Genomic analysis of extensively drug-resistant (XDR) typhoid isolates in Pakistan revealed numerous XDR variants circulating in the country, a team of Pakistani and US researchers reported this week in the American Journal of Tropical Medicine and Hygiene.
To get a better understanding of the genetic diversity of the sublineage of XDR Salmonella enterica serovar Typhi that emerged in Pakistan's Sindh Province in 2016 and has subsequently spread to other parts of the country, the researchers conducted whole-genome sequencing (WGS) on 58 XDR Salmonella Typhi isolates collected from November 2018 to December 2020.
XDR typhoid is defined as resistant to all recommended antibiotics for typhoid fever, including third-generation cephalosporins and fluoroquinolones. Susceptibility testing showed all isolates were resistant to ampicillin and ceftriaxone, and 54 of 58 were resistant to ciprofloxacin.
WGS showed that all isolates were related to the outbreak strain that emerged in Sindh, that multiple XDR variants exist, and that nearly one third of the isolates had integrated the plasmid containing the extended-spectrum beta-lactamase (ESBL) gene blaCTX-M-15 into the chromosome, which could enable them to acquire additional drug resistance and virulence genes.
"Our results reveal there are many circulating typhoid variants in Pakistan that have lost the IncY plasmid after integrating the ESBL into the chromosome," the study authors wrote. "These could acquire new plasmids to make them resistant to the few antibiotics to which it is susceptible (pan-resistant)."
These could acquire new plasmids to make them resistant to the few antibiotics to which it is susceptible (pan-resistant).
More than 15,000 cases of XDR typhoid have been reported in Pakistan since 2016. XDR strains have also been identified in Southeast Asia and eastern and southern Africa, and have been introduced into the United Kingdom, Canada, and the United States by travelers.
The authors say that, given the continued spread of XDR typhoid and the associated genomic diversity, countries need to take steps to reduce the burden of typhoid, which is transmitted by contaminated food and water and person-to-person contact and tends to spread in areas with poor sanitation. Among the steps they recommend are improving vaccination rates and the quality of drinking water and promoting good hygiene.