Global diversity and evolution ofSalmonellaPanama, an understudied serovar causing gastrointestinal and invasive disease worldwide: a genomic epidemiology study

Abstract

Background Nontyphoidal Salmonella (NTS) is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some NTS serovars can also colonise normally sterile sites in humans to cause invasive NTS (iNTS) disease. One understudied Salmonella enterica serovar which is responsible for a significant number of cases of iNTS disease is Panama. Despite global dissemination, numerous outbreaks, and a reported association with iNTS disease, S. enterica serovar Panama (S. Panama) has not been investigated in detail. Methods Using combined epidemiological and whole genome sequencing data we analysed 836 S. Panama isolates from all inhabited continents collected between 1931 and 2019. A combination of phylodynamic approaches were used to determine population structure & evolutionary history, and to infer geo-temporal dissemination. Subsequently, we characterised geographic and clade-specific trends in antimicrobial resistance (AMR), and genetic markers for invasiveness using epidemiological and bioinformatic approaches. Findings We identified the presence of multiple geographically linked S. Panama clades, and regional trends in antimicrobial resistance profiles. Most isolates were pan-susceptible to antibiotics and belonged to clades circulating in the United States of America, Latin America, and the Caribbean. Multidrug resistant (MDR) isolates belonged to two phylogenetic clades circulating in Europe and Asia/Oceania, which exhibited the highest invasiveness indices based on the conservation of 196 extra-intestinal predictor genes. Interpretation This first large-scale phylogenetic analysis of S. Panama revealed important information about population structure, AMR, global ecology, and genetic markers of invasiveness of the identified genomic subtypes. Our findings provide an important baseline for understanding S. Panama infection in the future. The presence of MDR clades with an elevated invasiveness index should be monitored by ongoing surveillance as such clades may pose an increased public health risk.