1
|
Mokrousov I. Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration. Mol Phylogenet Evol 2024; 195:108045. [PMID: 38447923 DOI: 10.1016/j.ympev.2024.108045] [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: 07/11/2023] [Revised: 01/04/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.
Collapse
Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia; Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China.
| |
Collapse
|
2
|
Bakuła Z, Wuyep VB, Bartocha Ł, Vyazovaya A, Ikeh EI, Bielecki J, Mokrousov I, Jagielski T. Molecular snapshot of drug-resistant Mycobacterium tuberculosis strains from the Plateau State, Nigeria. PLoS One 2022; 17:e0266837. [PMID: 35609028 PMCID: PMC9129033 DOI: 10.1371/journal.pone.0266837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular epidemiology of Mycobacterium tuberculosis in this country. The aim of this work was to analyze the genetic structure of drug-resistant (DR) M. tuberculosis population in the Plateau State (central Nigeria), with the results placed in the broader context of West Africa. The study sample included 67 DR M. tuberculosis isolates, recovered from as many TB patients between November 2015 and January 2016, in the Plateau State. The isolates were subjected to spoligotyping and MIRU-VNTR typing. A total of 20 distinct spoligotypes were obtained, split into 3 clusters (n = 50, 74.6%, 2–33 isolates per cluster) and 17 (25.4%) unique patterns. The Cameroon clade was the largest lineage (62.7%) followed by T (28.3%), LAM (3%), and Haarlem (3%) clades. Upon MIRU-VNTR typing, the isolates produced 31 profiles, i.e. 7 clusters (n = 43, 64.2%, 2–17 isolates per cluster) and 24 singletons. A combined spoligotyping and MIRU-VNTR typing analysis showed 20.9% of the cases clustered and estimated the recent transmission rate at 11.9%. In conclusion, two lineages, namely Cameroon, and T accounted for the majority (91%) of cases. No association was observed between the most prevalent Cameroon lineage and drug resistance, including multidrug resistant (MDR) phenotype, or any of the patient demographic characteristics.
Collapse
Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Łukasz Bartocha
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Eugene I. Ikeh
- Department of Medical Microbiology, School of Medical and Health Sciences, College of Medical Sciences, University of Jos, Jos, Nigeria
| | - Jacek Bielecki
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- * E-mail: (IM); (TJ)
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (IM); (TJ)
| |
Collapse
|
3
|
Salvato RS, Reis AJ, Schiefelbein SH, Gómez MAA, Salvato SS, da Silva LV, Costa ERD, Unis G, Dias CF, Viveiros M, Portugal I, von Groll A, da Silva PEA, Kritski AL, Perdigão J, Rossetti MLR. Genomic-based surveillance reveals high ongoing transmission of multi-drug-resistant Mycobacterium tuberculosis in Southern Brazil. Int J Antimicrob Agents 2021; 58:106401. [PMID: 34289403 DOI: 10.1016/j.ijantimicag.2021.106401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/28/2021] [Accepted: 07/03/2021] [Indexed: 11/30/2022]
Abstract
Genomic-based surveillance on the occurrence of drug resistance and its transmission dynamics has emerged as a powerful tool for the control of tuberculosis (TB). A whole-genome sequencing approach, phenotypic testing and clinical-epidemiological investigation were used to undertake a retrospective population-based study on drug-resistant (DR)-TB in Rio Grande do Sul, the largest state in Southern Brazil. The analysis included 305 resistant Mycobacterium tuberculosis strains sampled statewide from 2011 to 2014, and covered 75.7% of all DR-TB cases identified in this period. Lineage 4 was found to be predominant (99.3%), with high sublineage-level diversity composed mainly of 4.3.4.2 [Latin American and Mediterranean (LAM)/RD174], 4.3.3 (LAM/RD115) and 4.1.2.1 (Haarlem/RD182) sublineages. Genomic diversity was also reflected in resistance of the variants to first-line drugs. A large number of distinct resistance-conferring mutations, including variants that have not been reported previously in any other setting worldwide, and 22 isoniazid-monoresistant strains with mutations described as disputed in the rpoB gene but causing rifampicin resistance generally missed by automated phenotypic tests as BACTEC MGIT. Using a cut-off of five single nucleotide polymorphisms, the estimated recent transmission rate was 55.1%, with 168 strains grouped into 28 genomic clusters. The most worrying fact concerns multi-drug-resistant (MDR) strains, of which 73.4% were clustered. Different resistance profiles and acquisition of novel mutations intraclusters revealed important amplification of resistance in the region. This study described the diversity of M. tuberculosis strains, the basis of drug resistance, and ongoing transmission dynamics across the largest state in Southern Brazil, stressing the urgent need for MDR-TB transmission control state-wide.
Collapse
Affiliation(s)
- Richard Steiner Salvato
- Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Ana Júlia Reis
- Medical Microbiology Research Center, Faculdade de Medicina, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Sun Hee Schiefelbein
- Programa de Pós-graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - Michael Andrés Abril Gómez
- Medical Microbiology Research Center, Faculdade de Medicina, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Stéphanie Steiner Salvato
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Larissa Vitória da Silva
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Elis Regina Dalla Costa
- Programa Acadêmico de Tuberculose, Faculdade de Medicina e complexo hospitalar HUCFF-IDT, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gisela Unis
- Hospital Sanatório Partenon, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Isabel Portugal
- iMed.ULisboa - Research Institute for Medicine, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Andrea von Groll
- Medical Microbiology Research Center, Faculdade de Medicina, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Pedro Eduardo Almeida da Silva
- Medical Microbiology Research Center, Faculdade de Medicina, Programa de Pós-graduação em Ciências da Saúde, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose, Faculdade de Medicina e complexo hospitalar HUCFF-IDT, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - João Perdigão
- iMed.ULisboa - Research Institute for Medicine, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Lucia Rosa Rossetti
- Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| |
Collapse
|