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.
Highlights
Nontyphoidal Salmonella enterica is a significant public health problem and one of the most frequent cause of bacterial gastroenteritis worldwide [1, 2]
Whole genome sequencing data used for the current work were downloaded from public repositories (NCBI and Enterobase), while metadata used for data collection and management were collected from Florida Department of Health (FDOH) and the US Department of Agriculture Food Safety and Inspection Service (USDA FSIS)
We present a retrospective analysis of whole genome sequencing data of Salmonella enterica isolates from Florida in the years 2017–2018
Summary
Nontyphoidal Salmonella enterica (hereafter referred to as Salmonella) is a significant public health problem and one of the most frequent cause of bacterial gastroenteritis worldwide [1, 2]. PFGE has been the gold standard method for the subtyping of Salmonella [5], and gained widespread adoption under PulseNet USA, a surveillance network of public health laboratories across the United States and other countries [6]. For S. enterica serotype Enteritidis, reported as one of the most prevalent serotypes among laboratory confirmed cases [7], a considerable number of isolates (45%) received by PulseNet USA belonged to indistinguishable PFGE patterns using the XbaI restriction enzyme [8], whereas, 74% of S. Despite offering better discrimination, MLVA has had limited use because of its inability to differentiate common patterns [11], and standardized PulseNet protocols have been established for serotypes Enteritidis and Typhimurium only. The use of only seven housekeeping genes fails to capture genetic heterogeneity within strains of the same serotype and suffers from lower discriminatory power [14]
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