Abstract
Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:– and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.
Highlights
Salmonella enterica is an important zoonotic pathogen that causes over one million illnesses in the United States each year (Scallan et al, 2011)
The main features associated with S. enterica evolution include acquisition and recombination of mobile genetic elements such as genomic islands, transposons, integrons, and plasmids, among others (Partridge et al, 2018)
We describe the use of Pacific Biosciences (PacBio) long-read sequencing to characterize 134 isolates, representing 33 Salmonella serotypes, isolated from raw meats and food animals
Summary
Salmonella enterica is an important zoonotic pathogen that causes over one million illnesses in the United States each year (Scallan et al, 2011). While many serotypes may be capable of causing infections in humans and animals, a limited number of serotypes cause most human infections in the United States. Recent advancements in whole genome sequencing (WGS) offer a unique opportunity to dissect and investigate Salmonella serotypes at the nucleotide level and to further our understanding about notable evolutionary changes. The main features associated with S. enterica evolution include acquisition and recombination of mobile genetic elements such as genomic islands, transposons, integrons, and plasmids, among others (Partridge et al, 2018). An in-depth analysis of these features will help us to understand drivers of resistance, host and environmental adaptations, and sources of resistant Salmonella infections
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