Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018

Abstract

The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.

Salmonella serovars in sheep and goats and their probable zoonotic potential to humans in Suez Canal Area, Egypt

“…It seems that this serotype and/or S. Typhimurium are common nontyphoidal Salmonella spp. among Egyptians as reported in recent studies [40], which was also the case in Greece [41], Nigeria [42], and Florida (USA) [43]. In the present study, S. Apeyeme and S. Chester were identified in diarrheic and non-diarrheic patients, respectively, although they were not identified in animals.…”

Molecular Characterization of Quinolone Resistance Determinants in Non-Typhoidal Salmonella Strains Isolated in Tehran, Iran

“…In previous investigations conducted in Iran, S. enterica serotype Enteritidis was found to be the most common serotype of Salmonella in people. Moreover, in a comprehensive study conducted in China, United States, and Taiwan, S. enterica serotype Enteritidis was the most prevalent strain serotype among human isolates (19)(20)(21)(22). These results are in agreement with our results, which revealed that S. enterica serotype Enteritidis was the predominant serotype.…”

Geographical distribution and space–time clustering of human illnesses with major Salmonella serotypes in Florida, USA, 2017–2018

“…The distribution of clusters of genetically related Salmonella isolates detected in our previous phylogenetic work [10] was consistent with the geographical pattern of areas with a highincidence rate of illness from varying serotypes. The hierarchical clusters based on cgMLST-clustered isolates were based solely on their genetic relatedness, without considering the spatial and temporal components in the data.…”

“…The five most common serotypes identified through the FoodNet surveillance system in the USA are Enteritidis, Typhimurium, Newport, Javiana and I 4, [5],12:i:-, a monophasic variant of Typhimurium [9], while the major serotypes occurring in Florida are Enteritidis, Newport, Javiana, Sandiego and Braenderup [6]. In our previous work, we conducted a phylogenetic analysis of Salmonella isolates from five dominant serotypes in Florida and identified the geographical distribution of clusters of genetically related isolates using core genome multi-locus sequence typing (cgMLST), a subtyping approach that provides high resolution to distinguish isolates within the same serotype [10]. Eight clusters of genetically related isolates from four serotypes (Enteritidis, Newport, I 4, [5],12:i:-and Bareilly) involved more than 10 isolates and were investigated.…”