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Klopper M, van der Merwe CJ, van der Heijden YF, Folkerts M, Loubser J, Streicher EM, Mekler K, Hayes C, Engelthaler DM, Metcalfe JZ, Warren RM. The Hidden Epidemic of Isoniazid-Resistant Tuberculosis in South Africa. Ann Am Thorac Soc 2024; 21:1391-1397. [PMID: 38935769 PMCID: PMC11451881 DOI: 10.1513/annalsats.202312-1076oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 06/29/2024] Open
Abstract
Rationale: Isoniazid-resistant tuberculosis (Hr-TB) is often overlooked in diagnostic algorithms because of reliance on first-line molecular assays testing only for rifampicin resistance. Objectives: To determine the prevalence, outcomes, and molecular mechanisms associated with rifampin-susceptible, isoniazid-resistant TB (Hr-TB) in the Eastern Cape, South Africa. Methods: Between April 2016 and October 2017, sputum samples were collected from patients with rifampin-susceptible TB at baseline and at Weeks 7 and 23 of drug-susceptible TB treatment. We performed isoniazid phenotypic and genotypic drug susceptibility testing, including FluoroTypeMTBDR, Sanger sequencing, targeted next-generation sequencing, and whole-genome sequencing. Results: We analyzed baseline isolates from 766 patients with rifampin-susceptible TB. Of 89 patients (11.7%) who were found to have Hr-TB, 39 (44%) had canonical katG or inhA promoter mutations; 35 (39%) had noncanonical katG mutations (including 5 with underlying large deletions); 4 (5%) had mutations in other candidate genes associated with isoniazid resistance. For 11 (12.4%), no cause of resistance was found. Conclusions: Among patients with rifampin-susceptible TB who were diagnosed using first-line molecular TB assays, there is a high prevalence of Hr-TB. Phenotypic drug susceptibility testing remains the gold standard. To improve the performance of genetic-based phenotyping tests, all isoniazid resistance-associated regions should be included, and such tests should have the ability to identify underlying mutations.
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Affiliation(s)
- Marisa Klopper
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
| | - Charnay J. van der Merwe
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and University of Cape Town Lung Institute, Cape Town, South Africa
| | - Yuri F. van der Heijden
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee
- The Aurum Institute, Johannesburg, South Africa
| | - Megan Folkerts
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
| | - Elizabeth M. Streicher
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
| | | | - Cindy Hayes
- National Health Laboratory Services, Port Elizabeth, South Africa; and
| | - David M. Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona
| | - John Z. Metcalfe
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, California
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
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Zhou J, Li J, Hu Y, Li S. Epidemiological characteristics, diagnosis and treatment effect of rifampicin-resistant pulmonary tuberculosis (RR-PTB) in Guizhou Province. BMC Infect Dis 2024; 24:1058. [PMID: 39333894 PMCID: PMC11429120 DOI: 10.1186/s12879-024-09976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Rifampicin-resistant pulmonary tuberculosis (RR-PTB) presents a significant threat to global public health security. China bears a substantial burden of RR-PTB cases globally, with Guizhou Province experiencing particularly alarming trends, marked by a continual increase in patient numbers. Understanding the population characteristics and treatment modalities for RR-PTB is crucial for mitigating morbidity and mortality associated with this disease. METHODS We gathered epidemiological, diagnostic, and treatment data of all RR-PTB cases recorded in Guizhou Province from January 1, 2017 to December 31, 2023. Utilizing composition ratios as the analytical metric, we employed Chi-square tests to examine the spatiotemporal distribution patterns of RR-PTB patients and the evolving trends among different patient classifications over the study period. RESULTS In our study, 3396 cases of RR-PTB were analyzed, with an average age of 45 years. The number of RR-PTB patients rose significantly from 176 in 2017 to 960 in 2023, peaking notably among individuals aged 23-28 and 44-54, with a rising proportion in the 51-80 age group (P < 0.001). Since 2021, there has been a notable increase in the proportion of female patients. While individuals of Han ethnic group comprised the largest group, their proportion decreased over time (P < 0.001). Conversely, the Miao ethnicity showed an increasing trend (P < 0.05). The majority of patients were farmers, with their proportion showing an upward trajectory (P < 0.001), while students represented 4.33% of the cases. Geographically, most patients were registered in Guiyang and Zunyi, with a declining trend (P < 0.001), yet household addresses primarily clustered in Bijie, Tongren, and Zunyi. The proportion of floating population patients gradually decreased, alongside an increase in newly treated patients and those without prior anti-tuberculosis therapy. Additionally, there was a notable rise in molecular biological diagnostic drug sensitivity (real-time PCR and melting curve analysis) (P < 0.001). However, the cure rate declined, coupled with an increasing proportion of RR-PTB patients lost to follow-up and untreated (P < 0.05). CONCLUSIONS Enhanced surveillance is crucial for detecting tuberculosis patients aged 23-28 and 44-54 years. The distribution of cases varies among nationalities and occupations, potentially influenced by cultural and environmental factors. Regional patterns in RR-PTB incidence suggest tailored prevention and control strategies are necessary. Despite molecular tests advances, challenges persist with low cure rates and high loss to follow-up. Strengthening long-term management, resource allocation, and social support systems for RR-PTB patients is essential.
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Affiliation(s)
- Jian Zhou
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guiyang city, 550025, Guizhou Province, China
- Guizhou Center for Disease Control and Prevention, No.73, Bageyan Road, Yunyan District, Guiyang city, 550004, Guizhou Province, China
| | - Jinlan Li
- Guizhou Center for Disease Control and Prevention, No.73, Bageyan Road, Yunyan District, Guiyang city, 550004, Guizhou Province, China.
| | - Yong Hu
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guiyang city, 550025, Guizhou Province, China.
| | - Shijun Li
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guiyang city, 550025, Guizhou Province, China.
- Guizhou Center for Disease Control and Prevention, No.73, Bageyan Road, Yunyan District, Guiyang city, 550004, Guizhou Province, China.
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Naidoo K, Perumal R, Cox H, Mathema B, Loveday M, Ismail N, Omar SV, Georghiou SB, Daftary A, O'Donnell M, Ndjeka N. The epidemiology, transmission, diagnosis, and management of drug-resistant tuberculosis-lessons from the South African experience. THE LANCET. INFECTIOUS DISEASES 2024; 24:e559-e575. [PMID: 38527475 DOI: 10.1016/s1473-3099(24)00144-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Drug-resistant tuberculosis (DR-TB) threatens to derail tuberculosis control efforts, particularly in Africa where the disease remains out of control. The dogma that DR-TB epidemics are fueled by unchecked rates of acquired resistance in inadequately treated or non-adherent individuals is no longer valid in most high DR-TB burden settings, where community transmission is now widespread. A large burden of DR-TB in Africa remains undiagnosed due to inadequate access to diagnostic tools that simultaneously detect tuberculosis and screen for resistance. Furthermore, acquisition of drug resistance to new and repurposed drugs, for which diagnostic solutions are not yet available, presents a major challenge for the implementation of novel, all-oral, shortened (6-9 months) treatment. Structural challenges including poverty, stigma, and social distress disrupt engagement in care, promote poor treatment outcomes, and reduce the quality of life for people with DR-TB. We reflect on the lessons learnt from the South African experience in implementing state-of-the-art advances in diagnostic solutions, deploying recent innovations in pharmacotherapeutic approaches for rapid cure, understanding local transmission dynamics and implementing interventions to curtail DR-TB transmission, and in mitigating the catastrophic socioeconomic costs of DR-TB. We also highlight globally relevant and locally responsive research priorities for achieving DR-TB control in South Africa.
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Affiliation(s)
- Kogieleum Naidoo
- SAMRC-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Rubeshan Perumal
- SAMRC-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Helen Cox
- Institute of Infectious Diseases and Molecular Medicine, Wellcome Centre for Infectious Disease Research and Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Marian Loveday
- South African Medical Research Council, Durban, South Africa
| | - Nazir Ismail
- School of Pathology, University of Witwatersrand, Johannesburg, South Africa
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Amrita Daftary
- SAMRC-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; School of Global Health and Dahdaleh Institute of Global Health Research, York University, Toronto, ON, Canada
| | - Max O'Donnell
- SAMRC-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York City, NY, USA; Department of Epidemiology, Columbia University Irving Medical Center, New York City, NY, USA
| | - Norbert Ndjeka
- TB Control and Management, Republic of South Africa National Department of Health, Pretoria, South Africa
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Blankson HNA, Kamara RF, Barilar I, Andres S, Conteh OS, Dallenga T, Foray L, Maurer F, Kranzer K, Utpatel C, Niemann S. Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone. Microbiol Spectr 2024; 12:e0240523. [PMID: 38289066 PMCID: PMC10923214 DOI: 10.1128/spectrum.02405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 03/06/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) management has become a serious global health challenge. Understanding its epidemic determinants on the regional level is crucial for developing effective control measures. We used whole genome sequencing data of 238 of Mycobacterium tuberculosis complex (MTBC) strains to determine drug resistance profiles, phylogeny, and transmission dynamics of MDR/rifampicin-resistant (RR) MTBC strains from Sierra Leone. Forty-two strains were classified as RR, 196 as MDR, 5 were resistant to bedaquiline (BDQ) and clofazimine (CFZ), but none was found to be resistant to fluoroquinolones. Sixty-one (26%) strains were resistant to all first-line drugs, three of which had additional resistance to BDQ/CFZ. The strains were classified into six major MTBC lineages (L), with strains of L4 being the most prevalent, 62% (n = 147), followed by L6 (Mycobacterium africanum) strains, (21%, n = 50). The overall clustering rate (using ≤d12 single-nucleotide polymorphism threshold) was 44%, stratified into 31 clusters ranging from 2 to 16 strains. The largest cluster (n = 16) was formed by sublineage 2.2.1 Beijing Ancestral 3 strains, which developed MDR several times. Meanwhile, 10 of the L6 strains had a primary MDR transmission. We observed a high diversity of drug resistance mutations, including borderline resistance mutations to isoniazid and rifampicin, and mutations were not detected by commercial assays. In conclusion, one in five strains investigated was resistant to all first-line drugs, three of which had evidence of BDQ/CFZ resistance. Implementation of interventions such as rapid diagnostics that prevent further resistance development and stop MDR-TB transmission chains in the country is urgently needed. IMPORTANCE A substantial proportion of MDR-TB strains in Sierra Leone were resistant against all first line drugs; however this makes the all-oral-six-month BPaLM regimen or other 6-9 months all oral regimens still viable, mainly because there was no FQ resistance.Resistance to BDQ was detected, as well as RR, due to mutations outside of the hotspot region. While the prevalence of those resistances was low, it is still cause for concern and needs to be closely monitored.
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Affiliation(s)
- Harriet N. A. Blankson
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
| | - Rashidatu Fouad Kamara
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Ousman S. Conteh
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Tobias Dallenga
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- Cellular Microbiology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Lynda Foray
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Florian Maurer
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
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Grazian C. Clustering minimal inhibitory concentration data through Bayesian mixture models: An application to detect Mycobacterium tuberculosis resistance mutations. Stat Methods Med Res 2023; 32:2423-2439. [PMID: 37920984 PMCID: PMC10710010 DOI: 10.1177/09622802231211010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers are attempting to contrast it by developing both new antibiotics and patient-specific treatments. In the second case, whole-genome sequencing has had a huge impact in two ways: first, it is becoming cheaper and faster to perform whole-genome sequencing, and this makes it competitive with respect to standard phenotypic tests; second, it is possible to statistically associate the phenotypic patterns of resistance to specific mutations in the genome. Therefore, it is now possible to develop catalogues of genomic variants associated with resistance to specific antibiotics, in order to improve prediction of resistance and suggest treatments. It is essential to have robust methods for identifying mutations associated to resistance and continuously updating the available catalogues. This work proposes a general method to study minimal inhibitory concentration distributions and to identify clusters of strains showing different levels of resistance to antimicrobials. Once the clusters are identified and strains allocated to each of them, it is possible to perform regression method to identify with high statistical power the mutations associated with resistance. The method is applied to a new 96-well microtiter plate used for testing Mycobacterium tuberculosis.
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Affiliation(s)
- Clara Grazian
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
- ARC Training Centre in Data Analytics for Resources and Environments (DARE), Australia
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Georghiou SB, de Vos M, Velen K, Miotto P, Colman RE, Cirillo DM, Ismail N, Rodwell TC, Suresh A, Ruhwald M. Designing molecular diagnostics for current tuberculosis drug regimens. Emerg Microbes Infect 2023; 12:2178243. [PMID: 36752055 PMCID: PMC9980415 DOI: 10.1080/22221751.2023.2178243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/04/2023] [Indexed: 02/09/2023]
Abstract
Diagnostic development must occur in parallel with drug development to ensure the longevity of new treatment compounds. Despite an increasing number of novel and repurposed anti-tuberculosis compounds and regimens, there remains a large number of drugs for which no rapid and accurate molecular diagnostic option exists. The lack of rapid drug susceptibility testing for linezolid, bedaquiline, clofazimine, the nitroimidazoles (i.e pretomanid and delamanid) and pyrazinamide at any level of the healthcare system compromises the effectiveness of current tuberculosis and drug-resistant tuberculosis treatment regimens. In the context of current WHO tuberculosis treatment guidelines as well as promising new regimens, we identify the key diagnostic gaps for initial and follow-on tests to diagnose emerging drug resistance and aid in regimen selection. Additionally, we comment on potential gene targets for inclusion in rapid molecular drug susceptibility assays and sequencing assays for novel and repurposed drug compounds currently prioritized in current regimens, and evaluate the feasibility of mutation detection given the design of existing technologies. Based on current knowledge, we also propose design priorities for next generation molecular assays to support triage of tuberculosis patients to appropriate and effective treatment regimens. We encourage assay developers to prioritize development of these key molecular assays and support the continued evolution, uptake, and utility of sequencing to build knowledge of tuberculosis resistance mechanisms and further inform rapid treatment decisions in order to curb resistance to critical drugs in current regimens and achieve End TB targets.Trial registration: ClinicalTrials.gov identifier: NCT05117788..
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Affiliation(s)
| | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rebecca E. Colman
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Timothy C. Rodwell
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Anita Suresh
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
| | - Morten Ruhwald
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
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7
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Napier G, Couvin D, Refrégier G, Guyeux C, Meehan CJ, Sola C, Campino S, Phelan J, Clark TG. Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data. Sci Rep 2023; 13:11368. [PMID: 37443186 PMCID: PMC10345134 DOI: 10.1038/s41598-023-38384-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host-pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strain-types, though recent advances in whole genome sequencing (WGS) technology have led to their characterization using SNP-based sub-lineage nomenclature. Notwithstanding, spoligotyping remains an important tool and there is a need to study the congruence between spoligotyping-based and SNP-based sub-lineage assignation. To achieve this, an in silico spoligotype prediction method ("Spolpred2") was developed and integrated into TB-Profiler. Lineage and spoligotype predictions were generated for > 28 k isolates and the overlap between strain-types was characterized. Major spoligotype families detected were Beijing (25.6%), T (18.6%), LAM (13.1%), CAS (9.4%), and EAI (8.3%), and these broadly followed known geographic distributions. Most spoligotypes were perfectly correlated with the main MTBC lineages (L1-L7, plus animal). Conversely, at lower levels of the sub-lineage system, the relationship breaks down, with only 65% of spoligotypes being perfectly associated with a sub-lineage at the second or subsequent levels of the hierarchy. Our work supports the use of spoligotyping (membrane or WGS-based) for low-resolution surveillance, and WGS or SNP-based systems for higher-resolution studies.
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Affiliation(s)
- Gary Napier
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - David Couvin
- Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- CNRS, UMR ESE, AgroParisTech, 91405, Orsay, France
| | - Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | | | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- IAME, UMR1137, Université Paris-Cité, INSERM, Paris, France
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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Mokrousov I, Vyazovaya A, Shitikov E, Badleeva M, Belopolskaya O, Bespiatykh D, Gerasimova A, Ioannidis P, Jiao W, Khromova P, Masharsky A, Naizabayeva D, Papaventsis D, Pasechnik O, Perdigão J, Rastogi N, Shen A, Sinkov V, Skiba Y, Solovieva N, Tafaj S, Valcheva V, Kostyukova I, Zhdanova S, Zhuravlev V, Ogarkov O. Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster. BMC Infect Dis 2023; 23:426. [PMID: 37353765 PMCID: PMC10288800 DOI: 10.1186/s12879-023-08413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND . The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in the Far Eastern region of Russia. Here, we aimed to analyze its pathogenomic features and phylogeographic pattern. RESULTS . The study collection included M. tuberculosis DNA collected between 1996 and 2020 in different world regions. The bacterial DNA was subjected to genotyping and whole genome sequencing followed by bioinformatics and phylogenetic analysis. The PCR-based assay to detect specific SNPs of the Beijing 14717-15-cluster was developed and used for its screening in the global collections. Phylogenomic and phylogeographic analysis confirmed endemic prevalence of the Beijing 14717-15-cluster in the Asian part of Russia, and distant common ancestor with isolates from Korea (> 115 SNPs). The Beijing 14717-15-cluster isolates had two common resistance mutations RpsL Lys88Arg and KatG Ser315Thr and belonged to spoligotype SIT269. The Russian isolates of this cluster were from the Asian Russia while 4 isolates were from the Netherlands and Spain. The cluster-specific SNPs that significantly affect the protein function were identified in silico in genes within different categories (lipid metabolism, regulatory proteins, intermediary metabolism and respiration, PE/PPE, cell wall and cell processes). CONCLUSIONS . We developed a simple method based on real-time PCR to detect clinically significant MDR and hypervirulent Beijing 14717-15-cluster. Most of the identified cluster-specific mutations were previously unreported and could potentially be associated with increased pathogenic properties of this hypervirulent M. tuberculosis strain. Further experimental study to assess the pathobiological role of these mutations is warranted.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
- Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Egor Shitikov
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria Badleeva
- Department of Infectious Diseases, Dorji Banzarov Buryat State University, Ulan-Ude, Buryatia, Russia
| | - Olesya Belopolskaya
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Genogeography, Vavilov Institute of General Genetics Russian Academy of Sciences Moscow, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Panayotis Ioannidis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Weiwei Jiao
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Aleksey Masharsky
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
| | - Dinara Naizabayeva
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dimitrios Papaventsis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - João Perdigão
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Adong Shen
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
- Henan Children's Hospital, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Yuriy Skiba
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Silva Tafaj
- National Mycobacteria Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Violeta Valcheva
- Laboratory of Molecular Genetics of Mycobacteria, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irina Kostyukova
- Bacteriology laboratory, Clinical Tuberculosis Dispensary, Omsk, Russia
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
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9
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
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10
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Mesfin EA, Merker M, Beyene D, Tesfaye A, Shuaib YA, Addise D, Tessema B, Niemann S. Prediction of drug resistance by Sanger sequencing of Mycobacterium tuberculosis complex strains isolated from multidrug resistant tuberculosis suspect patients in Ethiopia. PLoS One 2022; 17:e0271508. [PMID: 35930613 PMCID: PMC9355188 DOI: 10.1371/journal.pone.0271508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Background Ethiopia is one of the high multidrug-resistant tuberculosis (MDR-TB) burden countries. However, phenotypic drug susceptibility testing can take several weeks due to the slow growth of Mycobacterium tuberculosis complex (MTBC) strains. In this study, we assessed the performance of a Sanger sequencing approach to predict resistance against five anti-tuberculosis drugs and the pattern of resistance mediating mutations. Methods We enrolled 226 MTBC culture-positive MDR-TB suspects and collected sputum specimens and socio-demographic and TB related data from each suspect between June 2015 and December 2016 in Addis Ababa, Ethiopia. Phenotypic drug susceptibility testing (pDST) for rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin using BACTEC MGIT 960 was compared with the results of a Sanger sequencing analysis of seven resistance determining regions in the genes rpoB, katG, fabG-inhA, pncA, embB, rpsL, and rrs. Result DNA isolation for Sanger sequencing was successfully extracted from 92.5% (209/226) of the MTBC positive cultures, and the remaining 7.5% (17/226) strains were excluded from the final analysis. Based on pDST results, drug resistance proportions were as follows: isoniazid: 109/209 (52.2%), streptomycin: 93/209 (44.5%), rifampicin: 88/209 (42.1%), ethambutol: 74/209 (35.4%), and pyrazinamide: 69/209 (33.0%). Resistance against isoniazid was mainly mediated by the mutation katG S315T (97/209, 46.4%) and resistance against rifampicin by rpoB S531L (58/209, 27.8%). The dominating resistance-conferring mutations for ethambutol, streptomycin, and pyrazinamide affected codon 306 in embB (48/209, 21.1%), codon 88 in rpsL (43/209, 20.6%), and codon 65 in pncA (19/209, 9.1%), respectively. We observed a high agreement between phenotypic and genotypic DST, such as 89.9% (at 95% confidence interval [CI], 84.2%–95.8%) for isoniazid, 95.5% (95% CI, 91.2%–99.8%) for rifampicin, 98.6% (95% CI, 95.9–100%) for ethambutol, 91.3% (95% CI, 84.6–98.1%) for pyrazinamide and 57.0% (95% CI, 46.9%–67.1%) for streptomycin. Conclusion We detected canonical mutations implicated in resistance to rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin. High agreement with phenotypic DST results for all drugs renders Sanger sequencing promising to be performed as a complementary measure to routine phenotypic DST in Ethiopia. Sanger sequencing directly from sputum may accelerate accurate clinical decision-making in the future.
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Affiliation(s)
- Eyob Abera Mesfin
- Ethiopian Public Health Institute, National Laboratory Capacity Building Directorate, Addis Ababa, Ethiopia
- * E-mail:
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- Evolution of the Resistome, Research Center Borstel, Sülfeld, Germany
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abreham Tesfaye
- Addis Ababa City Administration Health Bureau Health Research and Laboratory Services, Addis Ababa, Ethiopia
| | - Yassir Adam Shuaib
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- College of Veterinary Medicine, Sudan University of Science and Technology, Khartoum North, Sudan
| | - Desalegn Addise
- Ethiopian Public Health Institute, National Laboratory Capacity Building Directorate, Addis Ababa, Ethiopia
| | - Belay Tessema
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck- Borstel-Riems, Hamburg, Germany
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11
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Bainomugisa A, Lavu E, Pandey S, Majumdar S, Banamu J, Coulter C, Marais B, Coin L, Graham SM, du Cros P. Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea. BMC Infect Dis 2022; 22:437. [PMID: 35524232 PMCID: PMC9077924 DOI: 10.1186/s12879-022-07414-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular mechanisms determining the transmission and prevalence of drug resistant tuberculosis (DR-TB) in Papua New Guinea (PNG) are poorly understood. We used genomic and drug susceptibility data to explore the evolutionary history, temporal acquisition of resistance and transmission dynamics of DR-TB across PNG. METHODS We performed whole genome sequencing on isolates from Central Public Health Laboratory, PNG, collected 2017-2019. Data analysis was done on a composite dataset that also included 100 genomes previously sequenced from Daru, PNG (2012-2015). RESULTS Sampled isolates represented 14 of the 22 PNG provinces, the majority (66/94; 70%) came from the National Capital District (NCD). In the composite dataset, 91% of strains were Beijing 2.2.1.1, identified in 13 provinces. Phylogenetic tree of Beijing strains revealed two clades, Daru dominant clade (A) and NCD dominant clade (B). Multi-drug resistance (MDR) was repeatedly and independently acquired, with the first MDR cases in both clades noted to have emerged in the early 1990s, while fluoroquinolone resistance emerged in 2009 (95% highest posterior density 2000-2016). We identified the presence of a frameshift mutation within Rv0678 (p.Asp47fs) which has been suggested to confer resistance to bedaquiline, despite no known exposure to the drug. Overall genomic clustering was significantly associated with rpoC compensatory and inhA promoter mutations (p < 0.001), with high percentage of most genomic clusters (12/14) identified in NCD, reflecting its role as a potential national amplifier. CONCLUSIONS The acquisition and evolution of drug resistance among the major clades of Beijing strain threaten the success of DR-TB treatment in PNG. With continued transmission of this strain in PNG, genotypic drug resistance surveillance using whole genome sequencing is essential for improved public health response to outbreaks. With occurrence of resistance to newer drugs such as bedaquiline, knowledge of full drug resistance profiles will be important for optimal treatment selection.
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Affiliation(s)
| | - Evelyn Lavu
- University of Papua New Guinea, Port Moresby, Papua New Guinea.,Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Sushil Pandey
- Queensland Mycobacteria Reference Laboratory, Brisbane, QLD, Australia
| | - Suman Majumdar
- Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.,University of Melbourne Department of Paediatrics and Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Jennifer Banamu
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Chris Coulter
- Queensland Mycobacteria Reference Laboratory, Brisbane, QLD, Australia
| | - Ben Marais
- University of Sydney, Sydney, NSW, Australia
| | - Lachlan Coin
- Peter Doherty Institute, Melbourne, VIC, Australia
| | - Stephen M Graham
- Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.,University of Melbourne Department of Paediatrics and Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Philipp du Cros
- Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.
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12
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Oostvogels S, Ley SD, Heupink TH, Dippenaar A, Streicher EM, De Vos E, Meehan CJ, Dheda K, Warren R, Van Rie A. Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa. Microb Genom 2022; 8. [PMID: 35471145 PMCID: PMC9453078 DOI: 10.1099/mgen.0.000815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Extensively drug-resistant tuberculosis (XDR-TB), defined as resistance to at least isoniazid (INH), rifampicin (RIF), a fluoroquinolone (FQ) and a second-line injectable drug (SLID), is difficult to treat and poses a major threat to TB control. The transmission dynamics and distribution of XDR Mycobacterium tuberculosis (Mtb) strains have not been thoroughly investigated. Using whole genome sequencing data on 461 XDR-Mtb strains, we aimed to investigate the geographical distribution of XDR-Mtb strains in the Western Cape Province of South Africa over a 10 year period (2006–2017) and assess the association between Mtb sub-lineage, age, gender, geographical patient location and membership or size of XDR-TB clusters. First, we identified transmission clusters by excluding drug resistance-conferring mutations and using the 5 SNP cutoff, followed by merging clusters based on their most recent common ancestor. We then consecutively included variants conferring resistance to INH, RIF, ethambutol (EMB), pyrazinamide (PZA), SLIDs and FQs in the cluster definition. Cluster sizes were classified as small (2–4 isolates), medium (5–20 isolates), large (21–100 isolates) or very large (>100 isolates) to reflect the success of individual strains. We found that most XDR-TB strains were clustered and that including variants conferring resistance to INH, RIF, EMB, PZA and SLIDs in the cluster definition did not significantly reduce the proportion of clustered isolates (85.5–82.2 %) but increased the number of patients belonging to small clusters (4.3–12.4 %, P=0.56). Inclusion of FQ resistance-conferring variants had the greatest effect, with 11 clustered isolates reclassified as unique while the number of clusters increased from 17 to 37. Lineage 2 strains (lineage 2.2.1 typical Beijing or lineage 2.2.2 atypical Beijing) showed the large clusters which were spread across all health districts of the Western Cape Province. We identified a significant association between residence in the Cape Town metropole and cluster membership (P=0.016) but no association between gender, age and cluster membership or cluster size (P=0.39). Our data suggest that the XDR-TB epidemic in South Africa probably has its origin in the endemic spread of MDR Mtb and pre-XDR Mtb strains followed by acquisition of FQ resistance, with more limited transmission of XDR Mtb strains. This only became apparent with the inclusion of drug resistance-conferring variants in the definition of a cluster. In addition to the prevention of amplification of resistance, rapid diagnosis of MDR, pre-XDR and XDR-TB and timely initiation of appropriate treatment is needed to reduce transmission of difficult-to-treat TB.
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Affiliation(s)
- Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- *Correspondence: Selien Oostvogels,
| | - Serej D. Ley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Present address: Sefunda AG, Muttenz, Switzerland
| | - Tim H. Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Elizabeth M. Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Elise De Vos
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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13
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Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, Cui Z, Chongsuvivatwong V, Palittapongarnpim P. Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2. Microb Genom 2021; 7. [PMID: 34787541 PMCID: PMC8743535 DOI: 10.1099/mgen.0.000697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) lineage 2 (L2) strains are present globally, contributing to a widespread tuberculosis (TB) burden, particularly in Asia where both prevalence of TB and numbers of drug resistant TB are highest. The increasing availability of whole-genome sequencing (WGS) data worldwide provides an opportunity to improve our understanding of the global genetic diversity of Mtb L2 and its association with the disease epidemiology and pathogenesis. However, existing L2 sublineage classification schemes leave >20 % of the Modern Beijing isolates unclassified. Here, we present a revised SNP-based classification scheme of L2 in a genomic framework based on phylogenetic analysis of >4000 L2 isolates from 34 countries in Asia, Eastern Europe, Oceania and Africa. Our scheme consists of over 30 genotypes, many of which have not been described before. In particular, we propose six main genotypes of Modern Beijing strains, denoted L2.2.M1–L2.2.M6. We also provide SNP markers for genotyping L2 strains from WGS data. This fine-scale genotyping scheme, which can classify >98 % of the studied isolates, serves as a basis for more effective monitoring and reporting of transmission and outbreaks, as well as improving genotype-phenotype associations such as disease severity and drug resistance. This article contains data hosted by Microreact.
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Affiliation(s)
- Yuttapong Thawornwattana
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose 204-8533, Japan
| | - Htet Myat Win Maung
- National TB Control Programme, Department of Public Health, Ministry of Health and Sports, Naypyitaw 15011, Myanmar.,Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Had Yai 90110, Thailand
| | - Zhezhe Cui
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Had Yai 90110, Thailand.,Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, 530028, PR China
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,National Science and Technology Development Agency, Pathumthani 12120, Thailand
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14
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Ismail N, Rivière E, Limberis J, Huo S, Metcalfe JZ, Warren RM, Van Rie A. Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis. THE LANCET MICROBE 2021; 2:e604-e616. [PMID: 34796339 PMCID: PMC8597953 DOI: 10.1016/s2666-5247(21)00175-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background Methods Findings Interpretation Funding
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15
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Saati AA, Khurram M, Faidah H, Haseeb A, Iriti M. A Saudi Arabian Public Health Perspective of Tuberculosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10042. [PMID: 34639342 PMCID: PMC8508237 DOI: 10.3390/ijerph181910042] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/30/2021] [Accepted: 09/16/2021] [Indexed: 12/02/2022]
Abstract
Tuberculosis is a global health challenge due to its spreading potential. The Kingdom of Saudi Arabia (KSA) faces a challenge in the spread of tuberculosis from migrant workers, but the foremost threat is the huge number of pilgrims who travel to visit sacred sites of the Islamic world located in the holy cities of Makkah and Al Madina. Pilgrims visit throughout the year but especially in the months of Ramadan and Zul-Hijah. The rise of resistance in Mycobacterium tuberculosis is an established global phenomenon that makes such large congregations likely hotspots in the dissemination and spread of disease at a global level. Although very stringent and effective measures exist, the threat remains due to the ever-changing dynamics of this highly pathogenic disease. This overview primarily highlights the current public health challenges posed by this disease to the Saudi health system, which needs to be highlighted not only to the concerned authorities of KSA, but also to the concerned global quarters since the pilgrims and migrants come from all parts of the world with a majority coming from high tuberculosis-burdened countries.
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Affiliation(s)
- Abdullah A. Saati
- Department of Community Medicine & Pilgrims Healthcare, Faculty of Medicine, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
| | - Muhammad Khurram
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al Qura University, Makkah 24382, Saudi Arabia;
| | - Abdul Haseeb
- Department of Clinical Pharmacy, College of Pharmacy, Umm Al Qura University, Makkah 24382, Saudi Arabia;
| | - Marcello Iriti
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, 20133 Milano, Italy
- Phytochem Lab, Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, 20133 Milano, Italy
- Center for Studies on Bioispired Agro-Environmental Technology (BAT Center), Università degli Studi di Napoli “Federico II”, 80055 Portici, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Firenze, Italy
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16
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Molecular Analysis of Streptomycin Resistance Genes in Clinical Strains of Mycobacterium tuberculosis and Biocomputational Analysis of the MtGidB L101F Variant. Antibiotics (Basel) 2021; 10:antibiotics10070807. [PMID: 34356728 PMCID: PMC8300841 DOI: 10.3390/antibiotics10070807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/30/2022] Open
Abstract
Globally, tuberculosis (TB) remains a prevalent threat to public health. In 2019, TB affected 10 million people and caused 1.4 million deaths. The major challenge for controlling this infectious disease is the emergence and spread of drug-resistant Mycobacterium tuberculosis, the causative agent of TB. The antibiotic streptomycin is not a current first-line anti-TB drug. However, WHO recommends its use in patients infected with a streptomycin-sensitive strain. Several mutations in the M. tuberculosisrpsL, rrs and gidB genes have proved association with streptomycin resistance. In this study, we performed a molecular analysis of these genes in clinical isolates to determine the prevalence of known or novel mutations. Here, we describe the genetic analysis outcome. Furthermore, a biocomputational analysis of the MtGidB L101F variant, the product of a novel mutation detected in gidB during molecular analysis, is also reported as a theoretical approach to study the apparent genotype-phenotype association.
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17
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Alame Emane AK, Guo X, Takiff HE, Liu S. Highly transmitted M. tuberculosis strains are more likely to evolve MDR/XDR and cause outbreaks, but what makes them highly transmitted? Tuberculosis (Edinb) 2021; 129:102092. [PMID: 34102584 DOI: 10.1016/j.tube.2021.102092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Multi-Drug-Resistant strains of Mycobacterium tuberculosis (MDR-TB) are a serious obstacle to global TB eradication. While most MDR-TB strains are infrequently transmitted, a few cause large transmission clusters that contribute substantially to local MDR-TB burdens. Here we examine whether the known mutations in these strains can explain their success. Drug resistance mutations differ in fitness costs and strains can also acquire compensatory mutations (CM) to restore fitness, but some highly transmitted MDR strains have no CM. The acquisition of resistance mutations that maintain high transmissibility seems to occur by chance and are more likely in strains that are intrinsically highly transmitted and cause many cases. Modern Beijing lineage strains have caused several large outbreaks, but MDR outbreaks are also caused by ancient Beijing and lineage 4 strains, suggesting the lineage is less important than the characteristics of the individual strain. The development of fluoroquinolone resistance appears to represent another level of selection, in which strains must surmount unknown fitness costs of gyrA mutations. The genetic determinants of high transmission are poorly defined but may involve genes encoding proteins involved in molybdenum acquisition and the Esx systems. In addition, strains eliciting lower cytokine responses and producing more caseating granulomas may have advantages for transmission. Successful MDR/XDR strains generally evolve from highly transmitted drug sensitive parent strains due to selection pressures from deficiencies in local TB control programs. Until TB incidence is considerably reduced, there will likely be highly transmitted strains that develop resistance to any new antibiotic.
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Affiliation(s)
- Amel Kevin Alame Emane
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Xujun Guo
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Howard E Takiff
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China; Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, 28 Rue du Dr Roux, Paris, 75015, France; Laboratorio de Genética Molecular, CMBC, IVIC, Km. 11 Carr. Panamericana, Caracas, Venezuela.
| | - Shengyuan Liu
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
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18
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Alame Emane AK, Guo X, Takiff HE, Liu S. Drug resistance, fitness and compensatory mutations in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2021; 129:102091. [PMID: 34090078 DOI: 10.1016/j.tube.2021.102091] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/26/2023]
Abstract
For tuberculosis to be eradicated, the transmission of Multi-Drug-Resistant and eXtensively Drug Resistant strains of Mycobacterium tuberculosis (MDR and XDR-TB) must be considerably reduced. Drug resistant strains were initially thought to have reduced fitness, and the majority of resistant strains may actually have compromised fitness because they are found in only one or a few patients. In contrast, some MDR/XDR-TB strains are highly transmitted and cause large outbreaks. Most antibiotics target essential bacterial functions and the mutations that confer resistance to anti-TB drugs can incur fitness costs manifested as slower growth and reduced viability. The fitness costs vary with different resistance mutations and the bacilli can also accumulate secondary mutations that compensate for the compromised functions and partially or fully restore lost fitness. The compensatory mutations (CM) are different for each antibiotic, as they mitigate the deleterious effects of the specific functions compromised by the resistance mutations. CM are generally more common in strains with resistance mutations incurring the greatest fitness costs, but for RIF resistance, CM are most frequent in strains with the mutation carrying the least fitness cost, Ser450Leu. Here, we review what is known about fitness costs, CM and mechanisms of resistance to the drugs that define a strain as MDR or XDR-TB. The relative fitness costs of the resistance mutations and the mitigating effects of CM largely explain why certain mutations are frequently found in highly transmitted clusters while others are less frequently, rarely or never found in clinical isolates. The CM illustrate how drug resistance affects bacteria and how bacteria evolve to overcome the effects of the antibiotics, and thus a paradigm for how mycobacteria can evolve in response to stress.
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Affiliation(s)
- Amel Kevin Alame Emane
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China. 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China
| | - Xujun Guo
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China. 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China
| | - Howard E Takiff
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China. 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China; Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, 28 Rue du Dr Roux, Paris, 75015, France; CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela.
| | - Shengyuan Liu
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China. 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
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Fernandez Do Porto DA, Monteserin J, Campos J, Sosa EJ, Matteo M, Serral F, Yokobori N, Benevento AF, Poklepovich T, Pardo A, Wainmayer I, Simboli N, Castello F, Paul R, Martí M, López B, Turjanski A, Ritacco V. Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment. BMC Infect Dis 2021; 21:394. [PMID: 33926375 PMCID: PMC8082761 DOI: 10.1186/s12879-021-06069-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution -the genetic variability of M. tuberculosis at short time scales- of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. CASE PRESENTATION In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. CONCLUSIONS This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.
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Affiliation(s)
- Darío A Fernandez Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Mario Matteo
- Instituto de Tisioneumonología Raúl F. Vaccarezza, Hospital de Infecciosas Dr. F. J. Muñiz, Buenos Aires, Argentina
| | - Federico Serral
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Noemí Yokobori
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Fernández Benevento
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Tomás Poklepovich
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Agustín Pardo
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Ingrid Wainmayer
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Florencia Castello
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina.
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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Miyahara R, Smittipat N, Juthayothin T, Yanai H, Disratthakit A, Imsanguan W, Intralawan D, Nedsuwan S, Chaiyasirinroje B, Bupachat S, Tokunaga K, Mahasirimongkol S, Palittapongarnpim P. Risk factors associated with large clusters of tuberculosis patients determined by whole-genome sequencing in a high-tuberculosis-burden country. Tuberculosis (Edinb) 2020; 125:101991. [DOI: 10.1016/j.tube.2020.101991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/26/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022]
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21
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Nimmo C, Millard J, van Dorp L, Brien K, Moodley S, Wolf A, Grant AD, Padayatchi N, Pym AS, Balloux F, O'Donnell M. Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis. THE LANCET. MICROBE 2020; 1:e165-e174. [PMID: 32803174 PMCID: PMC7416634 DOI: 10.1016/s2666-5247(20)30031-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Bedaquiline and clofazimine are important drugs in the treatment of drug-resistant tuberculosis and are commonly used across southern Africa, although drug susceptibility testing is not routinely performed. In this study, we did a genotypic and phenotypic analysis of drug-resistant Mycobacterium tuberculosis isolates from cohort studies in hospitals in KwaZulu-Natal, South Africa, to identify resistance-associated variants (RAVs) and assess the extent of clofazimine and bedaquiline cross-resistance. We also used a comprehensive dataset of whole-genome sequences to investigate the phylogenetic and geographical distribution of bedaquiline and clofazimine RAVs in southern Africa. METHODS In this study, we included M tuberculosis isolates reported from the PRAXIS study of patients with drug-resistant tuberculosis treated with bedaquiline (King Dinuzulu Hospital, Durban) and three other cohort studies of drug-resistant tuberculosis in other KwaZulu-Natal hospitals, and sequential isolates from six persistently culture-positive patients with extensively drug-resistant tuberculosis at the KwaZulu-Natal provincial referral laboratory. Samples were collected between 2013 and 2019. Microbiological cultures were done as part of all parent studies. We sequenced whole genomes of included isolates and measured bedaquiline and clofazimine minimum inhibitory concentrations (MICs) for isolates identified as carrying any Rv0678 variant or previously published atpE, pepQ, and Rv1979c RAVs, which were the subject of the phenotypic study. We combined all whole-genome sequences of M tuberculosis obtained in this study with publicly available sequence data from other tuberculosis studies in southern Africa (defined as the countries of the Southern African Development Community), including isolates with Rv0678 variants identified by screening public genomic databases. We used this extended dataset to reconstruct phylogenetic relationships across lineage 2 and 4 M tuberculosis isolates. FINDINGS We sequenced the whole genome of 648 isolates from 385 patients with drug-resistant tuberculosis recruited into cohort studies in KwaZulu-Natal, and 28 isolates from six patients from the KwaZulu-Natal referral laboratory. We identified 30 isolates with Rv0678 RAVs from 16 (4%) of 391 patients. We did not identify any atpE, pepQ, or Rv1979c RAVs. MICs were measured for 21 isolates with Rv0678 RAVs. MICs were above the critical concentration for bedaquiline resistance in nine (43%) of 21 isolates, in the intermediate category in nine (43%) isolates, and within the wild-type range in three (14%) isolates. Clofazimine MICs in genetically wild-type isolates ranged from 0·12-0·5 μg/mL, and in isolates with RAVs from 0·25-4·0 μg/mL. Phylogenetic analysis of the extended dataset including M tuberculosis isolates from southern Africa resolved multiple emergences of Rv0678 variants in lineages 2 and 4, documented two likely nosocomial transmission events, and identified the spread of a possibly bedaquiline and clofazimine cross-resistant clone in eSwatini. We also identified four patients with pepQ frameshift mutations that may confer resistance. INTERPRETATION Bedaquiline and clofazimine cross-resistance in southern Africa is emerging repeatedly, with evidence of onward transmission largely due to Rv0678 mutations in M tuberculosis. Roll-out of bedaquiline and clofazimine treatment in the setting of limited drug susceptibility testing could allow further spread of resistance. Designing strong regimens would help reduce the emergence of resistance. Drug susceptibility testing is required to identify where resistance does emerge. FUNDING Wellcome Trust, National Institute of Allergy and Infectious Diseases and National Center for Advancing Translational Sciences of the National Institutes of Health.
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
- Africa Health Research Institute, Durban, South Africa
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | | | - Allison Wolf
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
- School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- CAPRISA-MRC HIV-TB Pathogenesis and Treatment Research Unit, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, KwaZulu-Natal, South Africa
| | | | | | - Max O'Donnell
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
- CAPRISA-MRC HIV-TB Pathogenesis and Treatment Research Unit, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, KwaZulu-Natal, South Africa
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