1
|
Rudeeaneksin J, Bunchoo S, Phetsuksiri B, Srisungngam S, Khummin R, Thapa J, Nakajima C, Suzuki Y. The first insight into Mycobacterium tuberculosis complex isolates in the lower northern region in Thailand. Trans R Soc Trop Med Hyg 2024; 118:527-536. [PMID: 38554067 DOI: 10.1093/trstmh/trae014] [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: 11/19/2023] [Revised: 01/21/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) remains an important infectious disease and different genotypes have been reported. This study aimed to investigate the genetic diversity and molecular epidemiology of TB in the lower northern region of Thailand, where genotyping data are limited. METHODS A total of 159 Mycobacterium tuberculosis complex (MTBC) isolates from this region were genotyped by spoligotyping and the major spoligotypes were further subdivided by the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method. RESULTS Spoligotyping identified 34 types and classified them into 14 clusters. East African-Indian (EAI) groups were the most frequent (44.7%), followed by Beijing (36.5%), with a higher prevalence of drug resistance. By 15-loci MIRU-VNTR typing, the major groups of the Beijing and EAI2_NTB were further differentiated into 44 and 21 subtypes forming 9 and 5 subclusters with cluster rates of 0.26 and 0.44, respectively. The Hunter-Gaston Discriminatory Index among the Beijing and EAI2_NTB groups were 0.987 and 0.931, respectively, indicating high diversity. CONCLUSIONS This is the first look at the MTBC genotypes in the lower northern region of Thailand, which could aid in understanding the distribution and potential spread of MTBC and Mycobacterium bovis in the target region to support TB control in Thailand.
Collapse
Affiliation(s)
- Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
- Medical Sciences Technical Office, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Ratchaneeporn Khummin
- Office of Disease Prevention and Control Region 2 Phitsanulok, Department of Disease Control, Ministry of Public Health, Phitsanulok 65000, Thailand
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| |
Collapse
|
2
|
Quan Z, Li M, Chen Y, Liang J, Takiff H, Gao Q. Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection. Eur J Clin Microbiol Infect Dis 2024; 43:297-304. [PMID: 38041721 DOI: 10.1007/s10096-023-04720-8] [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: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate. METHODS We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering. RESULTS The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.
Collapse
Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Yiwang Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Jialei Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
| |
Collapse
|
3
|
Saeed DK, Ashraf J, Hasan Z, Shakoor S, Kanji A, Hasan R. Bedaquiline resistant Mycobacterium tuberculosis clinical isolates with and without rv0678 mutations have similar growth patterns under varying BDQ drug pressure. Tuberculosis (Edinb) 2022; 137:102266. [PMID: 36195000 DOI: 10.1016/j.tube.2022.102266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023]
Abstract
Resistance associated mutations have been reported to alter the growth of Mycobacterium tuberculosis (MTB) isolates under drug pressure. However, there is little information on the growth characteristics of bedaquiline (BDQ) resistant isolates in the presence of BDQ. To further understand the role of rv0678, we aimed to study whether the presence of rv0678 variants in BDQ resistant isolates alters the killing effect of BDQ. We, therefore, selected BDQ resistant clinical MTB isolates with (n = 6) and without (n = 3) variants in rv0678 gene. Using time kill assays, growth inhibition; taken as the relative change in log average colony forming unit (CFU)/ml at selected time points (24-96 h), was studied at Minimum Inhibitory Concentrations (MICs): 0x, 1x, 2.5x, 5x, 7.5x, 10x for these isolates. Growth inhibition was then analyzed using Kruskal Wallis and Kolmogorov Smirnov tests in PRISM vr.9. During the 24-96 h lag phase isolates with and without variants in rv0678 showed a similar growth inhibition pattern. No difference was noted in growth inhibition between BDQ resistant isolates and H37Rv. These findings suggest that role of alternate mechanisms in contributing to BDQ tolerance needs to be explored.
Collapse
Affiliation(s)
- Dania Khalid Saeed
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, UK.
| |
Collapse
|
4
|
Whole-Genome Sequencing for Resistance Prediction and Transmission Analysis of Mycobacterium tuberculosis Complex Strains from Namibia. Microbiol Spectr 2022; 10:e0158622. [PMID: 36165641 PMCID: PMC9603870 DOI: 10.1128/spectrum.01586-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Namibia is among 30 countries with a high burden of tuberculosis (TB), with an estimated incidence of 460 per 100,000 population and around 800 new multidrug-resistant (MDR) TB cases per year. Still, data on the transmission and evolution of drug-resistant Mycobacterium tuberculosis complex (Mtbc) strains are not available. Whole-genome sequencing data of 136 rifampicin-resistant (RIFr) Mtbc strains obtained from 2016 to 2018 were used for phylogenetic classification, resistance prediction, and cluster analysis and linked with phenotypic drug susceptibility testing (pDST) data. Roughly 50% of the strains investigated were resistant to all first-line drugs. Furthermore, 13% of the MDR Mtbc strains were already pre-extensively drug resistant (pre-XDR). The cluster rates were high, at 74.6% among MDR and 85% among pre-XDR strains. A significant proportion of strains had borderline resistance-conferring mutations, e.g., inhA promoter mutations or rpoB L430P. Accordingly, 25% of the RIFr strains tested susceptible by pDST. Finally, we determined a potentially new bedaquiline resistance mutation (Rv0678 D88G) occurring in two independent clusters. High rates of resistance to first-line drugs in line with emerging pre-XDR and likely bedaquiline resistance linked with the ongoing recent transmission of MDR Mtbc clones underline the urgent need for the implementation of interventions that allow rapid diagnostics to break MDR TB transmission chains in the country. A borderline RIFr mutation in the dominant outbreak strain causing discrepancies between phenotypic and genotypic resistance testing results may require breakpoint adjustments but also may allow individualized regimens with high-dose treatment. IMPORTANCE The transmission of drug-resistant tuberculosis (TB) is a major problem for global TB control. Using genome sequencing, we showed that 13% of the multidrug-resistant (MDR) M. tuberculosis complex strains from Namibia are already pre-extensively drug resistant (pre-XDR), which is substantial in an African setting. Our data also indicate that the ongoing transmission of MDR and pre-XDR strains contributes significantly to the problem. In contrast to other settings with higher rates of drug resistance, we found a high proportion of strains having so-called borderline low-level resistance mutations, e.g., inhA promoter mutations or rpoB L430P. This led to the misclassification of 25% of the rifampicin-resistant strains as susceptible by phenotypic drug susceptibility testing. This observation potentially allows individualized regimens with high-dose treatment as a potential option for patients with few treatment options. We also found a potentially new bedaquiline resistance mutation in rv0678.
Collapse
|
5
|
Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3. Genes (Basel) 2022; 13:genes13060990. [PMID: 35741753 PMCID: PMC9222951 DOI: 10.3390/genes13060990] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Tuberculosis still causes 1.5 million deaths annually and is mainly caused by Mycobacterium tuberculosis complex strains belonging to three evolutionary modern lineages (Lineages 2–4). While Lineage 2 and Lineage 4 virtually conquered the world, Lineage 3 is particularly successful in Northern and Eastern Africa, as well as in Southern Asia, the suspected evolutionary origin of these strains. Here, we sought to understand how Lineage 3 strains came to the African continent. To this end, we performed routine genotyping to characterize over 2500 clinical isolates from 38 countries. We then selected a representative collection of 373 isolates for a whole-genome analysis and a modeling approach to infer the geographic origin of different sublineages. In fact, the origin of Lineage 3 could be located in India, and we found evidence for independent introductions of four distinct sublineages into North/East Africa, in line with known ancient exchanges and migrations between both world regions. Our study illustrates that the evolutionary history of humans and their pathogens are closely connected and further provides a systematic understanding of the genomic diversity of Lineage 3, which could be important for the development of new tuberculosis vaccines or new therapeutics. Abstract Mycobacterium tuberculosis complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates.
Collapse
|
6
|
Molecular Epidemiology of Mycobacterium tuberculosis Complex Strains in Urban and Slum Settings of Nairobi, Kenya. Genes (Basel) 2022; 13:genes13030475. [PMID: 35328028 PMCID: PMC8953814 DOI: 10.3390/genes13030475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
Kenya is a country with a high tuberculosis (TB) burden. However, knowledge on the genetic diversity of Mycobacterium tuberculosis complex (MTBC) strains and their transmission dynamics is sparsely available. Hence, we used whole-genome sequencing (WGS) to depict the genetic diversity, molecular markers of drug resistance, and possible transmission clusters among MTBC strains in urban and slum settings of Nairobi. We analyzed 385 clinical MTBC isolates collected between 2010 and 2015 in combination with patients’ demographics. We showed that the MTBC population mainly comprises strains of four lineages (L1–L4). The two dominating lineages were L4 with 55.8% (n = 215) and L3 with 25.7% (n = 99) of all strains, respectively. Genome-based cluster analysis showed that 30.4% (117/385) of the strains were clustered using a ≤5 single-nucleotide polymorphism (SNP) threshold as a surrogate marker for direct patient-to-patient MTBC transmission. Moreover, 5.2% (20/385) of the strains were multidrug-resistant (MDR), and 50.0% (n = 10) were part of a genome-based cluster (i.e., direct MDR MTBC transmission). Notably, 30.0% (6/20) of the MDR strains were resistant to all first-line drugs and are part of one molecular cluster. Moreover, TB patients in urban living setting had 3.8 times the odds of being infected with a drug-resistant strain as compared to patients from slums (p-value = 0.002). Our results show that L4 strains are the main causative agent of TB in Nairobi and MDR strain transmission is an emerging concern in urban settings. This emphasizes the need for more focused infection control measures and contact tracing of patients with MDR TB to break the transmission chains.
Collapse
|
7
|
Survival of hypoxia-induced dormancy is not a common feature of all strains of the Mycobacterium tuberculosis complex. Sci Rep 2021; 11:2628. [PMID: 33514768 PMCID: PMC7846770 DOI: 10.1038/s41598-021-81223-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022] Open
Abstract
While persistence in a dormant state is crucial for the life cycle of Mycobacterium tuberculosis, no investigation regarding dormancy survival of different strains across different lineages was performed so far. We analyzed responses to oxygen starvation and recovery in terms of growth, metabolism, and transcription. All different strains belonging to the Euro-American lineage (L4) showed similar survival and resuscitation characteristics. Different clinical isolates from the Beijing (L2), East African-Indian (L3), and Delhi/Central Asian (L1) lineage did not survive oxygen starvation. We show that dormancy survival is lineage-dependent. Recovery from O2 starvation was only observed in strains belonging to the Euro-American (L4) lineage but not in strains belonging to different lineages (L1, L2, L3). Thus, resuscitation from dormancy after oxygen starvation is not a general feature of all M. tuberculosis strains as thought before. Our findings are of key importance to understand infection dynamics of non-Euro-American vs Euro-American strains and to develop drugs targeting the dormant state.
Collapse
|
8
|
Population Structure of Mycobacterium bovis in Germany: a Long-Term Study Using Whole-Genome Sequencing Combined with Conventional Molecular Typing Methods. J Clin Microbiol 2020; 58:JCM.01573-20. [PMID: 32817084 DOI: 10.1128/jcm.01573-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/10/2020] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of domestic animal and wildlife species and humans. In Germany, bTB still emerges sporadically in cattle herds, free-ranging wildlife, diverse captive animal species, and humans. In order to understand the underlying population structure and estimate the population size fluctuation through time, we analyzed 131 M. bovis strains from animals (n = 38) and humans (n = 93) in Germany from 1999 to 2017 by whole-genome sequencing (WGS), mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing, and spoligotyping. Based on WGS data analysis, 122 out of the 131 M. bovis strains were classified into 13 major clades, of which 6 contained strains from both human and animal cases and 7 only strains from human cases. Bayesian analyses suggest that the M. bovis population went through two sharp anticlimaxes, one in the middle of the 18th century and another one in the 1950s. WGS-based cluster analysis grouped 46 strains into 13 clusters ranging in size from 2 to 11 members and involving strains from distinct host types, e.g., only cattle and also mixed hosts. Animal strains of four clusters were obtained over a 9-year span, pointing toward autochthonous persistent bTB infection cycles. As expected, WGS had a higher discriminatory power than spoligotyping and MIRU-VNTR typing. In conclusion, our data confirm that WGS and suitable bioinformatics constitute the method of choice to implement prospective molecular epidemiological surveillance of M. bovis The population of M. bovis in Germany is diverse, with subtle, but existing, interactions between different host groups.
Collapse
|
9
|
Phylogenetic diversity of Mycobacterium tuberculosis in two geographically distinct locations in Botswana - The Kopanyo Study. INFECTION GENETICS AND EVOLUTION 2020; 81:104232. [PMID: 32028055 DOI: 10.1016/j.meegid.2020.104232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) is divided into several major phylogenetic lineages, with differential distribution globally. Using population-based data collected over a three year period, we performed 24-locus Mycobacterial Interspersed Repeat Unit - Variable Number Tandem Repeat (MIRU-VNTR) genotyping on all culture isolates from two districts of the country that differ in tuberculosis (TB) incidence (Gaborone, the capital, and Ghanzi in the Western Kalahari). The study objective was to characterize the molecular epidemiology of TB in these districts. Overall phylogenetic diversity mirrored that reported from neighboring Republic of South Africa, but differences in the two districts were marked. All four major lineages of M. tuberculosis were found in Gaborone, but only three of the four major lineages were found in Ghanzi. Strain diversity was lower in Ghanzi, with a large proportion (38%) of all isolates having an identical MIRU-VNTR result, compared to 6% of all isolates in Gaborone with the same MIRU-VNTR result. This study demonstrates localized differences in strain diversity by two districts in Botswana, and contributes to a growing characterization of MTBC diversity globally.
Collapse
|
10
|
Arandjelović I, Merker M, Richter E, Kohl TA, Savić B, Soldatović I, Wirth T, Vuković D, Niemann S. Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia. Emerg Infect Dis 2019; 25:555-558. [PMID: 30789133 PMCID: PMC6390760 DOI: 10.3201/eid2503.181220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A retrospective population-based molecular epidemiologic study of multidrug-resistant Mycobacterium tuberculosis complex strains in Serbia (2008–2014) revealed an outbreak of TUR genotype strains in a psychiatric hospital starting around 1990. Drug unavailability, poor infection control, and schizophrenia likely fueled acquisition of additional resistance and bacterial fitness–related mutations over 2 decades.
Collapse
|
11
|
Makhado NA, Matabane E, Faccin M, Pinçon C, Jouet A, Boutachkourt F, Goeminne L, Gaudin C, Maphalala G, Beckert P, Niemann S, Delvenne JC, Delmée M, Razwiedani L, Nchabeleng M, Supply P, de Jong BC, André E. Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study. THE LANCET. INFECTIOUS DISEASES 2018; 18:1350-1359. [DOI: 10.1016/s1473-3099(18)30496-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
|
12
|
Al-Ghafli H, Kohl TA, Merker M, Varghese B, Halees A, Niemann S, Al-Hajoj S. Drug-resistance profiling and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis in Saudi Arabia revealed by whole genome sequencing. Infect Drug Resist 2018; 11:2219-2229. [PMID: 30519060 PMCID: PMC6237142 DOI: 10.2147/idr.s181124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background In Saudi Arabia, cross-border transmission of multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains might be particularly fostered by high immigration rates. Herein, we aimed to elucidate the transmission dynamics of MDR-MTBC strains and reveal a detailed prediction of all resistance-conferring mutations for the first- and second-line drugs. Methods We investigated all MDR-MTBC strains collected between 2015 and 2017 from provincial mycobacteria referral laboratories and compared demographic and clinical parameters to a cohort of non-MDR-TB patients using a whole genome sequencing approach. Clusters were defined based on a maximum strain-to-strain genetic distance of five single-nucleotide polymorphisms (SNPs) as surrogate marker for recent transmission, and then investigated molecular drug-resistance markers (37 genes). Results Forty-eight (67.6%) MDR-MTBC strains were grouped in 14 different clusters, ranging in size from two to six strains; 22.5% (16/71) of all MDR-MTBC isolates were predicted to be fully resistant to all five first-line drugs, and five strains (7.0%) exhibited fluoroquinolone resistance. Moreover, we revealed the presence of 12 compensatory mutations as well as 26 non-synonymous SNPs in the rpoC gene and non-hotspot region in rpoB, respectively. Conclusion Optimized TB molecular surveillance, diagnosis, and patient management are urgently needed to contain MDR-MTBC transmission and prevent the development of additional drug resistance.
Collapse
Affiliation(s)
- Hawra Al-Ghafli
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Bright Varghese
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| | - Anason Halees
- Data and Information Office, Anfas Medical Centre, Hittin District, Riyadh, Saudi Arabia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Sahal Al-Hajoj
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| |
Collapse
|
13
|
Kohl TA, Utpatel C, Niemann S, Moser I. Mycobacterium bovis Persistence in Two Different Captive Wild Animal Populations in Germany: a Longitudinal Molecular Epidemiological Study Revealing Pathogen Transmission by Whole-Genome Sequencing. J Clin Microbiol 2018; 56:e00302-18. [PMID: 29950330 PMCID: PMC6113487 DOI: 10.1128/jcm.00302-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/15/2018] [Indexed: 11/20/2022] Open
Abstract
Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a transmissible disease notifiable to the World Organization for Animal Health and to the European Union, with ongoing efforts of surveillance and eradication in every EU member state. In Germany, a country which has been declared officially free from bovine tuberculosis since 1997 by the EU, M. bovis infections still occur sporadically in cattle and other mammals, including humans. Here, the transmission routes of a bTB outbreak in a wildlife park in Germany affecting different cervid species, bison, lynx, and pot-bellied pigs were followed by employing whole-genome sequencing (WGS) combined with spoligotyping and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. One single M. bovis strain persisted from 2002 to 2015, and transmission between the park and a distantly located captive cervid farm was verified. The spoligotyping patterns remained identical, while MIRU-VNTR typing of 24 loci of the standardized panel and locus 2163a as an additional locus revealed one change at locus 2165 in a strain from a fallow deer and one at locus 2461 in isolates from red deer over the whole time period. WGS analysis confirmed the close relatedness of the isolates, with a maximum of 12 single nucleotide polymorphisms (SNPs) detected between any two sequenced isolates. In conclusion, our data confirm a longitudinal outbreak of M. bovis in a German wildlife park and provide the first insights into the dynamics of different genotyping markers in M. bovis.
Collapse
Affiliation(s)
- Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Irmgard Moser
- Friedrich-Loeffler-Institut, Federal Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| |
Collapse
|
14
|
Kohl TA, Harmsen D, Rothgänger J, Walker T, Diel R, Niemann S. Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System. EBioMedicine 2018; 34:131-138. [PMID: 30115606 PMCID: PMC6116475 DOI: 10.1016/j.ebiom.2018.07.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
Background Global tuberculosis (TB) control is challenged by uncontrolled transmission of Mycobacterium tuberculosis complex (Mtbc) strains, esp. of multidrug (MDR) or extensively resistant (XDR) variants. Precise analysis of transmission networks is the basis to trace outbreak M/XDR clones and improve TB control. However, classical genotyping tools lack discriminatory power due to the high similarity of strains of particular successful lineages, e.g. Beijing or outbreak strains. This can be overcome by whole genome sequencing (WGS) approaches, but these are not yet standardized to facilitate larger investigations encompassing different laboratories or outbreak tracing across borders. Methods We established and improved a whole genome gene-by-gene multi locus sequence typing approach encompassing a stable set of core genome genes (cgMLST) and linked it to a web-based nomenclature server (cgMLST.org) facilitating assignment and storage of allele numbers. Findings We evaluated and refined a previously suggested cgMLST schema by using a reference strain set (n = 251) reflecting the global diversity of the Mtbc. A set of 2891 genes showed excellent performance with at least 97% of the genes reliably identified in strains of all Mtbc lineages and in discriminating outbreak strains. cgMLST allele numbers were automatically retrieved from and stored at cgMLST.org. Interpretation The refined cgMLST schema provides high resolution genome-based typing of clinical strains of all Mtbc lineages. Combined with a web-based nomenclature server, it facilitates rapid, high-resolution, and harmonized tracing of clinical Mtbc strains needed for prospective local and global surveillance.
Collapse
Affiliation(s)
- Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Dag Harmsen
- Department of Periodontology and Restorative Dentistry, University Hospital Münster, 48149 Münster, Germany
| | | | - Timothy Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, 24105 Kiel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany; German Center for Infection Research, Borstel Site, 23845 Borstel, Germany.
| |
Collapse
|
15
|
Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A, Mahasirimongkol S, Yanai H, Yamada N, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Toyo-Oka L, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruengchai W, Palittapongarnpim P, Juthayothin T, Tongsima S, Tokunaga K. Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. Sci Rep 2018; 8:11597. [PMID: 30072734 PMCID: PMC6072702 DOI: 10.1038/s41598-018-29986-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022] Open
Abstract
Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-evolution between the host and M. tuberculosis may also play a role. Here, we reported the genomic analysis of 480 L1 isolates from patients in northern Thailand. The studied bacterial population was genetically diverse, allowing the identification of a total of 18 sublineages distributed into three major clades. The majority of isolates belonged to L1.1 followed by L1.2.1 and L1.2.2. Comparison of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be partially resolved if the entire DR region is investigated. Using the information to map L1 diversity across Southeast Asia highlighted differences in the dominant strain-types in each individual country, despite extensive interactions between populations over time. This finding supported the hypothesis that there is co-evolution between the bacteria and the host, and have implications for tuberculosis disease control.
Collapse
Affiliation(s)
- Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand.
| | - Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Wasna Viratyosin
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Nat Smittipat
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Areeya Disratthakit
- Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Nonthaburi, Thailand
| | | | - Hideki Yanai
- TB-HIV Research Foundation, Chiangrai, Thailand
- Fukujuji Hospital, Japan Anti-tuberculosis Association (JATA), Kiyose, Japan
| | - Norio Yamada
- Research Institute of Tuberculosis, JATA, Kiyose, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Worarat Imasanguan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Pacharee Kantipong
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | | | | | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Wuthiwat Ruengchai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | | | - Tada Juthayothin
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Sissades Tongsima
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| |
Collapse
|
16
|
Godfroid M, Dagan T, Kupczok A. Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts. Genome Biol Evol 2018; 10:1920-1926. [PMID: 30010866 PMCID: PMC6086087 DOI: 10.1093/gbe/evy143] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
DNA acquisition via genetic recombination is considered advantageous as it has the potential to bring together beneficial mutations that emerge independently within a population. Furthermore, recombination is considered to contribute to the maintenance of genome stability by purging slightly deleterious mutations. The prevalence of recombination differs among prokaryotic species and depends on the accessibility of DNA transfer mechanisms. An exceptional example is the human pathogen Mycobacterium tuberculosis (MTB) where no clear transfer mechanisms have been so far characterized and the presence of recombination is questioned. Here, we analyze completely assembled MTB genomes in search for evidence of recombination. We find that putative recombination events are enriched in strains reconstructed by reference-guided assembly and in regions with unreliable alignments. In addition, assembly and alignment artefacts introduce phylogenetic signals that are conflicting the established MTB phylogeny. Our results reveal that the so far reported recombination events in MTB are likely to stem from methodological artefacts. We conclude that no reliable signal of recombination is observed in the currently available MTB genomes. Moreover, our study demonstrates the limitations of reference-guided genome assembly for phylogenetic reconstructions. Rigorously de novo assembled genomes of high quality are mandatory in order to distinguish true evolutionary signal from noise, in particular for low diversity species such as MTB.
Collapse
Affiliation(s)
- Maxime Godfroid
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| |
Collapse
|
17
|
Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C, Yahayah AI, Baddoo A, Ansa GA, Aboagye SY, Asare P, Borrell S, Gehre F, Beckert P, Kohl TA, N'dira S, Beisel C, Antonio M, Niemann S, de Jong BC, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D. Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches. Sci Rep 2018; 8:11269. [PMID: 30050166 PMCID: PMC6062541 DOI: 10.1038/s41598-018-29620-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/16/2018] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches.
Collapse
Affiliation(s)
- Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Mireia Coscollá
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Leonor Sánchez-Busó
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Adwoa Asante-Poku
- 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
| | - Chloe Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Conor Meehan
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Audrey Forson
- Chest Clinic, Korle-Bu Teaching Hospital, Accra, Ghana
| | | | | | - Akosua Baddoo
- Chest Clinic, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Gloria Akosua Ansa
- Public Health Department, University of Ghana Hospital, Legon, Accra, Ghana
| | - Samuel Yaw Aboagye
- 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
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Florian Gehre
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Lübeck, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Lübeck, Germany
| | - Sanoussi N'dira
- National Reference Laboratory for Mycobacteria, Cotonou, Benin
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Antonio
- Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Lübeck, Germany
| | - Bouke C de Jong
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Simon R Harris
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana.
| |
Collapse
|
18
|
Lange C, Alghamdi WA, Al-Shaer MH, Brighenti S, Diacon AH, DiNardo AR, Grobbel HP, Gröschel MI, von Groote-Bidlingmaier F, Hauptmann M, Heyckendorf J, Köhler N, Kohl TA, Merker M, Niemann S, Peloquin CA, Reimann M, Schaible UE, Schaub D, Schleusener V, Thye T, Schön T. Perspectives for personalized therapy for patients with multidrug-resistant tuberculosis. J Intern Med 2018; 284:163-188. [PMID: 29806961 DOI: 10.1111/joim.12780] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
According to the World Health Organization (WHO), tuberculosis is the leading cause of death attributed to a single microbial pathogen worldwide. In addition to the large number of patients affected by tuberculosis, the emergence of Mycobacterium tuberculosis drug-resistance is complicating tuberculosis control in many high-burden countries. During the past 5 years, the global number of patients identified with multidrug-resistant tuberculosis (MDR-TB), defined as bacillary resistance at least against rifampicin and isoniazid, the two most active drugs in a treatment regimen, has increased by more than 20% annually. Today we experience a historical peak in the number of patients affected by MDR-TB. The management of MDR-TB is characterized by delayed diagnosis, uncertainty of the extent of bacillary drug-resistance, imprecise standardized drug regimens and dosages, very long duration of therapy and high frequency of adverse events which all translate into a poor prognosis for many of the affected patients. Major scientific and technological advances in recent years provide new perspectives through treatment regimens tailor-made to individual needs. Where available, such personalized treatment has major implications on the treatment outcomes of patients with MDR-TB. The challenge now is to bring these adances to those patients that need them most.
Collapse
Affiliation(s)
- C Lange
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - W A Alghamdi
- Department of Pharmacotherapy and Translational Research, Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - M H Al-Shaer
- Department of Pharmacotherapy and Translational Research, Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - S Brighenti
- Department of Medicine, Center for Infectious Medicine (CIM), Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - A H Diacon
- Task Applied Science, Bellville, South Africa
- Division of Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - A R DiNardo
- Section of Global and Immigrant Health, Baylor College of Medicine, Houston, TX, USA
| | - H P Grobbel
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - M I Gröschel
- Department of Pumonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | | | - M Hauptmann
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - J Heyckendorf
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - N Köhler
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - T A Kohl
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - M Merker
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - S Niemann
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - C A Peloquin
- Department of Pharmacotherapy and Translational Research, Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - M Reimann
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - U E Schaible
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
- Biochemical Microbiology & Immunochemistry, University of Lübeck, Lübeck, Germany
- LRA INFECTIONS'21, Borstel, Germany
| | - D Schaub
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - V Schleusener
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - T Thye
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - T Schön
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Linköping University, Linköping, Sweden
| |
Collapse
|
19
|
Hauck S, Maiden MCJ. Clonally Evolving Pathogenic Bacteria. MOLECULAR MECHANISMS OF MICROBIAL EVOLUTION 2018. [DOI: 10.1007/978-3-319-69078-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
20
|
Tyler AD, Randell E, Baikie M, Antonation K, Janella D, Christianson S, Tyrrell GJ, Graham M, Van Domselaar G, Sharma MK. Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut, Canada. PLoS One 2017; 12:e0185656. [PMID: 28982116 PMCID: PMC5628838 DOI: 10.1371/journal.pone.0185656] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
Canada has one of the lowest rates of tuberculosis (TB) in the world, however, among certain sub-populations, disease incidence rates approach those observed in sub-Saharan Africa, and other high incidence regions. In this study, we applied mycobacterial interspersed repetitive unit (MIRU) variable number of tandem repeat (VNTR) and whole genome sequencing (WGS) to the analysis of Mycobacterium tuberculosis isolates obtained from Northern communities in the territory of Nunavut. WGS was carried out using the Illumina MiSeq, with identified variants used to infer phylogenetic relationships and annotated to infer functional implications. Additionally, the sequencing data from these isolates were augmented with publically available WGS to evaluate data from the Nunavut outbreak in the broader Canadian context. In this study, isolates could be classified into four major clusters by MIRU-VNTR analysis. These could be further resolved into sub-clusters using WGS. No evidence for antimicrobial resistance, either genetic or phenotypic, was observed in this cohort. Among most subjects with multiple samples, reactivation/incomplete treatment likely contributed to recurrence. However, isolates from two subjects appeared more likely to have occurred via reinfection, based on the large number of genomic single nucleotide variants detected. Finally, although quite distinct from previously reported Canadian MTB strains, isolates obtained from Nunavut clustered most closely with a cohort of samples originating in the Nunavik region of Northern Quebec. This study demonstrates the benefit of using WGS for discriminatory analysis of MTB in Canada, especially in high incidence regions. It further emphasizes the importance of focusing epidemiological intervention efforts on interrupting transmission chains of endemic TB throughout Northern communities, rather than relying on strategies applied in regions where the majority of TB cases result from importation of foreign strains.
Collapse
Affiliation(s)
- Andrea D. Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | | | - Kym Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Debra Janella
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sara Christianson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Gregory J. Tyrrell
- The Division of Diagnostic and Applied Microbiology, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- The Provincial Laboratory for Public Health (Microbiology), Edmonton, Alberta, Canada
| | - Morag Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
21
|
Abstract
ABSTRACT
Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to
Mycobacterium tuberculosis
infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.
Collapse
|