Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam

Abstract Mycobacterium tuberculosis (Mtb) has different features depending on different geographic areas. We collected Mtb strains from patients with smear-positive pulmonary tuberculosis in Da Nang, central Vietnam. Using a whole genome sequencing platform, including genome assembly complemented by...

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Autores principales:	Nguyen Thi Le Hang, Minako Hijikata, Shinji Maeda, Akiko Miyabayashi, Keiko Wakabayashi, Shintaro Seto, Nguyen Thi Kieu Diem, Nguyen Thi Thanh Yen, Le Van Duc, Pham Huu Thuong, Hoang Van Huan, Nguyen Phuong Hoang, Satoshi Mitarai, Naoto Keicho, Seiya Kato
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4fdac76d29f448ecbedc2842b9397db2
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spelling	oai:doaj.org-article:4fdac76d29f448ecbedc2842b9397db22021-12-02T14:33:57ZPhenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam10.1038/s41598-021-92984-52045-2322https://doaj.org/article/4fdac76d29f448ecbedc2842b9397db22021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92984-5https://doaj.org/toc/2045-2322Abstract Mycobacterium tuberculosis (Mtb) has different features depending on different geographic areas. We collected Mtb strains from patients with smear-positive pulmonary tuberculosis in Da Nang, central Vietnam. Using a whole genome sequencing platform, including genome assembly complemented by long-read-sequencing data, genomic characteristics were studied. Of 181 Mtb isolates, predominant Vietnamese EAI4_VNM and EAI4-like spoligotypes (31.5%), ZERO strains (5.0%), and part of EAI5 (11.1%) were included in a lineage-1 (L1) sublineage, i.e., L1.1.1.1. These strains were found less often in younger people, and they genetically clustered less frequently than other modern strains. Patients infected with ZERO strains demonstrated less lung infiltration. A region in RD2bcg spanning six loci, i.e., PE_PGRS35, cfp21, Rv1985c, Rv1986, Rv1987, and erm(37), was deleted in EAI4_VNM, EAI4-like, and ZERO strains, whereas another 118 bp deletion in furA was specific only to ZERO strains. L1.1.1.1-sublineage-specific deletions in PE_PGRS4 and PE_PGRS22 were also identified. RD900, seen in ancestral lineages, was present in majority of the L1 members. All strains without IS6110 (5.0%) had the ZERO spoligo-pattern. Distinctive features of the ancestral L1 strains provide a basis for investigation of the modern versus ancestral Mtb lineages and allow consideration of countermeasures against this heterogeneous pathogen.Nguyen Thi Le HangMinako HijikataShinji MaedaAkiko MiyabayashiKeiko WakabayashiShintaro SetoNguyen Thi Kieu DiemNguyen Thi Thanh YenLe Van DucPham Huu ThuongHoang Van HuanNguyen Phuong HoangSatoshi MitaraiNaoto KeichoSeiya KatoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nguyen Thi Le Hang Minako Hijikata Shinji Maeda Akiko Miyabayashi Keiko Wakabayashi Shintaro Seto Nguyen Thi Kieu Diem Nguyen Thi Thanh Yen Le Van Duc Pham Huu Thuong Hoang Van Huan Nguyen Phuong Hoang Satoshi Mitarai Naoto Keicho Seiya Kato Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam
description	Abstract Mycobacterium tuberculosis (Mtb) has different features depending on different geographic areas. We collected Mtb strains from patients with smear-positive pulmonary tuberculosis in Da Nang, central Vietnam. Using a whole genome sequencing platform, including genome assembly complemented by long-read-sequencing data, genomic characteristics were studied. Of 181 Mtb isolates, predominant Vietnamese EAI4_VNM and EAI4-like spoligotypes (31.5%), ZERO strains (5.0%), and part of EAI5 (11.1%) were included in a lineage-1 (L1) sublineage, i.e., L1.1.1.1. These strains were found less often in younger people, and they genetically clustered less frequently than other modern strains. Patients infected with ZERO strains demonstrated less lung infiltration. A region in RD2bcg spanning six loci, i.e., PE_PGRS35, cfp21, Rv1985c, Rv1986, Rv1987, and erm(37), was deleted in EAI4_VNM, EAI4-like, and ZERO strains, whereas another 118 bp deletion in furA was specific only to ZERO strains. L1.1.1.1-sublineage-specific deletions in PE_PGRS4 and PE_PGRS22 were also identified. RD900, seen in ancestral lineages, was present in majority of the L1 members. All strains without IS6110 (5.0%) had the ZERO spoligo-pattern. Distinctive features of the ancestral L1 strains provide a basis for investigation of the modern versus ancestral Mtb lineages and allow consideration of countermeasures against this heterogeneous pathogen.
format	article
author	Nguyen Thi Le Hang Minako Hijikata Shinji Maeda Akiko Miyabayashi Keiko Wakabayashi Shintaro Seto Nguyen Thi Kieu Diem Nguyen Thi Thanh Yen Le Van Duc Pham Huu Thuong Hoang Van Huan Nguyen Phuong Hoang Satoshi Mitarai Naoto Keicho Seiya Kato
author_facet	Nguyen Thi Le Hang Minako Hijikata Shinji Maeda Akiko Miyabayashi Keiko Wakabayashi Shintaro Seto Nguyen Thi Kieu Diem Nguyen Thi Thanh Yen Le Van Duc Pham Huu Thuong Hoang Van Huan Nguyen Phuong Hoang Satoshi Mitarai Naoto Keicho Seiya Kato
author_sort	Nguyen Thi Le Hang
title	Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam
title_short	Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam
title_full	Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam
title_fullStr	Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam
title_full_unstemmed	Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam
title_sort	phenotypic and genotypic features of the mycobacterium tuberculosis lineage 1 subgroup in central vietnam
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4fdac76d29f448ecbedc2842b9397db2
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Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam

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