Genomic comparison of diverse Salmonella serovars isolated from swine

Abstract

Food animals act as a reservoir for many foodborne pathogens. Salmonella enterica is one of the leading pathogens that cause food borne illness in a broad host range including animals and humans. They can also be associated with a single host species or a subset of hosts, due to genetic factors associated with colonization and infection. Adult swine are often asymptomatic carriers of a broad range of Salmonella servoars and can act as an important reservoir of infections for humans. In order to understand the genetic variations among different Salmonella serovars, Whole Genome Sequences (WGS) of fourteen Salmonella serovars from swine products were analyzed. More than 75% of the genes were part of the core genome in each isolate and the higher fraction of gene assign to different functional categories in dispensable genes indicated that these genes acquired for better adaptability and diversity. High concordance (97%) was detected between phenotypically confirmed antibiotic resistances and identified antibiotic resistance genes from WGS. The resistance determinants were mainly located on mobile genetic elements (MGE) on plasmids or integrated into the chromosome. Most of known and putative virulence genes were part of the core genome, but a small fraction were detected on MGE. Predicted integrated phage were highly diverse and many harbored virulence, metal resistance, or antibiotic resistance genes. CRISPR (Clustered regularly interspaced short palindromic repeats) patterns revealed the common ancestry or infection history among Salmonella serovars. Overall genomic analysis revealed a great deal of diversity among Salmonella serovars due to acquired genes that enable them to thrive and survive during infection.

Genomic Epidemiology of Salmonella Infantis in Ecuador: From Poultry Farms to Human Infections

“…The long polar fimbrae (LfP), encoded by the lpf operon, was found as putative proteins in all isolates; it is believed that this protein is involved in adhesion and growth on the small intestine mucosa ( 76 ), evasion of the host immune system ( 77 ). Moreover, variations in these genes may also impact the host range of the bacteria ( 78 ). We also found the fim gene cluster that encodes type 1 fimbriae and it is involved in the initiation of biofilm formation ( 79 ).…”

Genomic network analysis of environmental and livestock F-type plasmid populations

“…In particular, their involvement in the dissemination of genes encoding extended-spectrum β-lactamases (ESBLs), such as bla CTX-M-15 , is of major clinical concern [ 14 , 15 ], and almost 40% of plasmid-borne carbapenemases are carried on F-type plasmids [ 16 ]. Additionally, F-type plasmids can also carry clinically important virulence genes [ 17 ] and colicin genes, sometimes together [ 18 ]. F-type plasmids are low copy-number and can be conjugative [ 19 ].…”

Recent Advances in the Detection of Antibiotic and Multi-Drug Resistant Salmonella: An Update

“…Whole genome sequencing (WGS) is a powerful, inexpensive open access epidemiological tool that can predict the genotypic and phenotypic resistance of a suspected bacterium in just a few days. Multi-locus sequence typing (MLST), multiple-locus variable number of tandem repeats analysis (MLVA), single-nucleotide polymorphism (SNP) analysis, [43], CRISPR-multi-locus virulence sequence typing (CRISPR-MVLST) [44] and nextgeneration sequencing (NGS) are some of the techniques [45] used in the sequencing of NTS antibiotic-resistant gene clusters, see Figure 3. In addition to labeled assays, non-labeled acoustic and optical LAMP assays have been used in the rapid detection (<1 h) of S. Typhimurium [41,42] in blood, saliva, nasal fluid (4 × 10 3 CFU/mL) and urine (5 CFU/mL) as well.…”

“…The arrow shows the orientation of the genes; genes are color-coded to define different classes of antibiotic resistance, mobile, and other gene categories. Copyright permission PLOS One [ 45 ].…”