Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

CJ Meehan, GA Goig, TA Kohl, L Verboven… - NATURE reviews …, 2019 - nature.com
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed
from a research tool to a clinical application for the diagnosis and management of …

PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph

G Gautreau, A Bazin, M Gachet, R Planel… - PLoS computational …, 2020 - journals.plos.org
The use of comparative genomics for functional, evolutionary, and epidemiological studies
requires methods to classify gene families in terms of occurrence in a given species. These …

Mycobacterium bovis: From Genotyping to Genome Sequencing

AMS Guimaraes, CK Zimpel - Microorganisms, 2020 - mdpi.com
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis.
Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the …

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples

TH Heupink, L Verboven, A Sharma… - PLoS Computational …, 2023 - journals.plos.org
Background Whole genome sequencing (WGS) holds great potential for the management
and control of tuberculosis. Accurate analysis of samples with low mycobacterial burden …

Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni

A Thépault, G Méric, K Rivoal, B Pascoe… - Applied and …, 2017 - Am Soc Microbiol
Campylobacter is among the most common worldwide causes of bacterial gastroenteritis.
This organism is part of the commensal microbiota of numerous host species, including …

Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

AL Manson, T Abeel, JE Galagan… - Clinical Infectious …, 2017 - academic.oup.com
Background. India is home to 25% of all tuberculosis cases and the second highest number
of multidrug resistant cases worldwide. However, little is known about the genetic diversity …

Genomic and metabolic features of the Bacillus amyloliquefaciens group–B. amyloliquefaciens, B. velezensis, and B. siamensis–revealed by pan-genome analysis

BH Chun, KH Kim, SE Jeong, CO Jeon - Food microbiology, 2019 - Elsevier
The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B.
amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan …

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in …

A Bainomugisa, T Duarte, E Lavu… - Microbial …, 2018 - microbiologyresearch.org
A better understanding of the genomic changes that facilitate the emergence and spread of
drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the …

The open pan-genome architecture and virulence landscape of Mycobacterium bovis

AC Reis, MV Cunha - Microbial Genomics, 2021 - microbiologyresearch.org
Animal tuberculosis (TB) is an emergent disease caused by Mycobacterium bovis, one of the
animal-adapted ecotypes of the Mycobacterium tuberculosis complex (MTC). In this work …

Complete Genome Sequencing of Mycobacterium bovis SP38 and Comparative Genomics of Mycobacterium bovis and M. tuberculosis Strains

CK Zimpel, PE Brandão, AF de Souza Filho… - Frontiers in …, 2017 - frontiersin.org
Mycobacterium bovis causes bovine tuberculosis and is the main organism responsible for
zoonotic tuberculosis in humans. We performed the sequencing, assembly and annotation …