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

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 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 E. coli strains classified by PCR as ExPEC and non-ExPEC. We observed very high concordance (average, 93.4%) between PCR and WGS findings, but WGS identified more alleles. In conclusion, the addition of 38 ExPEC-associated genes and the associated alleles to the E. coli VirulenceFinder database allows for a more complete characterization of E. coli isolates based on WGS data, which has become increasingly important considering the plasticity of the E. coli genome.

Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

“…Genes associated with biocide resistance were compared with BacMet database (Antibacterial Biocide and Metal Resistance Genes Database, http://bacmet.biomedicine.gu.se/, accessed on 30 April 2021) [129]. Virulence genes were identified using VirulenceFinder 2.0 (https://cge.cbs.dtu.dk/services/VirulenceFinder/, accessed on 30 April 2021) [130,131], CH types were characterized as mentioned above, and serogenotypes were analyzed by SerotypeFinder (https://cge.cbs.dtu.dk/services/ SerotypeFinder/, accessed on 30 April 2021) [132]. The presence of plasmids was determined using PlasmidFinder 2.1 (https://cge.cbs.dtu.dk/services/PlasmidFinder/, accessed on 30 April 2021) [133].…”

Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat

“…The developed PCR and sequencing techniques, especially whole genome sequencing methods, enable detailed screening of the occurrence of specific genes and open new possibilities to estimate the relationship between the presence of genes and pathogenicity of E. coli strains [ 29 , 38 ]. The VirulenceFinder software has been updated in 2020 and a broader spectrum of virulence genes encoding, e.g., adhesins, siderophores, toxins, and protectins have been included in multiple variants [ 39 ]. Therefore, at least three virulence genes were detected in the tested strains.…”

Complete Genome Sequence of Escherichia coli Strain FEX669, a ColV Plasmid-Containing Isolate from Retail Chicken Meat

“…A total of 27 virulence genes were identified on the FEX669 chromosome and plasmid using VirulenceFinder-2.0 software (with 90% threshold and 60% minimum length parameters) ( 9 ) (accessed 2 November 2020). They included genes for iron acquisition ( chuA , fyuA , iroN , sitA , iucC , irp2 , and iutA ), attachment ( hra, focC , sfaD , and yfcV ), and toxin production ( hlyF, vat , and usp ).…”