Abstract
The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in antimicrobial resistance has been expanding via plasmids as mobile genetic elements encoding antimicrobial resistance (AMR) genes that are transferred vertically and horizontally. This study focuses on Salmonella enterica, one of the leading foodborne pathogens in industrialized countries. S. enterica is known to carry several plasmids involved not only in virulence but also in AMR. In the current paper, we present an integrated strategy to detect plasmid scaffolds in whole genome sequencing (WGS) assemblies. We developed a two-step procedure to predict plasmids based on i) the presence of essential elements for plasmid replication and mobility, as well as ii) sequence similarity to a reference plasmid. Next, to confirm the accuracy of the prediction in 1750 S. enterica short-read sequencing data, we combined Oxford Nanopore MinION long-read sequencing with Illumina MiSeq short-read sequencing in hybrid assemblies for 84 isolates to evaluate the proportion of plasmid that has been detected. At least one scaffold with an origin of replication (ORI) was predicted in 61.3% of the Salmonella isolates tested. The results indicated that IncFII and IncI1 ORIs were distributed in many S. enterica serotypes and were the most prevalent AMR genes carrier, whereas IncHI2A/IncHI2 and IncA/C2 were more serotype restricted but bore several AMR genes. Comparison between hybrid and short-read assemblies revealed that 81.1% of plasmids were found in the short-read sequencing using our pipeline. Through this process, we established that plasmids are prevalent in S. enterica and we also substantially expand the AMR genes in the resistome of this species.
Highlights
Non-typhoidal Salmonella enterica is responsible for 88,000 cases of gastroenteritis in Canada each year
For each scaffold with an ORI identified by Plasmid-Gather, we identified the plasmid with the highest bit score using basic local alignement search tool (BLAST) against the National Center for Biotechnology Information (NCBI) Plasmid database (≥ 95% sequence identity, ≥ 15% query coverage per subject, and ≤ 550 kb of subject length)
A BLAST against the NCBI Nucleotide collection database of these genomic regions where mobility proteins were identified revealed they corresponded to partial plasmid sequences
Summary
Non-typhoidal Salmonella enterica is responsible for 88,000 cases of gastroenteritis in Canada each year. The symptoms of gastroenteritis can be mild to severe depending on the health conditions of individuals. The patient may recover without antibiotic treatment. Antibiotic intervention may be necessary for children, the elderly, and immunosuppressed patients. The Salmonella genus belongs to the Enterobacteriaceae family and includes two species, bongori and enterica. According to the Kauffman–White scheme, more than 2500 serotypes have been characterized [1]. As reported by the US Centers for Disease Control and Prevention (CDC), all S. enterica serotypes can cause disease in humans, less than 100 serotypes account for much of the infections
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