BacWGSTdb, a database for genotyping and source tracking bacterial pathogens

Whole genome sequencing has become one of the routine methods in molecular epidemiological practice. In this study, we present BacWGSTdb (http://bacdb.org/BacWGSTdb), a bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. This database borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens.

[1]  F. Lauro,et al.  Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients , 2014, Journal of Clinical Microbiology.

[2]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[3]  S. Peacock,et al.  Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory--pipe dream or reality? , 2012, The Journal of antimicrobial chemotherapy.

[4]  Federico Perez,et al.  New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis , 2014, mBio.

[5]  Mark J. Mandel,et al.  Genome-Wide Identification of Acinetobacter baumannii Genes Necessary for Persistence in the Lung , 2014, mBio.

[6]  E. Castro-Nallar,et al.  Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[7]  K. Jolley,et al.  Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[8]  K. Jolley,et al.  Using multilocus sequence typing to study bacterial variation: prospects in the genomic era. , 2014, Future microbiology.

[9]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[10]  Keith A. Jolley,et al.  A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter , 2012, Genes.

[11]  M. Achtman,et al.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Martin C. J. Maiden,et al.  BIGSdb: Scalable analysis of bacterial genome variation at the population level , 2010, BMC Bioinformatics.

[13]  Tim Kovacs,et al.  TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web , 2010, PloS one.

[14]  Yan Zhang,et al.  PATRIC, the bacterial bioinformatics database and analysis resource , 2013, Nucleic Acids Res..

[15]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[16]  C. Bertelli,et al.  Rapid bacterial genome sequencing: methods and applications in clinical microbiology. , 2013, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[17]  C. Chiu,et al.  Risk Factors and Outcome Analysis of Acinetobacter baumannii Complex Bacteremia in Critical Patients* , 2014, Critical care medicine.

[18]  P. O’Toole,et al.  Next-generation sequencing technologies and their impact on microbial genomics. , 2013, Briefings in functional genomics.

[19]  J. Marschall,et al.  Molecular Epidemiology of Carbapenem-Nonsusceptible Acinetobacter baumannii in the United States , 2011, Journal of Clinical Microbiology.

[20]  Mark Johnson,et al.  NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..

[21]  A. Friedrich,et al.  Overview of molecular typing methods for outbreak detection and epidemiological surveillance. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[22]  J. Bray,et al.  MLST revisited: the gene-by-gene approach to bacterial genomics , 2013, Nature Reviews Microbiology.

[23]  Yunsong Yu,et al.  Wide distribution of CC92 carbapenem-resistant and OXA-23-producing Acinetobacter baumannii in multiple provinces of China. , 2013, International journal of antimicrobial agents.

[24]  Richard Gibson,et al.  Content discovery and retrieval services at the European Nucleotide Archive , 2014, Nucleic Acids Res..

[25]  M. Nei,et al.  Prospects for inferring very large phylogenies by using the neighbor-joining method. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[26]  James A. Foster,et al.  Phylogenetics Clearcut : a fast implementation of relaxed neighbor joining , 2006 .

[27]  Daniel J. Wilson,et al.  Transforming clinical microbiology with bacterial genome sequencing , 2012, Nature Reviews Genetics.

[28]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[29]  David M. Aanensen,et al.  The multilocus sequence typing network: mlst.net , 2005, Nucleic Acids Res..

[30]  M. Maiden.  Multilocus sequence typing of bacteria. , 2006, Annual review of microbiology.