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Esteves LS, Gomes LL, Brites D, Fandinho FCO, Bhering M, Pereira MADS, Conceição EC, Salvato R, da Costa BP, Medeiros RFDM, Caldas PCDS, Redner P, Dalcolmo MP, Eldholm V, Gagneux S, Rossetti ML, Kritski AL, Suffys PN. Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing. Antibiotics (Basel) 2024; 13:496. [PMID: 38927163 PMCID: PMC11200758 DOI: 10.3390/antibiotics13060496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.
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Affiliation(s)
- Leonardo Souza Esteves
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Lia Lima Gomes
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Daniela Brites
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Fátima Cristina Onofre Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Marcela Bhering
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Márcia Aparecida da Silva Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Richard Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
| | - Bianca Porphirio da Costa
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Reginalda Ferreira de Melo Medeiros
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Redner
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Margareth Pretti Dalcolmo
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Vegard Eldholm
- Norwegian Institute of Public Health, 0213 Oslo, Norway;
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Maria Lucia Rossetti
- Laboratório de Biologia Molecular, Universidade Luterana do Brasil (ULBRA), Canoas 92425-020, RS, Brazil;
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
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2
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Busatto C, Possuelo LG, Bierhals D, de Oliveira CL, de Souza MQ, Fanfa D, Barreto É, Schwarzbold P, Von Groll A, Portugal I, Perdigão J, Croda J, Andrews JR, da Silva PA, Ramis IB. Spread of Mycobacterium tuberculosis in Southern Brazilian persons deprived of liberty: a molecular epidemiology study. Eur J Clin Microbiol Infect Dis 2023; 42:297-304. [PMID: 36701032 DOI: 10.1007/s10096-023-04546-4] [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: 08/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
To evaluate the genetic diversity and clustering rates of M. tuberculosis strains to better understand transmission among persons deprived of liberty (PDL) in Rio Grande do Sul (RS), southern Brazil. This is a cross-sectional study, including strains of M. tuberculosis isolated from PDL, stored at the Central Laboratory of RS, in the period from 2013 to 2018. The molecular characterization was performed using the MIRU-VNTR 15 loci method. A total of 598 M. tuberculosis strains were genotyped, and 37.5% were grouped into 53 clusters. Cluster sizes ranged from 2 to 34 strains. The largest cluster of the study had strains from 34 PDL, and 58.8% of the PDL of this cluster were in P01. Among the clusters formed, in 60.3%, there was at least one strain from P01. The most common strains in RS were LAM (53.2%) and Haarlem (31.1%). The LAM strain was the most likely to form clusters, and Haarlem was associated with anti-TB drug resistance. This was translational research, and the results can collaborate with the TB control programs, leading to improved strategies that allow the reduction of the TB burden in prisons.
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Affiliation(s)
- Caroline Busatto
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Lia Gonçalves Possuelo
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Dienefer Bierhals
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Carolina Larrosa de Oliveira
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Mariana Quaresma de Souza
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Dandara Fanfa
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Érika Barreto
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Pauline Schwarzbold
- 8ª Delegacia Penitenciária Regional, Superintendência Dos Serviços Penitenciários, Santa Cruz Do Sul, RS, Brazil
| | - Andrea Von Groll
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Isabel Portugal
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - João Perdigão
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Julio Croda
- Faculdade de Medicina, Universidade Federal Do Mato Grosso Do Sul, Campo Grande, Mato Grosso Do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, Palo Alto, CA, US
| | - Pedro Almeida da Silva
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil.
- Rua General Osório S/N, Centro, Rio Grande Do Sul, Rio Grande, 96200190, Brazil.
| | - Ivy Bastos Ramis
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
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Sousa EDO, Carneiro RTDO, Montes FCOF, Conceição EC, Bartholomay P, Marinho JM, Lima KVB, Natividade MSD, Araújo WND, Matos ED, Barbosa T. Laboratory-based study of drug resistance and genotypic profile of multidrug-resistant tuberculosis isolates in Salvador, Bahia, Brazil. Rev Soc Bras Med Trop 2022; 55:e00132022. [PMID: 35894395 PMCID: PMC9359346 DOI: 10.1590/0037-8682-0013-2022] [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: 01/10/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Surveillance of multidrug resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB) is essential to guide disease dissemination control measures. Brazil contributes to a significant fraction of tuberculosis (TB) cases worldwide, but only few reports addressed MDR/XDR-TB in the country. Methods: This cross-sectional, laboratory-based study describes the phenotypic resistance profiles of isolates obtained between January 2008 and December 2011 in Bahia, Brazil, and sociodemographic, epidemiological, and clinical characteristics (obtained from mandatory national registries) of the corresponding 204 MDR/XDR-TB patients. We analyzed the mycobacterial spoligotyping and variable number of tandem repeats of mycobacterial interspersed repetitive units in 12-loci profiles obtained from Salvador. Results: MDR/XDR-TB patients were predominantly male, had a median age of 43 years, belonged to black ethnicity, and failed treatment before MDR-TB diagnosis. Nearly one-third of the isolates had phenotypic resistance (evaluated by mycobacteria growth indicator tube assay) to second-line anti-TB drugs (64/204, 31%), of which 22% cases (14/64) were diagnosed as XDR-TB. Death was a frequent outcome among these individuals and was associated with resistance to second-line anti-TB drugs. Most isolates successfully genotyped belonged to the Latin-American Mediterranean (LAM) Family, with an unprecedented high proportion of LAM10-Cameroon subfamily bacilli. More than half of these isolates were assigned to a unique cluster by the genotyping methods performed. Large clusters of identical genotypes were also observed among LAM SIT42 and SIT376 strains. Conclusions: We highlight the need for strengthening local and national efforts to perform early detection of TB drug resistance and to prevent treatment discontinuation to limit the emergence of drug-resistant strains.
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Affiliation(s)
- Erivelton de Oliveira Sousa
- Laboratório Central de Saúde Pública Professor Gonçalo Moniz (LACEN-BA), Salvador, BA, Brasil.,Fundação Oswaldo Cruz, Instituto de Pesquisa Gonçalo Moniz, Salvador, BA, Brasil
| | | | | | - Emilyn Costa Conceição
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brasil
| | | | - Jamocyr Moura Marinho
- Escola Baiana de Medicina e Saúde Pública, Faculdade de Medicina, Salvador, Bahia, Brasil
| | | | | | | | - Eliana Dias Matos
- Escola Baiana de Medicina e Saúde Pública, Faculdade de Medicina, Salvador, Bahia, Brasil
| | - Theolis Barbosa
- Fundação Oswaldo Cruz, Instituto de Pesquisa Gonçalo Moniz, Salvador, BA, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
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Medeiros TF, Scheffer MC, Verza M, Salvato RS, Schörner MA, Barazzetti FH, Rovaris DB, Bazzo ML. Genomic characterization of variants on mycolic acid metabolism genes in Mycobacterium tuberculosis isolates from Santa Catarina, Southern Brazil. INFECTION GENETICS AND EVOLUTION 2021; 96:105107. [PMID: 34634381 DOI: 10.1016/j.meegid.2021.105107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 09/24/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis has a complex cell wall containing mycolic acids (MA), which play an important role in pathogenesis, virulence, and survival by protecting the cell against harsh environments. Studies have shown that genes encoding enzymes involved in MA synthesis are essential to mycobacterial functionality. Here, we used whole-genome sequencing to evaluate mutations in genes related to MA metabolism in M. tuberculosis isolates from pulmonary tuberculosis patients of the Florianópolis Metropolitan Area, Santa Catarina, Brazil, and assessed associations with clinical, epidemiological, and genotypic data. The mutations Rv3057c Asp112Ala (104/151), Rv3720 His70Arg (104/151), and Rv3802c Val50Phe (105/151) were identified in about 69% of the isolates and were related to the LAM lineage. SIT 216/LAM5 (13.2%, 20/151) had the highest frequency and presented the mutations accD2 Lys23Glu, kasA Gly269Ser, mmaA4 Asn165Ser, otsB1 Asp617Asn, Rv3057c Asp112Ala, Rv3720 His70Arg, Rv3802c Val50Phe, and tgs4 Ala216Glu. All SIT 73/T isolates (6.6%, 10/151) showed a characteristic and exclusive gene mutation pattern: amiD Rv3376 3790075G > A, fbpA-aftB 4266941G > A, echA11 Asn220fs, and otsB2 Ser110Arg. SITs 20/LAM1, 64/LAM6, 50/H3, 137/X2, and 119/X1 were also related to specific mutations. SITs from the LAM lineage differed in mutation profile from those of the T, Haarlem, and X lineages. Isolates from patients who had treatment failure showed mutations that do not seem to have a pattern related to this outcome. It was possible to identify a broad repertoire of single-nucleotide polymorphisms in genes related to MA metabolism in M. tuberculosis isolates. This study also described, for the first time, the variability between different SITs/sublineages of Lineage 4 circulating in Florianópolis Metropolitan Area.
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Affiliation(s)
- Taiane Freitas Medeiros
- Programa de Pós-graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil; Laboratório de Biologia Molecular, Microbiologia e Sorologia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Mara Cristina Scheffer
- Laboratório de Biologia Molecular, Microbiologia e Sorologia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Mirela Verza
- Programa de Pós-graduação em Clínica Médica, Faculdade de Medicina, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Richard Steiner Salvato
- Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marcos André Schörner
- Programa de Pós-graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil; Laboratório de Biologia Molecular, Microbiologia e Sorologia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Fernando Hartmann Barazzetti
- Laboratório de Biologia Molecular, Microbiologia e Sorologia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Darcita Buerger Rovaris
- Setor de Bacteriologia da Tuberculose, Laboratório Central do Estado de Santa Catarina (LACEN-SC), Florianópolis, Santa Catarina, Brazil
| | - Maria Luiza Bazzo
- Programa de Pós-graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil; Laboratório de Biologia Molecular, Microbiologia e Sorologia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil.
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5
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Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil. Sci Rep 2020; 10:12891. [PMID: 32732910 PMCID: PMC7393130 DOI: 10.1038/s41598-020-69755-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n = 6), 2.0% (n = 3) and 1.3% (n = 2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n = 1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n = 2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.
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6
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Tengan FM, Figueiredo GM, Leite OH, Nunes AK, Manchiero C, Dantas BP, Magri MC, Barone AA, Bernardo WM. Prevalence of multidrug-resistant tuberculosis in Latin America and the Caribbean: a systematic review and meta-analysis. Trop Med Int Health 2020; 25:1065-1078. [PMID: 32506718 DOI: 10.1111/tmi.13453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To evaluate the prevalence of multidrug-resistant tuberculosis (MDR-TB) in individuals living in Latin America and the Caribbean (LAC). METHODS We searched the MEDLINE, Embase and Literatura Latino Americana e do Caribe em Ciências da Saúde (Lilacs) databases until 08 August 2019 for all studies on the subject, without time or language restrictions. Original studies reporting the prevalence of infection with Mycobacterium tuberculosis resistant to isoniazid and rifampicin simultaneously (MDR) in LAC, the prevalence of resistance in cases with no previous treatment (new cases) and the prevalence of resistance in previously treated cases were selected. Considering the expected heterogeneity between studies, all analyses were performed using the random effects model, and heterogeneity was assessed using the I2 statistic. RESULTS We included 91 studies from 16 countries. The estimated overall prevalence was 13.0% (95% CI 12.0-14.0%), and the heterogeneity between studies was substantial (I2 = 96.1%). In the subgroup analyses, it was observed that the prevalence of MDR-TB among new cases was 7.0% (95% CI 6.0-7.0%) and in previously treated cases was 26.0% (95% CI 24.0-28.0%). CONCLUSIONS This review highlights multidrug resistance to antituberculosis drugs in LAC, indicating that prevention strategies have not been effective. Government institutions should invest heavily in strategies for early diagnosis and the rapid availability of effective treatments and prioritise adequate protection for health professionals. In addition, screening programmes should be adopted to prevent secondary cases.
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Affiliation(s)
- Fátima M Tengan
- Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.,Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Gerusa M Figueiredo
- Department of Preventive Medicine, University of São Paulo, São Paulo, Brazil
| | - Olavo Hm Leite
- Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Arielle Ks Nunes
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Carol Manchiero
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Bianca P Dantas
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Mariana C Magri
- Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Antonio A Barone
- Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.,Laboratory of Viral Medical Research in Hepatology, University of São Paulo, São Paulo, Brazil
| | - Wanderley M Bernardo
- School of Medicine, University of São Paulo, São Paulo, Brazil.,Brazilian Medical Association, São Paulo, Brazil
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7
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Bonin CR, Fochat RC, Leite ICG, Pereira TV, Fajardo MDO, Pinto CPG, Macedo RL, Silva MR, Menezes PPL, de Araújo NMJM, da Costa RR. Analysis of anti-tuberculosis drug resistance and sociodemographic and clinical aspects of patients admitted in a referral hospital. EINSTEIN-SAO PAULO 2019; 18:eAO4620. [PMID: 31664329 PMCID: PMC6896654 DOI: 10.31744/einstein_journal/2020ao4620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/05/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To determine the occurrence of anti-tuberculosis drug resistance and its association with sociodemographic and clinical characteristics of patients in a referral hospital. METHODS This was a cross-sectional study based on data from patients who had mycobacterial culture identified and defined antimicrobials sensitivity profile (June 2014 to February 2016). The descriptive statistical analysis and Fisher's exact test were used to compare proportions. RESULTS The study included 104 patients who had positive results for Mycobacterium tuberculosis . Bacilloscopy had high positivity (93.3%). A total of 15 patients (14.4%) had resistant strains and six (5.6%) multidrug-resistant. The sociodemographic and clinical characteristics were not related with resistance. CONCLUSION This study contributed to further the understandings about the tuberculosis patients' profile, the study also served as a tool for development of specific public policies. Patients diagnosed with resistant tuberculosis must be under greater supervision.
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Affiliation(s)
| | | | | | | | | | | | - Raquel Leite Macedo
- Hospital Universitário, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
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8
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Scheffer MC, Prim RI, Wildner LM, Medeiros TF, Maurici R, Kupek E, Bazzo ML. Performance of centralized versus decentralized tuberculosis treatment services in Southern Brazil, 2006-2015. BMC Public Health 2018; 18:554. [PMID: 29699537 PMCID: PMC5922025 DOI: 10.1186/s12889-018-5468-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 04/17/2018] [Indexed: 11/16/2022] Open
Abstract
Background Tuberculosis (TB) control programs face the challenges of decreasing incidence, mortality rates, and drug resistance while increasing treatment adherence. The Brazilian TB control program recommended the decentralization of patient care as a strategy for combating the disease. This study evaluated the performance of this policy in an area with high default rates, comparing epidemiological and operational indicators between two similar municipalities. Methods This study analyzed epidemiological and operational indicators on new cases of pulmonary tuberculosis reported in the Brazilian Notifiable Diseases Information System between 2006 and 2015. In addition, to characterize differences between the populations of the two studied municipalities, a prospective cohort study was conducted between 2014 and 2015, in which patients with new cases of culture-confirmed pulmonary tuberculosis were interviewed and monitored until the disease outcome. A descriptive analysis, the chi-square test, and a Poisson regression model were employed to compare TB treatment outcomes and health care indicators between the municipalities. Results Two thousand three hundred nine cases were evaluated, of which 207 patients were interviewed. Over the 2006–2015 period, TB incidence per 100,000 population in the municipality with decentralized care was significantly higher (39%, 95% CI 27–49%) in comparison to that of the municipality with centralized care. TB treatment default rate (45%, 95% CI 12–90%) was also higher in the municipality with decentralized care. During the two-year follow-up, significant differences were found between patients in centralized care and those in decentralized care regarding treatment success (84.5 vs. 66.1%), treatment default (10.7 vs. 25.8%), illicit drug use (27.7 vs. 45.9%), and homelessness (3.6 vs. 12.9%). The operational indicators revealed that the proportion of control smear tests, medical imaging, and HIV tests were all significantly higher in the centralized care. However, a significantly higher proportion of patients started treatment in the early stages of the disease in the municipality with decentralized care. Conclusions These data showed a low success rate in TB treatment in both municipalities. Decentralization of TB care, alone, did not improve the main epidemiological and operational indicators related to disease control when compared to centralized care. Full implementation of strategies already recommended is needed to improve TB treatment success rates.
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Affiliation(s)
- Mara Cristina Scheffer
- Departamento de Análises Clínicas for Programa de Pós-Graduação em Farmácia da, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rodrigo Ivan Prim
- Departamento de Análises Clínicas for Programa de Pós-Graduação em Farmácia da, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Leticia Muraro Wildner
- Departamento de Análises Clínicas for Programa de Pós-Graduação em Farmácia da, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Taiane Freitas Medeiros
- Departamento de Análises Clínicas for Programa de Pós-Graduação em Farmácia da, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rosemeri Maurici
- Departamento de Clínica Médica, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Emil Kupek
- Departamento de Saúde Pública, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Maria Luiza Bazzo
- Departamento de Análises Clínicas for Programa de Pós-Graduação em Farmácia da, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil. .,Laboratório de Biologia Molecular, Sorologia e Micobactérias, Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Campos Universitário- Trindade, Florianopolis, SC, 88040-900, Brazil.
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Medeiros TF, Nogueira CL, Prim RI, Scheffer MC, Alves EV, Rovaris DB, Zozio T, Rastogi N, Bazzo ML. Molecular epidemiology of Mycobacterium tuberculosis strains from prison populations in Santa Catarina, Southern Brazil. INFECTION GENETICS AND EVOLUTION 2017; 58:34-39. [PMID: 29248797 DOI: 10.1016/j.meegid.2017.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 11/24/2017] [Accepted: 12/13/2017] [Indexed: 11/19/2022]
Abstract
The Tuberculosis (TB) notification rates are 5 to 81 times higher in prisons worldwide when compared to the general population. The state of Santa Catarina (SC) has few epidemiological data regarding TB in prisons. The aim of this study was to evaluate the molecular epidemiology of circulating strains in prisons of SC. The study comprised 95 clinical samples from six prisons. Among the cases included, all subjects were male, predominantly caucasians, and young adults, with low education level. The positive smear in the TB diagnosis comprised 62.0% of cases. About 50% of subjects had some condition associated with TB. The Spoligotyping results showed that the most frequent lineages were LAM (50.7%), T (22.2%) and S (11.6%). The 12-loci MIRU generated 62 different genotypes. The MSTs showed evolutionary relationships between Mycobacterium tuberculosis spoligotypes from SC and evolutionary relationships between the prison isolates and studied parameters. This first study on TB in prison units of SC highlighted the predominance of SIT216/LAM5, and SIT34/S. Interestingly, his profile was found to be different from that observed in a previous study performed with the state's general population. This data shows the need for continued surveillance of episodes of TB occurring among prison inmates in an emerging country like Brazil.
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Affiliation(s)
- Taiane Freitas Medeiros
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Christiane Lourenço Nogueira
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Rodrigo Ivan Prim
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil.
| | - Mara Cristina Scheffer
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Eduardo Venâncio Alves
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Darcita Büerger Rovaris
- Laboratório Central do Estado de Santa Catarina (LACEN/SC), Florianópolis, Santa Catarina, Brazil
| | - Thierry Zozio
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
| | - Maria Luiza Bazzo
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil.
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Blanco-Guillot F, Delgado-Sánchez G, Mongua-Rodríguez N, Cruz-Hervert P, Ferreyra-Reyes L, Ferreira-Guerrero E, Yanes-Lane M, Montero-Campos R, Bobadilla-del-Valle M, Torres-González P, Ponce-de-León A, Sifuentes-Osornio J, Garcia-Garcia L. Molecular clustering of patients with diabetes and pulmonary tuberculosis: A systematic review and meta-analysis. PLoS One 2017; 12:e0184675. [PMID: 28902922 PMCID: PMC5597214 DOI: 10.1371/journal.pone.0184675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Many studies have explored the relationship between diabetes mellitus (DM) and tuberculosis (TB) demonstrating increased risk of TB among patients with DM and poor prognosis of patients suffering from the association of DM/TB. Owing to a paucity of studies addressing this question, it remains unclear whether patients with DM and TB are more likely than TB patients without DM to be grouped into molecular clusters defined according to the genotype of the infecting Mycobacterium tuberculosis bacillus. That is, whether there is convincing molecular epidemiological evidence for TB transmission among DM patients. Objective: We performed a systematic review and meta-analysis to quantitatively evaluate the propensity for patients with DM and pulmonary TB (PTB) to cluster according to the genotype of the infecting M. tuberculosis bacillus. Materials and methods We conducted a systematic search in MEDLINE and LILACS from 1990 to June, 2016 with the following combinations of key words “tuberculosis AND transmission” OR “tuberculosis diabetes mellitus” OR “Mycobacterium tuberculosis molecular epidemiology” OR “RFLP-IS6110” OR “Spoligotyping” OR “MIRU-VNTR”. Studies were included if they met the following criteria: (i) studies based on populations from defined geographical areas; (ii) use of genotyping by IS6110- restriction fragment length polymorphism (RFLP) analysis and spoligotyping or mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) or other amplification methods to identify molecular clustering; (iii) genotyping and analysis of 50 or more cases of PTB; (iv) study duration of 11 months or more; (v) identification of quantitative risk factors for molecular clustering including DM; (vi) > 60% coverage of the study population; and (vii) patients with PTB confirmed bacteriologically. The exclusion criteria were: (i) Extrapulmonary TB; (ii) TB caused by nontuberculous mycobacteria; (iii) patients with PTB and HIV; (iv) pediatric PTB patients; (v) TB in closed environments (e.g. prisons, elderly homes, etc.); (vi) diabetes insipidus and (vii) outbreak reports. Hartung-Knapp-Sidik-Jonkman method was used to estimate the odds ratio (OR) of the association between DM with molecular clustering of cases with TB. In order to evaluate the degree of heterogeneity a statistical Q test was done. The publication bias was examined with Begg and Egger tests. Review Manager 5.3.5 CMA v.3 and Biostat and Software package R were used. Results Selection criteria were met by six articles which included 4076 patients with PTB of which 13% had DM. Twenty seven percent of the cases were clustered. The majority of cases (48%) were reported in a study in China with 31% clustering. The highest incidence of TB occurred in two studies from China. The global OR for molecular clustering was 0.84 (IC 95% 0.40–1.72). The heterogeneity between studies was moderate (I2 = 55%, p = 0.05), although there was no publication bias (Beggs test p = 0.353 and Eggers p = 0.429). Conclusion There were very few studies meeting our selection criteria. The wide confidence interval indicates that there is not enough evidence to draw conclusions about the association. Clustering of patients with DM in TB transmission chains should be investigated in areas where both diseases are prevalent and focus on specific contexts.
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Affiliation(s)
- Francles Blanco-Guillot
- Doctorado en Ciencias en Enfermedades Infecciosas, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Norma Mongua-Rodríguez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Maestría en Ciencias Médicas con énfasis en Epidemiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Pablo Cruz-Hervert
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Leticia Ferreyra-Reyes
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Elizabeth Ferreira-Guerrero
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Mercedes Yanes-Lane
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, México
| | - Rogelio Montero-Campos
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Miriam Bobadilla-del-Valle
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Pedro Torres-González
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Alfredo Ponce-de-León
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - José Sifuentes-Osornio
- Dirección Médica, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Lourdes Garcia-Garcia
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- * E-mail:
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First Insight into the Molecular Epidemiology of Mycobacterium tuberculosis Isolates from the Minority Enclaves of Southwestern China. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2505172. [PMID: 28596961 PMCID: PMC5449728 DOI: 10.1155/2017/2505172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/09/2017] [Indexed: 01/04/2023]
Abstract
Yunnan is a province located in southwestern China. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis (MTB) strains circulating in Yunnan Province. We used spoligotyping and a 12-locus high-resolution VNTR set to identify a total of 271 MTB isolates collected from six prefectures' Yunnan. All the 271 patients were classified as 11 different ethnic groups, including 133 Han patients (49.1%) and 138 minority patients (50.9%). Spoligotyping analyses revealed that the largest two spoligotypes were SIT1 (Beijing family, n = 136) and SIT53 (T family, n = 35). Statistical analysis indicated that the proportion of Beijing genotype in Qujing was significantly higher than that in the ethnic enclaves (P ≤ 0.01). Compared with the percentage of Beijing-family isolates from patients under 25 years of age (72.7%), those from patients aged 45~64 years (44.6%, P < 0.01) and older than 64 years (48.1%) (P = 0.04) were significantly lower. Beijing genotype strains (23.8%, 36/151) showed higher clustering rate than non-Beijing genotype strains (16/120, 13.3%, P = 0.029). In conclusion, our data demonstrated that the Beijing genotype was the predominant genotype in Yunnan Province. The distribution of Beijing genotype strains showed geographic diversity. In addition, Beijing genotype was associated with recent transmission rather than drug resistance.
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Duarte TA, Nery JS, Boechat N, Pereira SM, Simonsen V, Oliveira M, Gomes MGM, Penha-Gonçalves C, Barreto ML, Barbosa T. A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil. Braz J Infect Dis 2017; 21:317-324. [PMID: 28238627 PMCID: PMC9427636 DOI: 10.1016/j.bjid.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/10/2017] [Indexed: 01/17/2023] Open
Abstract
Introduction The Mycobacterium tuberculosis East African-Indian (EAI) spoligotyping family (belonging to lineage 1, Indo-Oceanic, defined by the region of deletion RD239) is distributed worldwide, but is more prevalent in Southeast Asia, India, and East Africa. Studies in Latin America have rarely identified EAI. In this study, we describe the occurrence of the EAI family in Brazil. Methods EAI was identified in a systematic literature review of genetic diversity studies pertaining to M. tuberculosis in Brazil, as well as in a survey conducted in Salvador, Bahia, located in the northeastern region of this country. Results The EAI6-BGD1 spoligotyping family and the EAI5 Spoligotype International Type (SIT) 1983 clade were the most frequently reported, with wide distribution of this particular clade described in Brazil. The distribution of other EAI spoligotyping patterns with broader worldwide distribution was restricted to the southeastern region of the country. Conclusions EAI may be endemic at a low frequency in Brazil, with some clades indicating increased fitness with respect to this population.
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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