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Microorganisms
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Genomic Tools for the Surveillance and Investigation of Foodborne Disease...
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Genomic Tools for the Surveillance and Investigation of Foodborne Disease and Enteric Zoonoses

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 14882

Special Issue Editor

Dr. Sadjia Bekal

E-Mail Website
Guest Editor
Institut national de santé publique, Montreal, QC, Canada
Interests: foodborne pathogens; genomic; surveillance; outbreaks; virulence; bacterial resistance

Special Issue Information

Dear Colleagues,

Whole-genome sequencing (WGS) is rapidly replacing traditional typing methods that provide limited information and are usually pathogen-specific. By offering the highest resolution possible, genomic-based microbial typing tools can be used for pathogen tracking, outbreak control and source attribution, in addition to provide an all-in-one test for species identification, serotyping, resistance profiling and virulence detection useful for pathogen diagnostics and treatment decisions. However, WGS raises several challenges in terms of data extraction and its conversion to clinical and epidemiological information which include bioinformatic tool development, interpretation guideline definitions, harmonization and societal acceptance. This last challenge is covered by GE3LS by investigating economic, legal and societal questions at the intersection of genomics and society.

In the last few years, several methods have been developed for phylogenetic analysis based on single nucleotide polymorphism (SNP) or allelic (cgMLST or wgMLST) variation applied on the core- or the whole- genome. The use of core- or whole-genome sequences should take in consideration the genetic features of the pathogen in regards to genome size, evolution rate, plasticity and horizontally-transferred sequence content. The aim of this issue is to provide a reference collection of articles on the validation and the use of genomic tools for foodborne and zoonotic pathogen surveillance, outbreak investigation, source attribution, GE3LS and emerging challenges. Articles on the use of genomics for strain characterization, including virulence and resistance gene detection, are also accepted.

Dr. Sadjia Bekal
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Foodborne pathogens
  • Enteric zoonosis
  • Genomic analysis tools
  • Molecular Identification
  • Comparative genomic
  • GE3LS
  • Virulence
  • Antimicrobial Resistance
  • Epidemiology
  • Source attribution

Published Papers (4 papers)

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Research

15 pages, 839 KiB  
Article
Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations
by Christine A. Yanta, John R. Barta, Antoine Corbeil, Hervé Menan, Karine Thivierge, Robert Needle, Muhammad Morshed, Brent R. Dixon, James D. Wasmuth and Rebecca A. Guy
Microorganisms 2022, 10(2), 447; https://doi.org/10.3390/microorganisms10020447 - 15 Feb 2022
Cited by 5 | Viewed by 2350
Abstract
Cyclospora cayetanensis is an emerging foodborne parasite that causes cyclosporiasis, an enteric disease of humans. Domestically acquired outbreaks have been reported in Canada every spring or summer since 2013. To date, investigations into the potential sources of infection have relied solely on epidemiological [...] Read more.
Cyclospora cayetanensis is an emerging foodborne parasite that causes cyclosporiasis, an enteric disease of humans. Domestically acquired outbreaks have been reported in Canada every spring or summer since 2013. To date, investigations into the potential sources of infection have relied solely on epidemiological data. To supplement the epidemiological data with genetic information, we genotyped 169 Canadian cyclosporiasis cases from stool specimens collected from 2010 to 2021 using an existing eight-marker targeted amplicon deep (TADS) scheme specific to C. cayetanensis as previously described by the US Centers for Disease Control and Prevention (CDC). This is the first study to genotype Canadian Cyclospora cayetanensis isolates, and it focuses on evaluating the genotyping performance and genetic clustering. Genotyping information was successfully collected with at least part of one of the markers in the TADS assay for 97.9% of specimens, and 81.1% of cyclosporiasis cases met the minimum requirements to genetically cluster into 20 groups. The performance of the scheme suggests that examining cyclosporiasis cases genetically will be a valuable tool for supplementing epidemiological outbreak investigations and to minimize further infections. Further research is required to expand the number of discriminatory markers to improve genetic clustering. Full article
(This article belongs to the Special Issue Genomic Tools for the Surveillance and Investigation of Foodborne Disease and Enteric Zoonoses)
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19 pages, 2698 KiB  
Article
Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool
by Christy-Lynn Peterson, David Alexander, Julie Chih-Yu Chen, Heather Adam, Matthew Walker, Jennifer Ali, Jessica Forbes, Eduardo Taboada, Dillon O. R. Barker, Morag Graham, Natalie Knox and Aleisha R. Reimer
Microorganisms 2022, 10(2), 441; https://doi.org/10.3390/microorganisms10020441 - 15 Feb 2022
Cited by 5 | Viewed by 4282
Abstract
Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool [...] Read more.
Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories. Full article
(This article belongs to the Special Issue Genomic Tools for the Surveillance and Investigation of Foodborne Disease and Enteric Zoonoses)
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20 pages, 5520 KiB  
Article
Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella
by Ruimin Gao, Hongsheng Huang, Jérémie Hamel, Roger C. Levesque, Lawrence D. Goodridge and Dele Ogunremi
Microorganisms 2022, 10(2), 369; https://doi.org/10.3390/microorganisms10020369 - 5 Feb 2022
Cited by 3 | Viewed by 2504
Abstract
We have developed a targeted, amplicon-based next-generation sequencing method to detect and analyze 227 virulence genes (VG) of Salmonella (AmpliSeqSalm_227VG) for assessing the pathogenicity potential of Salmonella. The procedure was developed using 80 reference genomes representing 75 epidemiologically-relevant serovars associated [...] Read more.
We have developed a targeted, amplicon-based next-generation sequencing method to detect and analyze 227 virulence genes (VG) of Salmonella (AmpliSeqSalm_227VG) for assessing the pathogenicity potential of Salmonella. The procedure was developed using 80 reference genomes representing 75 epidemiologically-relevant serovars associated with human salmonellosis. We applied the AmpliSeqSalm_227VG assay to (a) 35 previously characterized field strains of Salmonella consisting of serovars commonly incriminated in foodborne illnesses and (b) 34 Salmonella strains with undisclosed serological or virulence attributes, and were able to divide Salmonella VGs into two groups: core VGs and variable VGs. The commonest serovars causing foodborne illnesses such as Enteritidis, Typhimurium, Heidelberg and Newport had a high number of VGs (217–227). In contrast, serovars of subspecies not commonly associated with human illnesses, such as houtenae, arizonae and salame, tended to have fewer VGs (177–195). Variable VGs were not only infrequent but, when present, displayed considerable sequence variation: safC, sseL, sseD, sseE, ssaK and stdB showed the highest variation and were linked to strain pathogenicity. In a chicken infection model, VGs belonging to rfb and sse operons showed differences and were linked with pathogenicity. The high-throughput, targeted NGS-based AmpliSeqSalm_227VG procedure provided previously unknown information about variation in select virulence genes that can now be applied to a much larger population of Salmonella for evaluating pathogenicity of various serovars of Salmonella and for risk assessment of foodborne salmonellosis. Full article
(This article belongs to the Special Issue Genomic Tools for the Surveillance and Investigation of Foodborne Disease and Enteric Zoonoses)
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10 pages, 256 KiB  
Article
Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr
by Amrita Bharat, Aaron Petkau, Brent P. Avery, Jessica C. Chen, Jason P. Folster, Carolee A. Carson, Ashley Kearney, Celine Nadon, Philip Mabon, Jeffrey Thiessen, David C. Alexander, Vanessa Allen, Sameh El Bailey, Sadjia Bekal, Greg J. German, David Haldane, Linda Hoang, Linda Chui, Jessica Minion, George Zahariadis, Gary Van Domselaar, Richard J. Reid-Smith and Michael R. Mulveyadd Show full author list remove Hide full author list
Microorganisms 2022, 10(2), 292; https://doi.org/10.3390/microorganisms10020292 - 26 Jan 2022
Cited by 61 | Viewed by 4971
Abstract
Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated [...] Read more.
Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5–100%), a specificity of 99.7% (98.6–100%), a positive predictive value of 95.4% (68.2–100%), and a negative predictive value of 99.1% (95.6–100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried aac(3)-IVa, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in Salmonella was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles. Full article
(This article belongs to the Special Issue Genomic Tools for the Surveillance and Investigation of Foodborne Disease and Enteric Zoonoses)
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