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Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Fowler PW, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Calisto Matias DVL, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TEA, Pinhata JMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson ER, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Smith G, Kohl TA, Solano W, Spitaleri A, Steyn AJC, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker AS, Walker TM, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. Nat Commun 2024; 15:488. [PMID: 38216576 PMCID: PMC10786857 DOI: 10.1038/s41467-023-44325-5] [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: 03/06/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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Karthik K, Subramanian S, Vinoli Priyadharshini M, Jawahar A, Anbazhagan S, Kathiravan RS, Thomas P, Babu RPA, Gopalan Tirumurugaan K, Raj GD. Whole genome sequencing and comparative genomics of Mycobacterium orygis isolated from different animal hosts to identify specific diagnostic markers. Front Cell Infect Microbiol 2023; 13:1302393. [PMID: 38188626 PMCID: PMC10770871 DOI: 10.3389/fcimb.2023.1302393] [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: 09/26/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Mycobacterium orygis, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members. Methods Isolation and whole genome sequencing of M. orygis was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference. Results M. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification. Conclusion The present study is yet another supportive evidence that M. orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.
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Affiliation(s)
- Kumaragurubaran Karthik
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, India
| | - Saraswathi Subramanian
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Michael Vinoli Priyadharshini
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Ayyaru Jawahar
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Subbaiyan Anbazhagan
- Indian Council of Medical Research (ICMR)-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, India
| | - Ramaiyan Selvaraju Kathiravan
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, Indian Council of Agricultural Research (ICAR)- India Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Ramasamy Parthiban Aravindh Babu
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Krishnaswamy Gopalan Tirumurugaan
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Gopal Dhinakar Raj
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
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Islam MR, Sharma MK, KhunKhun R, Shandro C, Sekirov I, Tyrrell GJ, Soualhine H. Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage Mycobacterium orygis. J Clin Microbiol 2023; 61:e0026023. [PMID: 37877705 PMCID: PMC10662373 DOI: 10.1128/jcm.00260-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphism (SNP) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of the MTBC species. WGS-based SNP analysis was performed for 61 isolates from different provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in the gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB 277 (A→G), gyrB 1478 (T→C), leuS 1064 (A→T), mmpL6 486 (T→C), and mmpS6 334 (C→G), are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that the studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high-confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.
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Affiliation(s)
- Md Rashedul Islam
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rupinder KhunKhun
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Cary Shandro
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Gregory J. Tyrrell
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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Brenner EP, Sreevatsan S. Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex. BMC Med Genomics 2023; 16:260. [PMID: 37875894 PMCID: PMC10598944 DOI: 10.1186/s12920-023-01695-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND While Mycobacterium tuberculosis complex (MTBC) variants are clonal, variant tuberculosis is a human-adapted pathogen, and variant bovis infects many hosts. Despite nucleotide identity between MTBC variants exceeding 99.95%, it remains unclear what drives these differences. Markers of adaptation into variants were sought by bacterial genome-wide association study of single nucleotide polymorphisms extracted from 6,362 MTBC members from varied hosts and countries. RESULTS The search identified 120 genetic loci associated with MTBC variant classification and certain hosts. In many cases, these changes are uniformly fixed in certain variants while absent in others in this dataset, providing good discriminatory power in distinguishing variants by polymorphisms. Multiple changes were seen in genes for cholesterol and fatty acid metabolism, pathways previously proposed to be important for host adaptation, including Mce4F (part of the fundamental cholesterol intake Mce4 pathway), 4 FadD and FadE genes (playing roles in cholesterol and fatty acid utilization), and other targets like Rv3548c and PTPB, genes shown essential for growth on cholesterol by transposon studies. CONCLUSIONS These findings provide a robust set of genetic loci associated with the split of variant bovis and variant tuberculosis, and suggest that adaptation to new hosts could involve adjustments in uptake and catabolism of cholesterol and fatty acids, like the proposed specialization to different populations in MTB lineages by alterations to host lipid composition. Future studies are required to elucidate how the associations between cholesterol profiles and pathogen utilization differences between hosts and MTBC variants, as well as the investigation of uncharacterized genes discovered in this study. This information will likely provide an understanding on the diversification of MBO away from humans and specialization towards a broad host range.
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Affiliation(s)
- Evan P Brenner
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA.
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Carter J. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. RESEARCH SQUARE 2023:rs.3.rs-3378915. [PMID: 37886522 PMCID: PMC10602118 DOI: 10.21203/rs.3.rs-3378915/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis; however, molecular diagnostics to date have focused largely on first-line drugs and predicting binary susceptibilities. We used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration in 15,211 Mycobacterium tuberculosis patient isolates from 23 countries across five continents. This identified 492 unique MIC-elevating variants across thirteen drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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Couvin D, Stattner E, Segretier W, Cazenave D, Rastogi N. simpiTB - a pipeline designed to extract meaningful information from whole genome sequencing data of Mycobacterium tuberculosis complex, allows to combine genomic, phylogenetic and clustering analyses in existing SITVIT databases. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105466. [PMID: 37331497 DOI: 10.1016/j.meegid.2023.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/20/2023]
Abstract
Data obtained from new sequencing technologies are evolving rapidly, leading to the development of specific bioinformatic tools, pipelines and softwares. Several algorithms and tools are today available allowing a better identification and description of Mycobacterium tuberculosis complex (MTBC) isolates worldwide. Our approach consists in applying existing methods to analyze DNA sequencing data (from FASTA or FASTQ files), and tentatively extract meaningful information that would facilitate identification as well as a better understanding and management of MTBC isolates (taking into account whole genome sequencing and classical genotyping data). The aim of this study is to propose a pipeline analysis allowing to potentially simplify MTBC data analysis by providing different ways to interpret genomic or genotyping information based on existing tools. Furthermore, we propose a "reconciledTB" list making a link with results directly obtained from whole genome sequencing (WGS) data and results obtained from classical genotyping analysis (data inferred from SpoTyping and MIRUReader). Data visualization graphics and trees generated provide additional elements to better understand and confer associations among information overlap analyses. Additionally, comparison between data entered in an international genotyping database (SITVITEXTEND) and ensuing data obtained from the pipeline not only provide meaningful information, but further suggest that simpiTB could also be suitable for new data integration in specific TB genotyping databases.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France; Transmission, Reservoir and Diversity of Pathogens Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France.
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Damien Cazenave
- Transmission, Reservoir and Diversity of Pathogens Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France
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Sumanth LJ, Suresh CR, Venkatesan M, Manesh A, Behr MA, Kapur V, Michael JS. Clinical features of human tuberculosis due to Mycobacterium orygis in Southern India. J Clin Tuberc Other Mycobact Dis 2023; 32:100372. [PMID: 37168873 PMCID: PMC10164920 DOI: 10.1016/j.jctube.2023.100372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Mycobacterium orygis is a member of the Mycobacterium tuberculosis complex (MTBC) and causes tuberculosis in a variety of animals, including humans in South Asia. Here, we describe the clinical features associated with 8 human cases of whole genome sequence (WGS) confirmed M. orygis from a tertiary care hospital in South India during 2018-2019. The patient ages ranged from 9 to 51 years, with 5 females and 3 males included. All the patients had extrapulmonary disease with 2 having concomitant pulmonary involvement. Clinical improvement was documented after a full course of anti-tuberculosis therapy in 6 cases for whom follow-up was available. Taken together, the results show that M. orygis causes human tuberculosis in India, with a predominant extrapulmonary disease. Standardized molecular assays of this emerging member of the MTBC are needed to provide further information on the frequency of M. orygis infection in India and other countries where it is found in livestock and domestic wildlife.
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Affiliation(s)
- Lydia Jennifer Sumanth
- Associate Physician, Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | | | - Manigandan Venkatesan
- Research Associate, Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Abi Manesh
- Associate Professor, Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Marcel A. Behr
- Professor of Medicine, McGill International TB Centre, Montreal, Quebec H4A 3S5, Canada
| | - Vivek Kapur
- Professor, Infectious Diseases and Microbiology, The Pennsylvania State University, State College, PA 16802-3500, USA
| | - Joy Sarojini Michael
- Professor, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu 632004, India
- Corresponding author.
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Morey-León G, Andrade-Molina D, Fernández-Cadena JC, Berná L. Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador. BMC Genomics 2022; 23:844. [PMID: 36544084 PMCID: PMC9769008 DOI: 10.1186/s12864-022-09042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. RESULTS Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. CONCLUSION This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.
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Affiliation(s)
- Gabriel Morey-León
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.442157.10000 0001 1183 0630Universidad de Guayaquil, Guayaquil, Ecuador ,grid.442156.00000 0000 9557 7590Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Derly Andrade-Molina
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Juan Carlos Fernández-Cadena
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Luisa Berná
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.11630.350000000121657640Facultad de Ciencias, Unidad de Genómica Evolutiva, Universidad de La República, Montevideo, Uruguay
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9
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Dale K, Globan M, Horan K, Sherry N, Ballard S, Tay EL, Bittmann S, Meagher N, Price DJ, Howden BP, Williamson DA, Denholm J. Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 28:100556. [PMID: 36034164 PMCID: PMC9405109 DOI: 10.1016/j.lanwpc.2022.100556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS. METHODS WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number. FINDINGS Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers. INTERPRETATION WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB. FUNDING The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.
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Affiliation(s)
- Katie Dale
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Victoria, Australia
| | - Simone Bittmann
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Justin Denholm
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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11
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Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis. Eur Respir J 2022; 60:2200239. [PMID: 35301246 PMCID: PMC9556810 DOI: 10.1183/13993003.00239-2022] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. While there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, it is necessary to measure the epidemiological cut-off values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-tuberculosis compounds, including bedaquiline and delamanid, derived from 20 637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex, and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression. The proposed ECOFF/ECVs were then validated by comparing with the MIC distributions of high-confidence genetic variants that confer resistance and with qualitative drug susceptibility tests obtained via the Mycobacterial Growth Indicator Tube (MGIT) system or Microscopic-Observation Drug Susceptibility (MODS) assay. These ECOFF/ECVs will inform and encourage the more widespread adoption of broth microdilution: this is a cheap culture-based method that tests the susceptibility of 12-14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.
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Affiliation(s)
- The CRyPTIC Consortium
- For a list of all members of the CRyPTIC Consortium and their affiliations, please see the section at the end of this article
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12
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Wetzstein N, Drummer AP, Bockey A, Herrmann E, Küpper-Tetzel CP, Graf C, Koch B, Goetsch U, Vehreschild MJGT, Guglielmetti L, Lange B, Wichelhaus TA, Stephan C. Occurrence of extrapulmonary tuberculosis is associated with geographical origin: spatial characteristics of the Frankfurt TB cohort 2013-2018. Infection 2022; 51:679-687. [PMID: 36181634 DOI: 10.1007/s15010-022-01921-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/02/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is caused by M. tuberculosis complex (MTB) and pulmonary tuberculosis (PTB) is its classical manifestation. However, in some regions of the world, extrapulmonary TB (EPTB) seems to be more frequent. METHODS We performed a retrospective cohort study of all TB patients treated at University Hospital Frankfurt, Germany, for the time period 2013-2018. Patient charts were reviewed and demographic, clinical, and microbiological data recorded. Patients were subdivided according to their geographic origins. RESULTS Of the 378 included patients, 309 were born outside Germany (81.7%). Three WHO regions were significantly associated with the occurrence of isolated EPTB: the South-East Asian Region (OR 3.37, CI 1.74-6.66, p < 0.001), the African Region (2.20, CI 1.25-3.90, p = 0.006), and the Eastern Mediterranean Region (OR 3.18, CI 1.78-5.76, p < 0.001). On a country level, seven countries of origin could be demonstrated to be significantly associated with the occurrence of isolated EPTB: India (OR 5.58, CI 2.30-14.20, p < 0.001), Nepal (OR 12.75, CI 1.73-259.28, p = 0.027), Afghanistan (OR 3.64, CI 1.14-11.98, p = 0.029), Pakistan (OR 3.64, CI 1.14-11.98, p = 0.029), Eritrea (OR 3.32, CI 1.52-7.47, p = 0.003), Somalia (OR 7.08, CI 2.77-19.43, p < 0.001), and Turkey (OR 9.56, CI 2.52-47.19, p = 0.002). CONCLUSION Geographical origin is a predictor for the occurrence of extrapulmonary TB. This might be linked to a delay in diagnosis in these patients, as well as specific responsible impairments of the host's immune system, possible virulence factors of MTB, and relevant comorbidities.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.
| | - Alena-Pauline Drummer
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Annabelle Bockey
- Department for Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modeling, Goethe University, Frankfurt am Main, Germany
| | - Claus Philippe Küpper-Tetzel
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christiana Graf
- Department of Internal Medicine, Gastroenterology and Hepatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Benjamin Koch
- Department of Internal Medicine, Nephrology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority, City of Frankfurt, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Lorenzo Guglielmetti
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, APHP, Groupe Hospitalier Universitaire Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Paris, France
| | - Berit Lange
- Department for Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christoph Stephan
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
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13
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Consistency of Mycobacterium tuberculosis Complex Spoligotyping between the Membrane-Based Method and In Silico Approach. Microbiol Spectr 2022; 10:e0022322. [PMID: 35467406 PMCID: PMC9241810 DOI: 10.1128/spectrum.00223-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To tackle the spread of tuberculosis (TB), epidemiological studies are undertaken worldwide to investigate TB transmission chains. Clustered regulatory interspaced short palindromic repeats (CRISPR) locus diversity, also called spoligotyping, is a widely used genotyping assay for the characterization of Mycobacterium tuberculosis complex (MTBC). We compared herein the spoligotyping of MTBC clinical isolates using a membrane-based method (following an initial PCR step) and whole-genome sequencing (WGS)-based method (i.e., in silico spoligotyping). All MTBC strains isolated at the Lyon University Hospital, France, between November 2016 and December 2020 were included (n = 597). Spoligotyping profiles were also used for species identification among the MTBC. Outputs of both methods were analyzed, and discrepant results were investigated thanks to CRISPRbuilder-TB. The overall agreement was 85.7%. Spacer discrepancies observed between the methods were due to the insertion of IS6110 within the direct repeat (DR) sequence upstream or downstream of spacers, mutated DR sequences, or truncated spacers. Discrepancies did not impact species identification. Although spoligotyping-based species identification was inconclusive for 29 isolates, SNP-based phylogeny conducted after WGS allowed the identification of 23 M. tuberculosis (Mtb), 2 M. canettii, and 4 mixed MTBC infections. WGS yielded very few discrepancies compared to membrane-based spoligotyping. Overall agreement was significantly improved (92.4%) by the CRISPR locus reconstruction using CRISPRbuilder-TB for the MTBC isolates with the shared international type 53 in silico spoligotyping. A smooth transition from the membrane-based to the in silico-based genotyping of M. tuberculosis isolates is, therefore, possible for TB diagnosis and epidemiologic survey. IMPORTANCE Whole-genome sequencing (WGS) has profoundly transformed the perspectives of tuberculosis (TB) diagnosis, providing a better discriminatory power to determine relatedness between Mycobacterium tuberculosis complex (MTBC) isolates. Previous genotyping approaches, such as spoligotyping consisting of an initial PCR step followed by reverse dot hybridization, are currently being replaced by WGS. Several pipelines have been developed to extract a spoligotype from WGS data (in silico spoligotyping) allowing for the continuity of MTBC molecular surveys before and after WGS implementation. The present study found very good overall agreement between hybridization to membrane-based spoligotyping and in silico spoligotyping, indicating the possibility of a smooth transition from the traditional to the in silico-based genotyping of MTBC isolates for TB diagnosis and epidemiological survey.
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14
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Smith TM, Youngblom MA, Kernien JF, Mohamed MA, Fry SS, Bohr LL, Mortimer TD, O'Neill MB, Pepperell CS. Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. eLife 2022; 11:e78454. [PMID: 35726854 PMCID: PMC9213004 DOI: 10.7554/elife.78454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/15/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.
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Affiliation(s)
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - John F Kernien
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Mohamed A Mohamed
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Sydney S Fry
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Mary B O'Neill
- Laboratoire de Biochimie (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL UniversitéParisFrance
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
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15
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de Neeling AJ, Jonckers Nieboer LF, Mulder A, Mariman R, Anthony RM, van Soolingen D. Tracking Mycobacterium tuberculosis sequencing samples using unique spikes of random DNA. J Microbiol Methods 2022; 197:106482. [PMID: 35551970 DOI: 10.1016/j.mimet.2022.106482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
In the Netherlands, local laboratories are involved in the primary diagnosis of tuberculosis. Positive Mycobacterium tuberculosis complex cultures are sent to the National Institute for Public Health and the Environment (RIVM) for species identification, epidemiological typing, and screening for resistance by Whole Genome Sequencing (WGS). Occasional sample-swaps and cross-contaminations are known to occur in the diagnostic procedures. Such errors may lead to incorrect diagnoses resulting in the unnecessary or sub-optimal treatment of patients. Internal controls throughout the process ideally allow the early detection of such mistakes.
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Affiliation(s)
- Albert J de Neeling
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
| | - Lucia F Jonckers Nieboer
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Arnout Mulder
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rob Mariman
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Richard M Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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16
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Balamurugan M, Banerjee R, Kasibhatla SM, Achalere A, Joshi R. Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches. Front Genet 2022; 13:800083. [PMID: 35495132 PMCID: PMC9043288 DOI: 10.3389/fgene.2022.800083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A total of two lineages of Mycobacterium tuberculosis var. africanum (Maf), L5 and L6, which are members of the Mycobacterium tuberculosis complex (MTBC), are responsible for causing tuberculosis in West Africa. Regions of difference (RDs) are usually used for delineation of MTBC. With increased data availability, single nucleotide polymorphisms (SNPs) promise to provide better resolution. Publicly available 380 Maf samples were analyzed for identification of “core-cluster-specific-SNPs,” while additional 270 samples were used for validation. RD-based methods were used for lineage-assignment, wherein 31 samples remained unidentified. The genetic diversity of Maf was estimated based on genome-wide SNPs using phylogeny and population genomics approaches. Lineage-based clustering (L5 and L6) was observed in the whole genome phylogeny with distinct sub-clusters. Population stratification using both model-based and de novo approaches supported the same observations. L6 was further delineated into three sub-lineages (L6.1–L6.3), whereas L5 was grouped as L5.1 and L5.2 based on the occurrence of RD711. L5.1 and L5.2 were further divided into two (L5.1.1 and L5.1.2) and four (L5.2.1–L5.2.4) sub-clusters, respectively. Unassigned samples could be assigned to definite lineages/sub-lineages based on clustering observed in phylogeny along with high-confidence posterior membership scores obtained during population stratification. Based on the (sub)-clusters delineated, “core-cluster-specific-SNPs” were derived. Synonymous SNPs (137 in L5 and 128 in L6) were identified as biomarkers and used for validation. Few of the cluster-specific missense variants in L5 and L6 belong to the central carbohydrate metabolism pathway which include His6Tyr (Rv0946c), Glu255Ala (Rv1131), Ala309Gly (Rv2454c), Val425Ala and Ser112Ala (Rv1127c), Gly198Ala (Rv3293) and Ile137Val (Rv0363c), Thr421Ala (Rv0896), Arg442His (Rv1248c), Thr218Ile (Rv1122), and Ser381Leu (Rv1449c), hinting at the differential growth attenuation. Genes harboring multiple (sub)-lineage-specific “core-cluster” SNPs such as Lys117Asn, Val447Met, and Ala455Val (Rv0066c; icd2) present across L6, L6.1, and L5, respectively, hinting at the association of these SNPs with selective advantage or host-adaptation. Cluster-specific SNPs serve as additional markers along with RD-regions for Maf delineation. The identified SNPs have the potential to provide insights into the genotype–phenotype correlation and clues for endemicity of Maf in the African population.
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17
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Couvin D, Cervera-Marzal I, David A, Reynaud Y, Rastogi N. SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis. Database (Oxford) 2022; 2022:6506437. [PMID: 35028657 PMCID: PMC8962452 DOI: 10.1093/database/baab081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022]
Abstract
Limited data are available for bovine tuberculosis and the infections it can cause in humans and other mammals. We therefore constructed a publicly accessible SITVITBovis database that incorporates genotyping and epidemiological data on Mycobacterium bovis. It also includes limited data on Mycobacterium caprae (previously synonymous with the name M. bovis subsp. Caprae) that can infect both animals and humans. SITVITBovis incorporates data on 25,741 isolates corresponding to 60 countries of origin (75 countries of isolation). It reports a total of 1000 spoligotype patterns: 537 spoligotype international types (SITs, containing 25 278 clinical isolates) and 463 orphan patterns, allowing a wide overview of the geographic distribution of various phylogenetical sublineages (BOV_1, BOV_2, BOV_3 and BOV_4-CAPRAE). The SIT identifiers of the SITVITBovis were compared to the SB numbers of the Mbovis.org database to facilitate crosscheck among databases. Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. Significant differences were observed when comparing age/gender of human isolates as well as various hosts. The database includes information on the regions where a strain was isolated as well as hosts involved, making it possible to see geographic trends. SITVITBovis is publicly accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis. Finally, a future second version is currently in progress to allow query of associated whole-genome sequencing data. Database URLhttp://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Iñaki Cervera-Marzal
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Audrey David
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Yann Reynaud
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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Mave V, Chen L, Ranganathan UD, Kadam D, Vishwanathan V, Lokhande R, S SK, Kagal A, Pradhan N, Shivakumar SVBY, Paradkar MS, Deshmukh S, Tornheim JA, Kornfeld H, Farhat M, Gupta A, Padmapriyadarsini C, Gupte N, Golub JE, Mathema B, Kreiswirth BN. Whole Genome Sequencing Assessing Impact of Diabetes Mellitus on Tuberculosis Mutations and Type of Recurrence in India. Clin Infect Dis 2022; 75:768-776. [PMID: 34984435 PMCID: PMC9477453 DOI: 10.1093/cid/ciab1067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evidence describing the impact of diabetes mellitus (DM) on the recurrence and mutation rate of Mycobacterium tuberculosis (Mtb) is limited. METHODS This study was nested in 3 cohort studies of tuberculosis (TB) patients with and without DM in India. Paired Mtb isolates recovered at baseline and treatment failure/recurrence underwent whole genome sequencing. We compared acquisition of single-nucleotide polymorphisms (SNPs), TB drug resistance mutations, and type of recurrence (endogenous reactivation [<8 SNPs] or exogenous reinfection [≥8 SNPs]) by DM status. RESULTS Of 1633 enrolled in the 3 parent cohorts, 236 (14.5%) had microbiologically confirmed TB treatment failure/recurrence; 76 Mtb isolate pairs were available for sequencing (22 in TB-DM and 54 in TB-only). The SNP acquisition rate was overall was 0.43 (95% confidence interval [CI], .25-.64) per 1 person-year (PY); 0.77 (95% CI, .40-1.35) per 1 PY, and 0.44 (95% CI, .19-.86) per 1 PY at treatment failure and recurrence, respectively. Significant difference in SNP rates by DM status was seen at recurrence (0.21 [95% CI, .04-.61]) per 1 PY for TB-only vs 1.28 (95% CI, .41-2.98) per 1 PY for TB-DM; P = .02). No significant difference in SNP rates by DM status was observed at treatment failure. Acquired TB drug resistance was seen in 4 of 18 (22%) in TB-DM vs 4 of 45 (9%) in TB-only (P = .21). Thirteen (17%) participants had exogenous reinfection; the reinfection rate at recurrence was 25% (3/12) for TB-DM vs 17% (4/24) in TB-only (P = .66). CONCLUSIONS Considerable intrahost Mtb mutation rates were present at recurrence among patients with DM in India. One-fourth of patients with DM had exogenous reinfection at recurrence.
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Affiliation(s)
- Vidya Mave
- Correspondence: V. Mave, Byramjee-Jeejeebhoy Medical College-Johns Hopkins University Clinical Research Site, Jai Prakash Narayan Road, First Floor, Pune, Maharashtra, India 411001 ()
| | - Liang Chen
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, New Jersey, USA
| | | | - Dileep Kadam
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | | | - Rahul Lokhande
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | - Siva Kumar S
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Anju Kagal
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | - Neeta N Pradhan
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India,Johns Hopkins India, Pune, India
| | | | - Mandar S Paradkar
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India,Johns Hopkins India, Pune, India
| | - Sona Deshmukh
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India,Johns Hopkins India, Pune, India
| | | | | | - Maha Farhat
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amita Gupta
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Nikhil Gupte
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Johns Hopkins India, Pune, India
| | - Jonathan E Golub
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Barry N Kreiswirth
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, New Jersey, USA
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20
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Freschi L, Vargas R, Husain A, Kamal SMM, Skrahina A, Tahseen S, Ismail N, Barbova A, Niemann S, Cirillo DM, Dean AS, Zignol M, Farhat MR. Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. Nat Commun 2021; 12:6099. [PMID: 34671035 PMCID: PMC8528816 DOI: 10.1038/s41467-021-26248-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 09/06/2021] [Indexed: 01/10/2023] Open
Abstract
Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.
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Affiliation(s)
- Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ashaque Husain
- Directorate General of Health Services, Ministry of Health and Family Welfare, Dhaka, Bangladesh
| | - S M Mostofa Kamal
- Department of Pathology and Microbiology, National Institute of Diseases of the Chest and Hospital, Dhaka, Bangladesh
| | - Alena Skrahina
- Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Sabira Tahseen
- National Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - Nazir Ismail
- National Institute for Communicable Diseases, Sandringham, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anna Barbova
- Central Reference Laboratory on Tuberculosis Microbiological Diagnostics, Ministry of Health, Kiev, Ukraine
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Borstel Research Centre, Borstel, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna S Dean
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Matteo Zignol
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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21
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Gupta A, Alland D. Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis. Nat Commun 2021; 12:4702. [PMID: 34349104 PMCID: PMC8339072 DOI: 10.1038/s41467-021-25055-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis can adapt to changing environments by non-heritable mechanisms. Frame-shifting insertions and deletions (indels) may also participate in adaptation through gene disruption, which could be reversed by secondary introduction of a frame-restoring indel. We present ScarTrek, a program that scans genomic data for indels, including those that together disrupt and restore a gene's reading frame, producing "frame-shift scars" suggestive of reversible gene inactivation. We use ScarTrek to analyze 5977 clinical M. tuberculosis isolates. We show that indel frequency inversely correlates with genomic linguistic complexity and varies with gene-position and gene-essentiality. Using ScarTrek, we detect 74 unique frame-shift scars in 48 genes, with a 3.74% population-level incidence of unique scar events. We find multiple scars in the ESX-1 gene cluster. Six scars show evidence of convergent evolution while the rest shared a common ancestor. Our results suggest that sequential indels are a mechanism for reversible gene silencing and adaptation in M. tuberculosis.
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Affiliation(s)
- Aditi Gupta
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, USA.
| | - David Alland
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, USA.
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22
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Abstract
Mycobacterium tuberculosis complex (MTBC) species are classic examples of genetically monomorphic microorganisms due to their low genetic variability. Whole-genome sequencing made it possible to describe both the main species within the complex and M. tuberculosis lineages and sublineages. This differentiation is based on single nucleotide polymorphisms (SNPs) and large sequence polymorphisms in the so-called regions of difference (RDs). Although a number of studies have been performed to elucidate RD localizations, their distribution among MTBC species, and their role in the bacterial life cycle, there are some inconsistencies and ambiguities in the localization of RDs in different members of the complex. To address this issue, we conducted a thorough search for all possible deletions in the WGS data collection comprising 721 samples representing the full MTBC diversity. Discovered deletions were compared with a list of all previously described RDs. As with the SNP-based analysis, we confirmed the specificities of 79 regions at the species, lineage, or sublineage level, 17 of which are described for the first time. We also present RDscan (https://github.com/dbespiatykh/RDscan), an open-source workflow, which detects deletions from short-read sequencing data and correlates the results with high-specificity RDs, curated in this study. Testing of the workflow on a collection comprising ∼7,000 samples showed a high specificity of the found RDs. This study provides novel details that can contribute to a better understanding of the species differentiation within the MTBC and can help to determine how individual clusters evolve within various MTBC species. IMPORTANCE Reductive genome evolution is one of the most important and intriguing adaptation strategies of different living organisms to their environment. Mycobacterium offers several notorious examples of either naturally reduced (Mycobacterium leprae) or laboratory-reduced (Mycobacterium bovis BCG) genomes. Mycobacterium tuberculosis complex has its phylogeny unambiguously framed by large sequence polymorphisms that present unidirectional unique event changes. In the present study, we curated all known regions of difference and analyzed both Mycobacterium tuberculosis and animal-adapted MTBC species. For 79 loci, we have shown a relationship with phylogenetic units, which can serve as a marker for diagnosing or studying biological effects. Moreover, intersections were found for some loci, which may indicate the nonrandomness of these processes and the involvement of these regions in the adaptation of bacteria to external conditions.
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23
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Bajaj AO, Saraswat S, Knuuttila JEA, Freeke J, Stielow JB, Barker AP. Accurate Identification of Closely Related Mycobacterium tuberculosis Complex Species by High Resolution Tandem Mass Spectrometry. Front Cell Infect Microbiol 2021; 11:656880. [PMID: 34239815 PMCID: PMC8259740 DOI: 10.3389/fcimb.2021.656880] [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: 01/21/2021] [Accepted: 05/07/2021] [Indexed: 11/22/2022] Open
Abstract
Rapid and accurate differentiation of Mycobacterium tuberculosis complex (MTBC) species from other mycobacterium is essential for appropriate therapeutic management, timely intervention for infection control and initiation of appropriate health care measures. However, routine clinical characterization methods for Mycobacterium tuberculosis (Mtb) species remain both, time consuming and labor intensive. In the present study, an innovative liquid Chromatography-Mass Spectrometry method for the identification of clinically most relevant Mycobacterium tuberculosis complex species is tested using a model set of mycobacterium strains. The methodology is based on protein profiling of Mycobacterium tuberculosis complex isolates, which are used as markers of differentiation. To test the resolving power, speed, and accuracy of the method, four ATCC type strains and 37 recent clinical isolates of closely related species were analyzed using this new approach. Using different deconvolution algorithms, we detected hundreds of individual protein masses, with a subpopulation of these functioning as species-specific markers. This assay identified 216, 260, 222, and 201 proteoforms for M. tuberculosis ATCC 27294™, M. microti ATCC 19422™, M. africanum ATCC 25420™, and M. bovis ATCC 19210™ respectively. All clinical strains were identified to the correct species with a mean of 95% accuracy. Our study successfully demonstrates applicability of this novel mass spectrometric approach to identify clinically relevant Mycobacterium tuberculosis complex species that are very closely related and difficult to differentiate with currently existing methods. Here, we present the first proof-of-principle study employing a fast mass spectrometry-based method to identify the clinically most prevalent species within the Mycobacterium tuberculosis species complex.
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Affiliation(s)
- Amol O Bajaj
- Research & Development, Associated Regional and University Pathologists, Inc. (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Suraj Saraswat
- Research & Development, Associated Regional and University Pathologists, Inc. (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Juha E A Knuuttila
- Research & Development, Thermo Fisher Scientific, Helsinki-Vantaa, Finland
| | - Joanna Freeke
- Centre for Infectious Diseases, Radboud University Medical Center (UMC), Nijmegen, Netherlands.,Research & Development, Thermo Fisher Scientific, Landsmeer, Netherlands
| | - J Benjamin Stielow
- Centre for Infectious Diseases, Radboud University Medical Center (UMC), Nijmegen, Netherlands.,Research & Development, Thermo Fisher Scientific, Landsmeer, Netherlands
| | - Adam P Barker
- Research & Development, Associated Regional and University Pathologists, Inc. (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
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24
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Bogaerts B, Delcourt T, Soetaert K, Boarbi S, Ceyssens PJ, Winand R, Van Braekel J, De Keersmaecker SCJ, Roosens NHC, Marchal K, Mathys V, Vanneste K. A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches. J Clin Microbiol 2021; 59:e00202-21. [PMID: 33789960 PMCID: PMC8316078 DOI: 10.1128/jcm.00202-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/27/2021] [Indexed: 01/18/2023] Open
Abstract
The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.
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Affiliation(s)
- Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Julien Van Braekel
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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25
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Zhao F, Zhang J, Wang X, Liu L, Gong J, Zhai Z, He L, Meng F, Xiao D. A multisite SNP genotyping and macrolide susceptibility gene method for Mycoplasma pneumoniae based on MALDI-TOF MS. iScience 2021; 24:102447. [PMID: 33997713 PMCID: PMC8105657 DOI: 10.1016/j.isci.2021.102447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/20/2021] [Accepted: 04/14/2021] [Indexed: 11/06/2022] Open
Abstract
In this study, a multisite SNP genotyping and macrolide (ML) susceptibility gene test method for Mycoplasma pneumoniae (M. pneumoniae) was developed based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The detection limit of this method for nucleic acids was 102 -103 copies/reaction. Six SNP site-based genotyping and 3 ML susceptibility sites could be detected simultaneously based on multiplex PCR and mass probe. Using the method constructed in this study, 141 Chinese clinical isolates were divided into 8 SNP types. All the SNP test results for the ML susceptibility gene were in line with those of the 23S rRNA sequencing results. With this method, the multisite SNP genotyping and ML susceptibility determination of M. pneumoniae can be completed simultaneously in one test, which greatly reduces the workload and cost, improves the genotyping ability of M. pneumoniae and deserves clinical application. An all-in-one genotyping and macrolide resistance testing method for M. pneumoniae Multisite SNP detection technology was used for genotyping and resistance testing The cost of M. pneumoniae genotyping and macrolide resistance detection was reduced
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Affiliation(s)
- Fei Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Jianzhong Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Xuemei Wang
- Intelligene Biosystems (Qingdao) Co., Ltd, Qingdao, China
| | - Liyong Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Jie Gong
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Zhixiang Zhai
- Intelligene Biosystems (Qingdao) Co., Ltd, Qingdao, China
| | - Lihua He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Fanliang Meng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Di Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
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26
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Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere ID, Asante-Poku A, Asare P, Sánchez-Busó L, Gehre F, Sanoussi CN, Antonio M, Affolabi D, Fyfe J, Beckert P, Niemann S, Alabi AS, Grobusch MP, Kobbe R, Parkhill J, Beisel C, Fenner L, Böttger EC, Meehan CJ, Harris SR, de Jong BC, Yeboah-Manu D, Brites D. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom 2021; 7:000477. [PMID: 33555243 PMCID: PMC8208692 DOI: 10.1099/mgen.0.000477] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
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Affiliation(s)
- Mireia Coscolla
- ISysBio, University of Valencia-FISABIO Joint Unit, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Florian Gehre
- Infectious Disease Epidemiology Department, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- Health Department, East African Community (EAC), Arusha, Tanzania
| | - C. N’Dira Sanoussi
- Laboratoire de Référence des Mycobactéries, Ministry of Health, Cotonou, Bénin
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Martin Antonio
- London School of Hygiene and Tropical Medicine, London, UK
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries, Ministry of Health, Cotonou, Bénin
| | - Janet Fyfe
- Mycobacterium Reference Laboratory, Victoria Infectious Diseases Reference Laboratory, Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research, Borstel, Germany
| | - Abraham S. Alabi
- Centre de Recherches Médicales en Lambaréné (Cermel), Lambaréné, Gabon
| | - Martin P. Grobusch
- Centre de Recherches Médicales en Lambaréné (Cermel), Lambaréné, Gabon
- Institut für Tropenmedizin, Deutsches Zentrum fuer Infektionsforschung, University of Tübingen, Tübingen, Germany
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, The Netherlands
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Germany
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Erik C. Böttger
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Conor J. Meehan
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Simon R. Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Microbiotica Limited, Bioinnovation Centre, Wellcome Genome Campus, Cambridge, CB10 1DR, UK
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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27
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Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, Chin VK. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery. Microbiol Res 2021; 246:126674. [PMID: 33549960 DOI: 10.1016/j.micres.2020.126674] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) refers to a group of mycobacteria encompassing nine members of closely related species that causes tuberculosis in animals and humans. Among the nine members, Mycobacterium tuberculosis (M. tuberculosis) remains the main causative agent for human tuberculosis that results in high mortality and morbidity globally. In general, MTBC species are low in diversity but exhibit distinctive biological differences and phenotypes among different MTBC lineages. MTBC species are likely to have evolved from a common ancestor through insertions/deletions processes resulting in species speciation with different degrees of pathogenicity. The pathogenesis of human tuberculosis is complex and remains poorly understood. It involves multi-interactions or evolutionary co-options between host factors and bacterial determinants for survival of the MTBC. Granuloma formation as a protection or survival mechanism in hosts by MTBC remains controversial. Additionally, MTBC species are capable of modulating host immune response and have adopted several mechanisms to evade from host immune attack in order to survive in humans. On the other hand, current diagnostic tools for human tuberculosis are inadequate and have several shortcomings. Numerous studies have suggested the potential of host biomarkers in early diagnosis of tuberculosis, in disease differentiation and in treatment monitoring. "Multi-omics" approaches provide holistic views to dissect the association of MTBC species with humans and offer great advantages in host biomarkers discovery. Thus, in this review, we seek to understand how the genetic variations in MTBC lead to species speciation with different pathogenicity. Furthermore, we also discuss how the host and bacterial players contribute to the pathogenesis of human tuberculosis. Lastly, we provide an overview of the journey of "omics" approaches in host biomarkers discovery in human tuberculosis and provide some interesting insights on the challenges and directions of "omics" approaches in host biomarkers innovation and clinical implementation.
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Affiliation(s)
- Renuga Devi Kanabalan
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Le Jie Lee
- Prima Nexus Sdn. Bhd., Menara CIMB, Jalan Stesen Sentral 2, Kuala Lumpur, Malaysia
| | - Tze Yan Lee
- Perdana University School of Liberal Arts, Science and Technology (PUScLST), Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan Damansara Heights, Kuala Lumpur, 50490, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, Subang Jaya, 47500, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Rosnah Ismail
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia.
| | - Voon Kin Chin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam Campus, Bandar Puncak Alam, Selangor, 42300, Malaysia.
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28
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Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex. mSystems 2021; 6:6/1/e00934-20. [PMID: 33468705 PMCID: PMC7820667 DOI: 10.1128/msystems.00934-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in M. tuberculosis strain genotyping, its evolutionary path in Mycobacteriaceae is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in M. tuberculosis complex (MTBC). Our global phylogenetic analysis of CRISPR repeats and Cas10 proteins offers evidence of horizontal gene transfer (HGT) of the CRISPR-Cas module in the last common ancestor of MTBC and Mycobacterium canettii from a Streptococcus-like environmental bacterium. Additionally, our results show that the variation of CRISPR-Cas organization in M. tuberculosis lineages, especially in the Beijing sublineage of lineage 2, is due to the transposition of insertion sequence IS6110 The direct repeat (DR) region of the CRISPR-Cas locus acts as a hot spot for IS6110 insertion. We show in M. tuberculosis H37Rv that the repeat at the 5' end of CRISPR1 of the forward strand is an atypical repeat made up partly of IS-terminal inverted repeat and partly CRISPR DR. By tracing an undetectable spacer sequence in the DR region, the two CRISPR loci could theoretically be joined to reconstruct the ancestral single CRISPR-Cas locus organization, as seen in M. canettii This study retracing the evolutionary events of HGT and IS6110-driven genomic deletions helps us to better understand the strain-specific variations in M. tuberculosis lineages.IMPORTANCE Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide. Recent evidence on the functionality of the CRISPR-Cas system in M. tuberculosis has brought back focus on these conserved genetic elements, present in many prokaryotes. Our study advances understanding of mycobacterial CRISPR-Cas origin and its diversity among the different species. We provide phylogenetic evidence of acquisition of CRISPR-Cas type III-A in the last common ancestor shared between MTBC and M. canettii, by HGT-mediated events. The most likely source of HGT was an environmental Firmicutes bacterium. Genomic mapping of the CRISPR loci showed the IS6110 transposition-driven variations in M. tuberculosis strains. Thus, this study offers insights into events related to the evolution of CRISPR-Cas in M. tuberculosis lineages.
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Couvin D, Segretier W, Stattner E, Rastogi N. Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families. Database (Oxford) 2020; 2020:baaa108. [PMID: 33320180 PMCID: PMC7737520 DOI: 10.1093/database/baaa108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/18/2022]
Abstract
Bioinformatic tools are currently being developed to better understand the Mycobacterium tuberculosis complex (MTBC). Several approaches already exist for the identification of MTBC lineages using classical genotyping methods such as mycobacterial interspersed repetitive units-variable number of tandem DNA repeats and spoligotyping-based families. In the recently released SITVIT2 proprietary database of the Institut Pasteur de la Guadeloupe, a large number of spoligotype families were assigned by either manual curation/expertise or using an in-house algorithm. In this study, we present two complementary data-driven approaches allowing fast and precise family prediction from spoligotyping patterns. The first one is based on data transformation and the use of decision tree classifiers. In contrast, the second one searches for a set of simple rules using binary masks through a specifically designed evolutionary algorithm. The comparison with the three main approaches in the field highlighted the good performances of our contributions and the significant runtime gain. Finally, we propose the 'SpolLineages' software tool (https://github.com/dcouvin/SpolLineages), which implements these approaches for MTBC spoligotype families' identification.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F-97183, Abymes, Guadeloupe, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, F-97154, Pointe-à-Pitre, Guadeloupe, France
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, F-97154, Pointe-à-Pitre, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F-97183, Abymes, Guadeloupe, France
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Napier G, Campino S, Merid Y, Abebe M, Woldeamanuel Y, Aseffa A, Hibberd ML, Phelan J, Clark TG. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med 2020; 12:114. [PMID: 33317631 PMCID: PMC7734807 DOI: 10.1186/s13073-020-00817-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages. METHODS To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach. RESULTS By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples. CONCLUSIONS The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform ( https://github.com/jodyphelan/TBProfiler ).
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Affiliation(s)
- Gary Napier
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Yared Merid
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Hawassa University College of Medicine and Health Sciences, Hawassa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Yimtubezinash Woldeamanuel
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Martin L. Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
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Capewell P, Krumrie S, Katzer F, Alexander CL, Weir W. Molecular Epidemiology of Giardia Infections in the Genomic Era. Trends Parasitol 2020; 37:142-153. [PMID: 33067130 DOI: 10.1016/j.pt.2020.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
Giardia duodenalis is a major gastrointestinal parasite of humans and animals across the globe. It is also of interest from an evolutionary perspective as it possesses many features that are unique among the eukaryotes, including its distinctive binucleate cell structure. While genomic analysis of a small number of isolates has provided valuable insights, efforts to understand the epidemiology of the disease and the population biology of the parasite have been limited by the molecular tools currently available. We review these tools and assess the impact of affordable and rapid genome sequencing systems increasingly being deployed in diagnostic settings. While these technologies have direct implications for public and veterinary health, they will also improve our understanding of the unique biology of this fascinating parasite.
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Affiliation(s)
- Paul Capewell
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Sarah Krumrie
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Frank Katzer
- Moredun Research Institute, Pentlands Science Park, Edinburgh, EH26 0PZ, UK
| | - Claire L Alexander
- Scottish Parasitology Diagnostic and Reference Laboratories, Glasgow, G31 2ER, UK
| | - William Weir
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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Colangeli R, Gupta A, Vinhas SA, Chippada Venkata UD, Kim S, Grady C, Jones-López EC, Soteropoulos P, Palaci M, Marques-Rodrigues P, Salgame P, Ellner JJ, Dietze R, Alland D. Mycobacterium tuberculosis progresses through two phases of latent infection in humans. Nat Commun 2020; 11:4870. [PMID: 32978384 PMCID: PMC7519141 DOI: 10.1038/s41467-020-18699-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/03/2020] [Indexed: 12/21/2022] Open
Abstract
Little is known about the physiology of latent Mycobacterium tuberculosis infection. We studied the mutational rates of 24 index tuberculosis (TB) cases and their latently infected household contacts who developed active TB up to 5.25 years later, as an indication of bacterial physiological state and possible generation times during latent TB infection in humans. Here we report that the rate of new mutations in the M. tuberculosis genome decline dramatically after two years of latent infection (two-sided p < 0.001, assuming an 18 h generation time equal to log phase M. tuberculosis, with latency period modeled as a continuous variable). Alternatively, assuming a fixed mutation rate, the generation time increases over the latency duration. Mutations indicative of oxidative stress do not increase with increasing latency duration suggesting a lack of host or bacterial derived mutational stress. These results suggest that M. tuberculosis enters a quiescent state during latency, decreasing the risk for mutational drug resistance and increasing generation time, but potentially increasing bacterial tolerance to drugs that target actively growing bacteria.
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Affiliation(s)
- Roberto Colangeli
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Aditi Gupta
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Solange Alves Vinhas
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | | | - Soyeon Kim
- Frontier Science Foundation, 1371 Beacon Street, Suite #203, Brookline, MA, 02446, USA
| | - Courtney Grady
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Edward C Jones-López
- Division of Infectious Diseases, Department of Medicine. Keck School of Medicine of USC, University of Southern California Los Angeles, Los Angeles, CA, USA
| | - Patricia Soteropoulos
- The Genomics Center, Rutgers-New Jersey Medical School, Newark, NJ, USA
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Moisés Palaci
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | | | - Padmini Salgame
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Jerrold J Ellner
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - David Alland
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA.
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Veyrier FJ, Nieves C, Lefrancois LH, Trigui H, Vincent AT, Behr MA. RskA Is a Dual Function Activator-Inhibitor That Controls SigK Activity Across Distinct Bacterial Genera. Front Microbiol 2020; 11:558166. [PMID: 33013790 PMCID: PMC7509140 DOI: 10.3389/fmicb.2020.558166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/14/2020] [Indexed: 01/25/2023] Open
Abstract
It has been previously shown that RskA, the anti-Sigma factor K of Mycobacterium tuberculosis, inhibits SigK and that mutations in RskA promote high expression of the SigK regulon. The latter observation led us to hypothesize that RskA mutations lead to loss of the anti-Sigma factor function. In this report, we used natural and artificial mutations in RskA to determine the basis of the SigK-RskA partnership. Consistent with predictions, the N-terminal cytoplasmic portion of RskA was sufficient on its own to inhibit SigK. Unexpectedly, RskA also served as an activator of SigK. This activation depended on the same N-terminal region and was enhanced by the membrane-extracellular portion of RskA. Based on this, we engineered similar truncations in a Gram-negative bacterium, namely Yersinia enterocolitica. Again, we observed that, with specific alterations of RskA, we were able to enhance SigK activity. Together these results support an alternative mechanism of anti-Sigma factor function, that we could term modulator (activator-inhibitor) in both Actinobacteria and Gram-negative bacteria, suggesting that Sigma factor activation by anti-Sigma factors could be under-recognized.
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Affiliation(s)
- Frédéric J Veyrier
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Cecilia Nieves
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Louise H Lefrancois
- McGill International TB Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Hana Trigui
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Antony T Vincent
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Marcel A Behr
- McGill International TB Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
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Jajou R, Kohl TA, Walker T, Norman A, Cirillo DM, Tagliani E, Niemann S, de Neeling A, Lillebaek T, Anthony RM, van Soolingen D. Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases. ACTA ACUST UNITED AC 2020; 24. [PMID: 31847944 PMCID: PMC6918587 DOI: 10.2807/1560-7917.es.2019.24.50.1900130] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Whole genome sequencing (WGS) is a reliable tool for studying tuberculosis (TB) transmission. WGS data are usually processed by custom-built analysis pipelines with little standardisation between them. Aim To compare the impact of variability of several WGS analysis pipelines used internationally to detect epidemiologically linked TB cases. Methods From the Netherlands, 535 Mycobacterium tuberculosis complex (MTBC) strains from 2016 were included. Epidemiological information obtained from municipal health services was available for all mycobacterial interspersed repeat unit-variable number of tandem repeat (MIRU-VNTR) clustered cases. WGS data was analysed using five different pipelines: one core genome multilocus sequence typing (cgMLST) approach and four single nucleotide polymorphism (SNP)-based pipelines developed in Oxford, United Kingdom; Borstel, Germany; Bilthoven, the Netherlands and Copenhagen, Denmark. WGS clusters were defined using a maximum pairwise distance of 12 SNPs/alleles. Results The cgMLST approach and Oxford pipeline clustered all epidemiologically linked cases, however, in the other three SNP-based pipelines one epidemiological link was missed due to insufficient coverage. In general, the genetic distances varied between pipelines, reflecting different clustering rates: the cgMLST approach clustered 92 cases, followed by 84, 83, 83 and 82 cases in the SNP-based pipelines from Copenhagen, Oxford, Borstel and Bilthoven respectively. Conclusion Concordance in ruling out epidemiological links was high between pipelines, which is an important step in the international validation of WGS data analysis. To increase accuracy in identifying TB transmission clusters, standardisation of crucial WGS criteria and creation of a reference database of representative MTBC sequences would be advisable.
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Affiliation(s)
- Rana Jajou
- These authors contributed equally.,Center of Epidemiology and Surveillance of infectious diseases, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Thomas A Kohl
- German Center for Infection Research, Borstel site, Borstel, Germany.,Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Borstel, Germany.,These authors contributed equally
| | - Timothy Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany.,Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Borstel, Germany
| | - Albert de Neeling
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Troels Lillebaek
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.,International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Richard M Anthony
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Goig GA, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Navarro D, Borrás R, Comas I. Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study. THE LANCET MICROBE 2020; 1:e175-e183. [DOI: 10.1016/s2666-5247(20)30060-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
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Duffy SC, Srinivasan S, Schilling MA, Stuber T, Danchuk SN, Michael JS, Venkatesan M, Bansal N, Maan S, Jindal N, Chaudhary D, Dandapat P, Katani R, Chothe S, Veerasami M, Robbe-Austerman S, Juleff N, Kapur V, Behr MA. Reconsidering Mycobacterium bovis as a proxy for zoonotic tuberculosis: a molecular epidemiological surveillance study. LANCET MICROBE 2020; 1:e66-e73. [PMID: 32642742 PMCID: PMC7325494 DOI: 10.1016/s2666-5247(20)30038-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Zoonotic tuberculosis is defined as human infection with Mycobacterium bovis. Although globally, India has the largest number of human tuberculosis cases and the largest cattle population, in which bovine tuberculosis is endemic, the burden of zoonotic tuberculosis is unknown. The aim of this study was to obtain estimates of the human prevalence of animal-associated members of the Mycobacterium tuberculosis complex (MTBC) at a large referral hospital in India. Methods We did a molecular epidemiological surveillance study of 940 positive mycobacteria growth indicator tube (MGIT) cultures, collected from patients visiting the outpatient department at Christian Medical College (Vellore, India) with suspected tuberculosis between Oct 1, 2018, and March 31, 2019. A PCR-based approach was applied to subspeciate cultures. Isolates identified as MTBC other than M tuberculosis or as inconclusive on PCR were subject to whole-genome sequencing (WGS), and phylogenetically compared with publicly available MTBC sequences from south Asia. Sequences from WGS were deposited in the National Center for Biotechnology Information Sequence Read Archive, accession number SRP226525 (BioProject database number PRJNA575883). Findings The 940 MGIT cultures were from 548 pulmonary and 392 extrapulmonary samples. A conclusive identification was obtained for all 940 isolates; wild-type M bovis was not identified. The isolates consisted of M tuberculosis (913 [97·1%] isolates), Mycobacterium orygis (seven [0·7%]), M bovis BCG (five [0·5%]), and non-tuberculous mycobacteria (15 [1·6%]). Subspecies were assigned for 25 isolates by WGS, which were analysed against 715 MTBC sequences from south Asia. Among the 715 genomes, no M bovis was identified. Four isolates of cattle origin were dispersed among human sequences within M tuberculosis lineage 1, and the seven M orygis isolates from human MGIT cultures were dispersed among sequences from cattle. Interpretation M bovis prevalence in humans is an inadequate proxy of zoonotic tuberculosis. The recovery of M orygis from humans highlights the need to use a broadened definition, including MTBC subspecies such as M orygis, to investigate zoonotic tuberculosis. The identification of M tuberculosis in cattle also reinforces the need for One Health investigations in countries with endemic bovine tuberculosis. Funding Bill & Melinda Gates Foundation, Canadian Institutes for Health Research.
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Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Sreenidhi Srinivasan
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Megan A Schilling
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, Ames, IA, USA
| | - Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Joy S Michael
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Nitish Bansal
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Sushila Maan
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Deepika Chaudhary
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Premanshu Dandapat
- Eastern Regional Station, Indian Veterinary Research Institute, Indian Council of Agricultural Research, Kolkata, India
| | - Robab Katani
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Shubhada Chothe
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, Ames, IA, USA
| | | | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Shockey AC, Dabney J, Pepperell CS. Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria. Front Genet 2019; 10:477. [PMID: 31214242 PMCID: PMC6558051 DOI: 10.3389/fgene.2019.00477] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.
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Affiliation(s)
- Abigail C. Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Jesse Dabney
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex. Antimicrob Agents Chemother 2019; 63:AAC.00159-19. [PMID: 30962348 DOI: 10.1128/aac.00159-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
Using 894 phylogenetically diverse genomes of the Mycobacterium tuberculosis complex (MTBC), we simulated in silico the ability of the Hain Lifescience GenoType MTBC assay to differentiate the causative agents of tuberculosis. Here, we propose a revised interpretation of this assay to reflect its strengths (e.g., it can distinguish some strains of Mycobacterium canettii and variants of Mycobacterium bovis that are not intrinsically resistant to pyrazinamide) and limitations (e.g., Mycobacterium orygis cannot be differentiated from Mycobacterium africanum).
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Jajou R, van der Laan T, de Zwaan R, Kamst M, Mulder A, de Neeling A, Anthony R, van Soolingen D. WGS more accurately predicts susceptibility of Mycobacterium tuberculosis to first-line drugs than phenotypic testing. J Antimicrob Chemother 2019; 74:2605-2616. [DOI: 10.1093/jac/dkz215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/12/2019] [Accepted: 04/22/2019] [Indexed: 01/13/2023] Open
Abstract
Abstract
Background
Drug-susceptibility testing (DST) of Mycobacterium tuberculosis complex (MTBC) isolates by the Mycobacteria Growth Indicator Tube (MGIT) approach is the most widely applied reference standard. However, the use of WGS is increasing in many developed countries to detect resistance and predict susceptibility. We investigated the reliability of WGS in predicting drug susceptibility, and analysed the discrepancies between WGS and MGIT against the first-line drugs rifampicin, isoniazid, ethambutol and pyrazinamide.
Methods
DST by MGIT and WGS was performed on MTBC isolates received in 2016/2017. Nine genes and/or their promotor regions were investigated for resistance-associated mutations: rpoB, katG, fabG1, ahpC, inhA, embA, embB, pncA and rpsA. Isolates that were discrepant in their MGIT/WGS results and a control group with concordant results were retested in the MGIT, at the critical concentration and a lower concentration, and incubated for up to 45 days after the control tube became positive in the MGIT.
Results
In total, 1136 isolates were included, of which 1121 were routine MTBC isolates from the Netherlands. The negative predictive value of WGS was ≥99.3% for all four first-line antibiotics. The majority of discrepancies for isoniazid and ethambutol were explained by growth at the lower concentrations, and for rifampicin by prolonged incubation in the MGIT, both indicating low-level resistance.
Conclusions
Applying WGS in a country like the Netherlands, with a low TB incidence and low prevalence of resistance, can reduce the need for phenotypic DST for ∼90% of isolates and accurately detect mutations associated with low-level resistance, often missed in conventional DST.
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Affiliation(s)
- Rana Jajou
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Tridia van der Laan
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rina de Zwaan
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Miranda Kamst
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arnout Mulder
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Albert de Neeling
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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