilola Odeyemi , College of Health Sciences, Department of Medicine, Osun State University, Osogbo, Osun, Nigeria 0 Views copyright © 2024 Odeyemi A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions I have no further comment to make. Competing Interests No competing interests were disclosed. Reviewer Expertise Lung infection and lung function in people with chronic illnesses. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Odeyemi AO. Peer Review Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.168666.r300687) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/12-1104/v2#referee-response-300687 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Odeyemi A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 06 Jun 2024 | for Version 1 Abiona Oluwadamilola Odeyemi , College of Health Sciences, Department of Medicine, Osun State University, Osogbo, Osun, Nigeria 0 Views copyright © 2024 Odeyemi A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Overall, it was a good research. It was technically sound and exhibited originality. It was also well structured and it gave adequate detail as to how the organisms were isolated. I would have attached the PDF file of the manuscript with my comments so that my comments on some aspects of the manuscript can be seen here . Thank you Is the work clearly and accurately presented and does it cite the current literature? Yes Is the study design appropriate and is the work technically sound? Yes Are sufficient details of methods and analysis provided to allow replication by others? Yes If applicable, is the statistical analysis and its interpretation appropriate? Yes Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Lung infection and lung function in people with chronic illnesses. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Odeyemi AO. Peer Review Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.148209.r276826) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/12-1104/v1#referee-response-276826 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Meena D. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 20 Mar 2024 | for Version 1 Durga Shankar Meena , All India Institute of Medical Sciences, Jodhpur, India 0 Views copyright © 2024 Meena D. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Not Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions 1. In 'abstract' section, patient with negative AFB and MPT 64 ag were analysed? What about AFB +, gene Xpert negative patients? Many of such patients might belonged to NTM group. 2. Line "Nairobi had 12.6% (21/167), Mombasa 10.8% (18/167), Kilifi and Meru each had 7.8% (13/167)." Please complete the sentence. 3. Conclusion of the abstract is not corroborative with objectives of study. It should be revised. 4. 'Introduction' last line - it seems unclear. 5. Methodology - Authors should clearly mention what were the inclusion and exclusion criteria for this study? 6. Results - Number of patients with HIV positivity and HIV coinfection both sentences are the same. 7. MAC was commonest species isolated. What were the possible factors for this? It should also be compared with other geographical/national prevalence. 8. What was the proportion of MAC in HIV patients in this study? How many patients had previous tuberculosis? Any data on clinical profile of these patients? Mortality ? Outcomes? 9. Please mention the proportion of rapid growers and slow grower NTM in this study. The major limitation of this study is lack of clinical data correlating to NTM isolation. Methodology is also unclear, how were these samples were selected for NTM isolation? Is the work clearly and accurately presented and does it cite the current literature? Partly Is the study design appropriate and is the work technically sound? No Are sufficient details of methods and analysis provided to allow replication by others? No If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise Infectious Diseases I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (1) Author Response 09 Jul 2024 George Kamau, Department of Preventive and Promotive Health (DPPH), Field Epidemiology Laboratory Training Program (FELTP), Nairobi, Kenya I addressed all the reviews and recommendations made and sent a revised version View more View less Competing Interests I do not have any competing interests reply Respond Report a concern Meena DS. Peer Review Report For: Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019 [version 2; peer review: 1 approved, 2 not approved] . F1000Research 2024, 12 :1104 ( https://doi.org/10.5256/f1000research.148209.r246327) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/12-1104/v1#referee-response-246327 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. 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