In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data.

Journal of Clinical Microbiology
Anna Maria Malberg TetzschnerFlemming Scheutz

Abstract

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause in humans of urinary tract infection and bacteremia. The previously published web tool VirulenceFinder (http://cge.cbs.dtu.dk/services/VirulenceFinder/) uses whole-genome sequencing (WGS) data for in silico characterization of E. coli isolates and enables researchers and clinical health personnel to quickly extract and interpret virulence-relevant information from WGS data. In this study, 38 ExPEC-associated virulence genes were added to the existing E. coli VirulenceFinder database. In total, 14,441 alleles were downloaded. A total of 1,890 distinct alleles were added to the database after removal of redundant sequences and analysis of the remaining alleles for open reading frames (ORFs). The database now contains 139 genes-of which 44 are related to ExPEC-and 2,826 corresponding alleles. Construction of the database included validation against 27 primer pairs from previous studies, a search for serotype-specific P fimbriae papA alleles, and a BLASTn confirmation of seven genes (etsC, iucC, kpsE, neuC, sitA, tcpC, and terC) not covered by the primers. The augmented database was evaluated using (i) a panel of nine control strains and (ii) 288 human-source ...Continue Reading

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Citations

Feb 6, 2021·Microorganisms·Michaela KubelováRenáta Karpíšková
Feb 25, 2021·Emerging Infectious Diseases·Federica GigliucciValeria Michelacci
Jun 3, 2021·International Journal of Molecular Sciences·Olivia M GrünzweilIgor Loncaric
Jun 5, 2021·Applied and Environmental Microbiology·Ana Carolina de Mello SantosTânia Aparecida Tardelli Gomes
Aug 10, 2021·International Journal of Medical Microbiology : IJMM·Nadine LercheAxel Kramer
Aug 28, 2021·Microorganisms·Tanja Bernreiter-HoferIgor Loncaric
Nov 18, 2021·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Lorena López-CereroÁlvaro Pascual

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Datasets Mentioned

BETA
PRJNA16235
U00096.3
JN688153.1
PRJEB38689
ERS4600802
ERS4600803
CP019944
ECOF165A
CP041623
CP028320

Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

MyDbFinder
VirulenceFinder
ExPECFinder
BLASTn
BLASTx
MUSCLE
BLAST
SerotypeFinder

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