Salmonella enterica serotypes causing infection in Kuwait during 2018-2021, determined by multi-locus sequence typing or whole genome sequencing

Abstract

Salmonellosis due to non-typhoidal Salmonellae (NTS) is a zoonotic infection that has epidemiological uniqueness in different settings. The current study aimed to determine the serotypes and the genetic diversity of human Salmonella enterica isolates causing infection in Kuwait. Isolates were obtained from feces of healthy adults and diarrheal patients between 2018 and 2021. Multi-locus sequence typing (MLST) was used to study sequence types (STs) and infer serotypes. Whole genome sequencing (WGS) was used to investigate six selected isolates, which included two isolates from a foodborne outbreak and two isolates whose serotypes could not be determined. Antibiotic susceptibility was studied by E-test and interpreted according to the Clinical and Laboratory Standards Institute guidelines. During the study period, 112/8,019 stool samples, 39/129,130 blood samples, 4/1,835 tissue samples, 3/1,209 pleural fluids, 3/9,388 pus samples, 4/80,799 urine samples, 1/7,053 endotracheal secretions, and 1/18 liver abscess samples were culture positive for Salmonella, yielding a total of 167 isolates with 30 different serotypes. S. Enteritidis (36.5%, n = 61), S. Typhimurium (14.97%, n = 25), S. Kentucky (5.9%, n = 10), and S. Newport (5.9%, n = 10) were the predominant serotypes. A new sequence type, ST 10217 corresponding to S. Schwarzengrund, was found by WGS. Two S. Enteritidis isolates from the foodborne outbreak showed a unique phylogenetic profile. In the phylogenetic analysis of serotypes, the number of clades was equal to the number of STs. No resistance to carbapenems was found among the isolates. This study provided data on the epidemiology of Salmonella serotypes causing infection in Kuwait.IMPORTANCEHuman salmonellosis due to nontyphoid Salmonellae is a major foodborne disease throughout the world. We determined the serotypes of isolates causing salmonellosis in Kuwait during the study period. We inferred the serotypes of isolates based on their sequence types as determined by multi-locus sequence typing, which is more amenable to laboratories than the traditional serotyping. By whole genome sequencing, we determined that the strain causing a foodborne outbreak was unique, and a new sequence type not in the serotyping scheme represented a rare serotype. We learnt the resistance pattern of isolates and lack of resistance to carbapenems that will be useful for treating multi-drug-resistant infection. Our data will contribute to planning strategies for treatment and control of salmonellosis and the epidemiology of salmonellosis in the Middle East.

Keywords: MLST; Salmonella; WGS; genomic surveillance; serotypes.