Virulence factors among isolates of extraintestinal Escherichia coli (ExPEC) from hospitals in the United Kingdom.

Abstract

182 genes associated with virulence were sought from the whole genome sequences of all non-duplicate isolates of Escherichia coli received by the UK Health Security Agencys Antimicrobial Resistance and HealthCare Associated Infections laboratory for typing between June 2019 and March 2021 from hospitals in the United Kingdom and Republic of Ireland (n=593). These were from healthcare associated investigations and were not associated with diarrhoeal disease. Genes that were very common or very rare were excluded from further analysis. The frequency of detection of genes was compared among isolates from invasive infection, screening, urine samples and from neonates. cnf1 (coding for cytotoxic necrotising factor), clbK (coding for colibactin), focCDF (coding for F1 fimbriae), kpsM_K1, neuBD (associated with the K1 capsule), mchBC, mcmA (coding for microcins), papG_alleleIII (part of a cluster encoding P fimbriae), pic (protein involved in intestinal colonization), sfaE/sfafoCDE (coding for S fimbriae), tcpC (encoding TLR domain containing-protein C) and vat (encoding toxin vacuolating autotransporter) were 4 to 28 times more prevalent among isolates from invasive infections than among those from carriage. Representatives of sequence types (ST) 12, 73, 998 and 127 carried multiple of these virulence factors, no matter whether they were from screening swabs or from blood or other infection sites. Isolates carrying multiple virulence factors were more prevalent from neonatal screens than those from general screens. Genes associated with the K1 capsule (ibeA, neuBD, kpsM_K1) were particularly found in STs 1193, 10, 998, 538, 80 and 141. Nanopore sequencing of 14 isolates representing 10 different STs showed that the virulence elements sought were largely carried in chromosomal genomic islands, which were mosaic in nature. Some 9 % of isolates carried more than six of the main virulence genes/gene sets sought, highlighting the potential for significant numbers of carriage isolates to cause extraintestinal infections.