Genomic epidemiology of emerging ESBL-producingSalmonellaKentuckyblaCTX-M-14bin Europe

Global dissemination of ciprofloxacin-resistantSalmonellaKentucky has been observed over the past decades. In recent years, there have been reports of extended-spectrum beta-lactamase (ESBL) producingS. Kentucky. Routine surveillance at the European Centre for Disease Prevention and Control (ECDC) detected cases with a ciprofloxacin-resistantS. Kentucky with the ESBL-genebla(CTX-M-14b). Ensuing research identified 78 cases in 2013-2018 in eight European countries. Compared to otherS. Kentucky and non-typhoidalSalmonellainfections, reported to the European Surveillance System, these cases were more likely to be elderly and to present urinary-tract infections. Bayesian time-scaled phylogeny on whole genome sequences of isolates from these cases and supplementary isolates from public sequence databases was used to infer the origin and spread of this clone. We dated the origin of thebla(CTX-M-14b)clone to approximately 2005 in Northern Africa, most likely in Egypt. The geographic origin predicted by the phylogenetic analysis is consistent with the patients' travel history. Next to multiple introductions of the clone to Europe from Egypt, our analysis suggests that in some parts of Europe the clone might have formed a stable population, from which further spread has occurred. Comparative genomics indicated that thebla(CTX-M-14b)gene is present on the bacterial chromosome, within the type VI secretion system region. Thebla(CTX-M-14b)gene is integrated downstream of thehcp1gene, on a 2854 bp plasmid fragment containing also ISEcp1. This is the first report of a chromosomally integrated CTX-M gene inSalmonellaspp. in Europe, previous studies having identified similar genes only on plasmids.