Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012

Rapid isolation of Salmonella from food is essential for faster typing and source tracking in an outbreak. The objective of this study was to investigate a rapid isolation method that would augment the standard U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) method. Food samples with low microbial load, including egg salad and ice cream, moderately high–microbial-load tomatoes, and high-microbial-load ground beef were intentionally inoculated with 2 to 48 CFU of Salmonella enterica serotype Typhimurium. The samples were preenriched in buffered peptone water for 6 h, and then selectively concentrated by immunomagnetic separation and plated for isolation on xylose-lysine-desoxycholate agar: the 6IX method. Salmonella Typhimurium was presumptively identified from approximately 97% of the low-microbial-load and moderately high–microbial-load samples by the 6IX method 2 days before the BAM standard method for isolation of Salmonella. In 49% of the beef samples, Salmonella Typhimurium was presumptively identified 1 or 2 days earlier by the 6IX method. Given the inocula used, our data clearly indicated that for most of the food samples tested, with the exception of ground beef, Salmonella Typhimurium could be isolated two laboratory days earlier with the 6IX method compared with the BAM method. In conclusion, this 6IX method may expedite Salmonella isolation and, therefore, has the potential to accelerate strain tracking for epidemiological analysis in a foodborne outbreak.

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Geography Shapes the Population Genomics of Salmonella enterica Dublin

Genome Biology and Evolution ◽

10.1093/gbe/evz158 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2220-2231 ◽

Cited By ~ 3

Author(s):

Gavin J Fenske ◽

Anil Thachil ◽

Patrick L McDonough ◽

Amy Glaser ◽

Joy Scaria

Keyword(s):

Population Structure ◽

Salmonella Enterica ◽

Core Genome ◽

Population Genomics ◽

Negative Impact ◽

Antibiotic Resistance Genes ◽

Virulence Plasmid ◽

Ancestral State ◽

Secretion Systems ◽

Data Set

Abstract Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated data set comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian, and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and are mediated by an IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, S. enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.

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Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

Journal of Clinical Microbiology ◽

10.1128/jcm.02200-15 ◽

2015 ◽

Vol 54 (2) ◽

pp. 289-295 ◽

Cited By ~ 54

Author(s):

S. Bekal ◽

C. Berry ◽

A. R. Reimer ◽

G. Van Domselaar ◽

G. Beaudry ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Salmonella Enterica ◽

Core Genome ◽

Phage Type ◽

Epidemiological Data ◽

Single Nucleotide Variant ◽

High Quality ◽

Typing Method ◽

Single Nucleotide ◽

Content Type

Salmonella entericaserovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for commonSalmonellaserovars, such asS. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonalS. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.

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Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2019.05.022 ◽

2019 ◽

Vol 304 ◽

pp. 68-74 ◽

Cited By ~ 1

Author(s):

Teerarat Prasertsee ◽

Phongsakorn Chuammitri ◽

Manu Deeudom ◽

Nipa Chokesajjawatee ◽

Pannita Santiyanont ◽

...

Keyword(s):

Sequence Analysis ◽

Genome Sequence ◽

Salmonella Enterica ◽

Core Genome ◽

Swine Production ◽

Production Chain ◽

Genome Sequence Analysis

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Draft Genome Sequences of 64 Salmonella enterica Serotype Enteritidis Isolates Obtained from Wild Mice

Genome Announcements ◽

10.1128/genomea.00953-17 ◽

2017 ◽

Vol 5 (36) ◽

Cited By ~ 4

Author(s):

Jean Guard ◽

Guojie Cao ◽

George J. Kastanis ◽

Sherrill Davison ◽

Michael McClelland ◽

...

Keyword(s):

Salmonella Enterica ◽

Draft Genome ◽

Foodborne Pathogen ◽

Genomic Diversity ◽

Genome Sequences ◽

Wild Mice ◽

Content Type ◽

Baseline Information ◽

Foodborne Outbreaks ◽

Global Concern

ABSTRACT Salmonella enterica serotype Enteritidis is a foodborne pathogen of global concern, because it is frequently isolated from foods and patients. Draft genome sequences are reported here for 64 S. Enteritidis strains isolated from the intestines and spleens of mice caught live on chicken farms in the U.S. Northeast. The availability of these genomes provides baseline information on the genomic diversity of S. Enteritidis during the 1990s, when foodborne outbreaks traced to internal contamination of eggs were prevalent.

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

F1000Research ◽

10.12688/f1000research.25540.1 ◽

2020 ◽

Vol 9 ◽

pp. 1142

Author(s):

Linto Antony ◽

Gavin Fenske ◽

Radhey S Kaushik ◽

Tiruvoor G Nagaraja ◽

Milton Thomas ◽

...

Keyword(s):

Population Structure ◽

Multidrug Resistance ◽

Salmonella Enterica ◽

Virulence Gene ◽

Economic Stress ◽

Phylogenomic Analysis ◽

Gene Repertoire ◽

Phenotypic Analysis ◽

Virulence Potential ◽

Foodborne Outbreaks

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.

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Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes

PLoS ONE ◽

10.1371/journal.pone.0255612 ◽

2021 ◽

Vol 16 (8) ◽

pp. e0255612

Author(s):

Rajesh Kumar Vaid ◽

Zoozeal Thakur ◽

Taruna Anand ◽

Sanjay Kumar ◽

Bhupendra Nath Tripathi

Keyword(s):

Genome Analysis ◽

Salmonella Enterica ◽

Core Genome ◽

Genomic Islands ◽

Economic Losses ◽

Genotypic Differences ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Genomic Features ◽

Antimicrobial Resistance Genes

Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.

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Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises

Veterinary Research ◽

10.1186/s13567-021-01001-0 ◽

2021 ◽

Vol 52 (1) ◽

Author(s):

Arnar K. S. Sandholt ◽

Aleksija Neimanis ◽

Anna Roos ◽

Jenny Eriksson ◽

Robert Söderlund

Keyword(s):

Salmonella Enterica ◽

Core Genome ◽

Opportunistic Infections ◽

Environmental Cues ◽

Loss Of Function ◽

Tissue Samples ◽

Clonal Population ◽

Genomic Signatures ◽

Group B ◽

Close Relatives

AbstractA type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (“Fulica-like”) has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections.

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