Dataset Information

Population structure of Salmonella enterica serotype Mbandaka reveals similar virulence potential irrespective of source and phylogenomic stratification.

ABSTRACT: Background: Salmonella enterica serotype Mbandaka ( Salmonella ser. Mbandaka) is a multi-host adapted Non-typhoidal Salmonella (NTS) that can cause foodborne illnesses in human. Outbreaks of Salmonella ser. Mbandaka contributed to the economic stress caused by NTS due to hospitalizations. Whole genome sequencing (WGS)-based phylogenomic analysis facilitates better understanding of the genomic features that may expedite the foodborne spread of Salmonella ser. Mbandaka. Methods: In the present study, we define the population structure, antimicrobial resistance (AMR), and virulence profile of Salmonella ser. Mbandaka using WGS data of more than 400 isolates collected from different parts of the world. We validated the genotypic prediction of AMR and virulence phenotypically using an available set of representative isolates. Results: Phylogenetic analysis of Salmonella ser. Mbandaka using Bayesian approaches revealed clustering of the population into two major groups; however, clustering of these groups and their subgroups showed no pattern based on the host or geographical origin. Instead, we found a uniform virulence gene repertoire in all isolates. Phenotypic analysis on a representative set of isolates showed a similar trend in cell invasion behavior and adaptation to a low pH environment. Both genotypic and phenotypic analysis revealed the carriage of multidrug resistance (MDR) genes in Salmonella ser. Mbandaka. Conclusions: Overall, our results show that the presence of multidrug resistance along with adaptation to broad range of hosts and uniformity in the virulence potential, isolates of Salmonella ser. Mbandaka from any source could have the potential to cause foodborne outbreaks as well as AMR dissemination.

SUBMITTER: Antony L

PROVIDER: S-EPMC7653644 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Population structure of Salmonella enterica serotype Mbandaka reveals similar virulence potential irrespective of source and phylogenomic stratification.

Antony Linto L Fenske Gavin G Kaushik Radhey S RS Nagaraja Tiruvoor G TG Thomas Milton M Scaria Joy J

F1000Research 20200916

Background: Salmonella enterica serotype Mbandaka ( Salmonella ser. Mbandaka) is a multi-host adapted Non-typhoidal Salmonella (NTS) that can cause foodborne illnesses in human. Outbreaks of Salmonella ser. Mbandaka contributed to the economic stress caused by NTS due to hospitalizations. Whole genome sequencing (WGS)-based phylogenomic analysis facilitates better understanding of the genomic features that may expedite the foodborne spread of Salmonella ...[more]

PMID: 33214877

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Project description:The prevalence, among human clinical cases, of Salmonella enterica serotype 4,5,12:i:-, a serotype antigenically similar to Salmonella enterica serotype Typhimurium but lacking second-phase flagellar antigens, has increased considerably over the last 10 years. To probe the evolution and ecology of this emerging serotype, we characterized 190 Salmonella isolates initially classified as Salmonella serotypes 4,5,12:i:- (n = 90) and Typhimurium (n = 100) and obtained from various sources in the United States and Spain. These isolates were characterized into six sequence types (determined by multilocus sequence typing [MLST]) and 79 pulsed-field gel electrophoresis types. The majority of Salmonella serotype 4,5,12:i:- and Typhimurium isolates (85 and 84 isolates, respectively) represented a single MLST type. Existing genome information revealed different genome deletions (which included genes responsible for phase 2 flagellum expression) in four Spanish Salmonella serotype 4,5,12:i:- isolates and one U.S. Salmonella serotype 4,5,12:i:- isolate. Fifty-nine isolates of both serotypes, representing different sources and geographical locations as well as different molecular subtypes, were thus screened for the presence of six genes and one specific region, all of which were previously found to show variable presence among Salmonella serotype 4,5,12:i:- and Typhimurium strains. All Salmonella serotype 4,5,12:i:- isolates lacked the phase 2 flagella genes fljA and fljB, which were present in all Salmonella serotype Typhimurium isolates. While all Spanish Salmonella serotype 4,5,12:i:- isolates carried the same deletion surrounding fljAB, all but two U.S. isolates showed a different genomic deletion; the two atypical U.S. isolates represented the "Spanish" deletion genotype and a unique deletion genotype. Salmonella serotype 4,5,12:i:- thus appears to represent at least two common clones, which cannot easily be differentiated with standard diagnostic procedures.

Project description:BackgroundThe emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium).ResultsAMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6')-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins.ConclusionsOur data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica.

Dataset Information

Population structure of Salmonella enterica serotype Mbandaka reveals similar virulence potential irrespective of source and phylogenomic stratification.

Publications

Population structure of <i>Salmonella enterica</i> serotype Mbandaka reveals similar virulence potential irrespective of source and phylogenomic stratification.

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