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Complete genome sequences of 17 Salmonella enterica serovar Schwarzengrund isolates carrying an IncFIB-IncFIC (FII) fusion plasmid.

ABSTRACT: Seventeen Salmonella enterica serovar Schwarzengrund isolates from chicken (n = 9) and clinical samples including stool (n = 6), urine (n = 1), and gallbladder (n = 1) were sequenced and found to carry an IncFIB-IncFIC (FII) fusion plasmid of approximately 145 Kb. This information provides reference genomic data for comparative studies of S. Schwarzengrund pathogenicity and plasmid genetics.

SUBMITTER: Sopovski D

PROVIDER: S-EPMC10868266 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Complete genome sequences of 17 Salmonella enterica serovar Schwarzengrund isolates carrying an IncFIB-IncFIC (FII) fusion plasmid.

Sopovski Danielle D Commichaux Seth S Zhao Shaohua S Grim Christopher J CJ Foley Steven L SL Khajanchi Bijay K BK

Microbiology resource announcements 20240117 2

Seventeen Salmonella enterica serovar Schwarzengrund isolates from chicken (n = 9) and clinical samples including stool (n = 6), urine (n = 1), and gallbladder (n = 1) were sequenced and found to carry an IncFIB-IncFIC (FII) fusion plasmid of approximately 145 Kb. This information provides reference genomic data for comparative studies of S. Schwarzengrund pathogenicity and plasmid genetics. ...[more]

PMID: 38231183

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Project description:Salmonella enterica serovar Schwarzengrund is one of the most frequently isolated Salmonella serotypes responsible for human and poultry infections in Taiwan, and it has raised public health concerns. To better facilitate the understanding of transmission patterns and the dynamics of epidemics, sharing molecular data on pathogen profiles is urgently needed. The objectives of the current study were to determine and establish baseline data of S. enterica serovar Schwarzengrund isolates from 23 epidemiologically unrelated sources from year 2000 to 2018 and examine their phenotypic and genotypic characteristics. Genomic DNA of the Salmonella isolates was extracted and subjected to whole-genome sequencing using an Illumina platform. Results showed that all selected isolates exhibited multidrug resistance, and six of those were resistant to ciprofloxacin phenotypically. Genotypically, these isolates carried genes resistant to aminoglycoside (100%), phenicol (91.3%), β-lactams (69.5%), folate pathway antagonist (100%), tetracycline (82.6%), and fluoroquinolone (4.3%). Moreover, these isolates harbor integrons with five different gene cassettes identified for the first time, which are associated with resistance to trimethoprim, streptomycin, tetracycline, sulfonamide, chloramphenicol, and gentamicin. Furthermore, prevalence of IncFIB plasmid was found among studied isolates, which may increase its ability to colonize the chicken cecum and cause extra-intestinal disease. Salmonella pathogenicity islands SPI-1 to SPI-5, SPI-13, and SPI-14, as well as C63PI locus, were also detected in all isolates. This study demonstrated that a considerable high antimicrobial resistance with high virulence levels of Salmonella were found from animal sources. Sharing data on these pathogen profiles can not only help increase the reproducibility and accessibility of genomic analysis but can also support surveillance and epidemiological investigations for salmonellosis in the region.

Project description:The global incidence of Salmonella enterica serovar Schwarzengrund has risen in recent years. This serotype has been isolated from poultry, retail meat, and other food products, leading to multiple outbreaks. Alongside the increase in infections, there are growing concerns about the increasing levels of antimicrobial resistance (AMR) among S. Schwarzengrund strains. This study aims to better understand the genetic factors possibly contributing to the rising prevalence of S. Schwarzengrund by analyzing the sequences of 2058 isolates from both human patients (N = 313) and food- and animal-associated sources, including chicken (N = 1145), turkey (N = 300), pork (N = 132), and other sources (N = 168). Data were obtained from GenBank and analyzed for AMR genes using AMRFinder. Additionally, putative virulence genes and plasmid transfer genes were assessed using the Virulence and AMR Plasmid Transfer Factor Database. AMR genes were found in 1269 (61.7%) of the isolates, with a total of 2478 AMR genes among the isolates, the most common being aph(3″)-Ib (N = 969, 47.1%), tet(A) (N = 190, 9.2%), and sul2 (N = 150, 7.3%), which are responsible for resistance to aminoglycoside, tetracycline, and sulfonamide, respectively. Additionally, 1060 (51.5%) isolates carried multiple plasmid transfer genes associated with IncFIB-FIC(FII) plasmids. Other plasmid types found in at least 1% of the strains included IncI1 (N = 101, 4.9%), IncHI2 (N = 62, 3.0%), or IncHI1 (N = 24, 1.2%). The virulence gene profiles of human isolates showed diversity but largely overlapped with those from different food sources. Notably, the aerobactin iron acquisition genes, associated with Salmonella's virulence and colonization, were highly prevalent among chicken isolates (N = 1019, 89.0%) but less frequent in isolates from other sources (N = 65, 7.2%). IncFIB-FIC(FII) plasmids, commonly harboring the aerobactin operon, were highly prevalent among chicken-related isolates and present in about 10% of human isolates. The diverse plasmid, AMR, and virulence gene profiles in human-associated isolates suggest that multiple factors may contribute to the increased virulence in S. Schwarzengrund.

Dataset Information

Complete genome sequences of 17 Salmonella enterica serovar Schwarzengrund isolates carrying an IncFIB-IncFIC (FII) fusion plasmid.

Publications

Complete genome sequences of 17 <i>Salmonella enterica</i> serovar Schwarzengrund isolates carrying an IncFIB-IncFIC (FII) fusion plasmid.

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