Chromosomal integration of resistance mechanisms in ESBL-producing XDR Salmonella Typhi

Passive genomic surveillance of Salmonella enterica serovar Typhi (S. Typhi) isolated from travellers returning to England from Pakistan between April 2014 and March 2020 revealed an intensification of the ongoing extended-spectrum beta-lactamase (ESBL)-producing extended drug resistant (XDR) S. Typhi outbreak. Of the 63 cases identified, 23 (36.5%) were reported in the first 3 months of 2020. Limited genetic diversity was observed between the outbreak isolates with the majority of the isolates (17/63) belonged to the ancestral Sindh outbreak haplotype. Enhanced surveillance of cases travel history reveals the outbreak has subsequently spread to multiple regions within Pakistan. All 63 isolates were resistant to ceftriaxzone and ceftazidime (ESBL phenotype), amoxicillin, and had reduced susceptibility to ciprofloxacin. One isolate was susceptible to chloramphenicol and two to trimethoprim whilst the remaining were resistant.The ESBL phenotype was conferred by the presence of blaCTX-M-15 (n=62) or blaCTX-M-55 (n=1). IncY plasmid harbouring the blaCTX-M-15 and qnr was detected in 54/63 isolates. In 9 isolates the IncY plasmid was absent and the 4kb ISEcpl-blaCTX-M-15–tnp gene cassette was inserted into the chromosome at 3 integration points:i) in yidA (6 isolates); ii) between aas and galR (1 isolate) and iii) between gutQ and norA ( 2 isolates).Phylogenetic analysis of the isolates without IncY plasmid suggests that the chromosomal integration of blaCTX-M-15 within the Sindh XDR outbreak isolates has occurred on at least six separate occasions since January 2019. These multiple integration events suggest a strong selective pressure driving the integration of the ESBL genotype into the chromosome. The emergence of resistance to third generation cephalosporins and fluoroquinolones is a challenge for the clinical management of typhoid fever.