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Conceição EC, da Conceição ML, Marcon DJ, Loubser J, Andrade GL, da Silva SP, Cruz ACR, Sharma A, Suffys P, Lima KVB. Genomic Diversity of the Rarely Observed Genotype of the Mycobacterium tuberculosis Central Asian (CAS) Lineage 3 from North Brazil. Microorganisms 2023; 11:microorganisms11010132. [PMID: 36677424 PMCID: PMC9862801 DOI: 10.3390/microorganisms11010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) Central Asian Strain (CAS) Lineage 3 (L3) genotype is predominantly found in East-Africa, Central-Asia, Western-Asia, and South-Asia; however, a new spoligotyping CAS/SIT2545 was found in northern regions of Brazil. We aimed to characterize and describe the genetic diversity and perform a phylogenetic assessment of this novel genotype. We performed 24-MIRU-VNTR loci and Whole-genome sequencing (WGS) of six Brazilian isolates previously spoligotyped. The libraries were prepared using a Nextera-XT kit and sequenced in a NextSeq 550 Illumina instrument. We performed lineage assignment and genomic characterization. From publicly available genomes of Mtb L3 and other lineages, we created a robust dataset to run the MTBSeq pipeline and perform a phylogenetic analysis. MIRU-VNTR and WGS confirmed CAS/SIT2545 belongs to L3. Out of 1691 genomes, 1350 (79.83%) passed in quality control (genomic coverage > 95%). Strain 431 differed in 52 single nucleotide variants (SNV), confirming it does not belong to the same transmission chain. The eight genomes from a global dataset clustered closer to Brazilian strains differed in >52 SNVs. We hypothesized L3 and L1 were introduced in Brazilian Northern in the same historical event; however, there is a need for additional studies exploring the genetic diversity of Mtb Brazilian Northern.
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Affiliation(s)
- 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, Tygerberg, Cape Town P.O. Box 241, South Africa
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Correspondence:
| | | | - Davi Josué Marcon
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Johannes Loubser
- 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, Tygerberg, Cape Town P.O. Box 241, South Africa
| | - Gabrielly Leite Andrade
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Departamento de Medicina, Centro Universitário do Pará—CESUPA, Belém 66613-903, PA, Brazil
| | - Sandro Patroca da Silva
- Seção de Arbovírus e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Ana Cecília Ribeiro Cruz
- Seção de Arbovírus e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Programa de Pós-graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém 66087-670, PA, Brazil
| | - Abhinav Sharma
- Faculty of Engineering and Technology, Liverpool John Moores University (LJMU), Liverpool L35UX, UK
- Seqera Labs, 08005 Bacelona, Spain
| | - Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactéria, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Karla Valéria Batista Lima
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Programa de Pós-graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém 66087-670, PA, Brazil
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Duan Q, Zhang Z, Tian D, Zhou M, Hu Y, Wu J, Wang T, Li Y, Chen J. Transmission of multidrug-resistant Mycobacterium tuberculosis in Wuhan, China: A retrospective molecular epidemiological study. Medicine (Baltimore) 2022; 101:e28751. [PMID: 35089253 PMCID: PMC8797475 DOI: 10.1097/md.0000000000028751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/13/2022] [Indexed: 01/05/2023] Open
Abstract
How multidrug-resistant tuberculosis (MDR-TB) spreads and expands in Wuhan population is not clear. The study aimed to determine the transmission patterns of MDR-TB in Wuhan city, China, including 149 patients with MDR-TB.Tuberculosis isolates were genotyped by deletion-targeted multiplex polymerase chain reaction, mycobacterial interspersed repetitive unit-variable number tandem repeat typing, and sequencing of drug resistance-associated genes. The risk factors of genomic-clustering were analyzed with logistic regression. The genomic-clustering patients were deeply investigated.The analysis identified 111 unique and 11 clustered genotypes (38 isolates). The clustering rate was 25.50% and the minimum estimate proportion of recent transmission was 18.12%. Two clusters (5 isolates) shared the same mutation, the remain 9 clusters (33 isolates) had different mutation. Logistic regression showed that older than 60 years (adjusted OR 2.360, 95% CI:1.052-5.292) was an independent factor associated with the genomic-clustering of MDR-TB. Among the 38 genomic-clustering cases, 14 cases had epidemiological transmission links. The most common type of transmission link was social contact.The local transmission of MDR-TB in Wuhan was really an issue. The elderly population might be the high-risk groups for transmission of MDR-TB, and the community or public transportation might be the main transmission places.
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Affiliation(s)
- Qionghong Duan
- Department of Tuberculosis Prevention, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Zhengbin Zhang
- Department of Tuberculosis Prevention, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Dan Tian
- Department of Tuberculosis Prevention, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Meilan Zhou
- Department of Tuberculosis Prevention, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Yanjie Hu
- Department of Clinical Laboratory, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Jun Wu
- Department of Supervision, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Tiantian Wang
- Department of Tuberculosis Prevention, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Yuehua Li
- Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Jun Chen
- Department of Clinical Laboratory, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
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