Evidence map›Paper›PMID 35744717›Full record

ArticleMicroorganisms2022

Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

Gopal R Gopinath, Hyein Jang, Junia Jean-Gilles Beaubrun, Jayanthi Gangiredla, Mark K Mammel, Andrea Müller, Sandeep Tamber, Isha R Patel, Laura Ewing, Leah M Weinstein and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microorganisms, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Genomic features ofFrontiers in veterinary science · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Gopal R GopinathCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.ORCID 0000-0003-2577-7548
Hyein JangCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Junia Jean-Gilles BeaubrunCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Jayanthi GangiredlaCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Mark K MammelCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Andrea MüllerInstitute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland.
Sandeep TamberFood Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada.
Isha R PatelCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Laura EwingCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Leah M WeinsteinCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Caroline Z WangCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Samantha FinkelsteinCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Flavia NegreteCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Tim MuruvandaCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA.
Marc AllardCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA.
Donald C SockettWisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, WI 53706, USA.
Franco PagottoFood Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada.
Ben D TallCenter of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
Roger StephanInstitute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland.ORCID 0000-0003-1002-4762

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.

Indexed as

phagesphylogenomicsplasmidsSalmonella Bovismorbificansvirulence factors

Identifiers

PMID35744717
PMCPMC9228720

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.