☆ 4.8 Article

BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking

NUCLEIC ACIDS RESEARCH (2021)

Journal

NUCLEIC ACIDS RESEARCH

Volume 49, Issue D1, Pages D644-D650

Publisher

OXFORD UNIV PRESS

DOI: 10.1093/nar/gkaa821

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Funding

National Natural Science Foundation of China [31670132]
Zhejiang Province Public Welfare Technology Application Research Project [LGF18H190001]

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Abstract

BacWGSTdb 2.0 is a free database for bacterial whole-genome sequence typing and source tracking, with new features such as core genome multi-locus sequence typing, multiple genome analysis module, and source tracking module. It has increased the number of species encompassed from 9 to 20, providing a user-friendly interface and visualization tools. This updated version continues to offer a one-stop solution for bacterial genome sequence analysis to users including epidemiologists, clinicians, and bench scientists.

An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.

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CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

Irene Ortega-Sanz, Jose A. Barbero-Aparicio, Antonio Canepa-Oneto, Jordi Rovira, Beatriz Melero

Summary: CamPype is a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria. It allows customization of stages and tools, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction, and identification of nucleotide variants. All results are presented in an interactive HTML report for better data visualization and interpretation. CamPype requires minimal user intervention and is suitable for microbiology laboratories without expertise in bioinformatics, serving as a first-line method for bacterial typing, epidemiological analyses, and comparative genomic analyses.

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