Special Issue "Genetics and Genomics of Foodborne Pathogens"
Deadline for manuscript submissions: 31 March 2018
Dr. Kieran Jordan
Food Safety Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
Interests: Occurrence and persistence of foodborne pathogens, Listeria monocytogenes, pathogenic E. coli, whole genome sequencing, control of pathogens
Dr. Avelino Alvarez-Ordonez
Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, León, Spain
Interests: Microbial stress responses, antimicrobial resistance, occurrence and persistence of foodborne pathogens, biofilms, biocontrol, metagenomics
Dr. Olivia McAuliffe
Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
Interests: Whole genome sequencing of foodborne pathogens and their bacteriophages, biocontrol and detection of foodborne pathogens with bacteriophages
Foodborne pathogens are a public health threat and their control is a challenge to the food industry. The occurrence and transcription of genes, which encode specialised functions, plays a vital role in survival of pathogens, growth under harsh conditions and in food, their ability to produce toxins and in virulence, pathogenicity and antimicrobial resistance. Controlling the expression of such genes can result in limiting the ability of pathogens to cause disease. Whole genome sequencing technologies are revolutionising epidemiology of foodborne pathogens and tracing of foodborne pathogens in food and the food processing environment. An increasing amount of information on genes, genomes and transcriptomes of foodborne pathogens is becoming available, which will lead to a greater understanding of survival and virulence of pathogens.
This Special Issue welcomes submissions on issues relating to the genetics and genomics of foodborne pathogens, including on topics such as persistence, virulence, gene detection, whole genome sequencing, transcriptomics, and characterisation of genes involved in toxin production, antimicrobial resistance and virulence, among others.
All contributions to this Special Issue must be in line with the scope of the journal. Manuscripts discovered, during any stage of peer review process, to be outside of the scope may be transferred to a suitable section or field, or withdrawn from review.
Dr. Kieran Jordan
Dr. Olivia McAuliffe
Dr. Avelino Alvarez-Ordonez
Manuscript Submission Information
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- Bacterial virulence
- Whole genome sequencing
- Toxin production
- Antimicrobial resistance
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Tentative title: Antibiotic resistance genetic markers and integrons in white soft cheese: aspects of clinical resistome and potentiality of horizontal gene spread.
Putative authors: Ana Caroline L. Paula, Julliane D. Medeiros, Analice C. Azevedo, Jessica A. Chagas, Vania L. Silva and Claudio G. Diniz
Affiliations: Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora MG, Brazil.
Abstract: Antibiotic resistance poses an important threat to global public health and has become a challenge to modern medicine. The occurrence of antibiotic-resistant bacteria in a broad range of foods has led to a growing concern about the impact that food may have as a reservoir of antibiotic resistance genes. Considering Minas Frescal Cheese (MFC), a typical Brazilian white soft cheese and its economic and cultural values, in this study medically relevant antimicrobial-resistance genetic markers (AR genes) were screened and the occurrence of integrons were evaluated in manufactured MFC, using culture-independent approaches. Through a fingerprinting analysis, the tested MFC were brand-clustered, indicating reproducibility along the production chain. We detected a common core of resistance markers to all brands evaluated related antimicrobials such as beta-lactams, tetracyclines, quinolones and sulfonamide. Several other markers, including efflux pumps and aminoglycosides-resistance were distributed among brands. Class 1 and 2 integrons were observed respectively in 77% and 97% of the samples. The presence of AR genes are of special interest due to their clinical relevance. Taken together the data may suggest that productive chain of MFC might be related to spread of putative drug-resistant bacteria with great impact on human health. Furthermore, detection of class 1 and class 2 integrons in MFC lead to discussions about resistance genes spread in this traditional cheese, providing evidences of potential horizontal transfer of AR genes to our transient and resident microbiota, especially in the gut.
Tentative title: Genotypic and phenotypic analysis of antimicrobial resistance among Listeria monocytogenes isolated from Australian food production chains
Putative authors: Annaleise Wilson, Jessica Gray, P. Scott Chandry, Edward M. Fox
Affiliation: CSIRO Agriculture and Food, Werribee, Victoria, Australia
Abstract: The current global crisis of antimicrobial resistance among important human bacterial pathogens has been amplified by an increased resistance prevalence. In recent years a number of reports have reported higher resistance levels among Listeria monocytogenes isolates, which has serious implications for treatment of listeriosis infection where resistance to key treatment antimicrobials is noted. This study examined the genotypic and phenotypic antimicrobial resistance (AMR) patterns of 100 L. monocytogenes isolates originating from food production supplies in Australia, and examined this in the context of global population trends. Low levels of resistance were noted to ciprofloxacin (2%) and erythromycin (1%), however no resistance was observed to penicillin G or tetracycline. Resistance to ciprofloxacin was associated with a mutation in the fepR gene in one isolate, however no genetic basis for resistance in the other isolate was identified. Resistance to erythromycin was correlated with the presence of the ermB resistance gene. Both resistant isolates belonged to clonal complex 1 (CC1), and analysis of these in the context of global CC1 isolates suggested they were more similar to isolates from India, rather than the other CC1 isolates included in this study. This study provides baseline AMR data for L. monocytogenes isolated in Australia, identifies key genetic markers underlying this resistance, and highlights the need for global molecular surveillance of resistance patterns to maintain control over the potential dissemination of AMR isolates.
Tentative title: Whole genome sequencing as a tool for strengthening foodborne disease surveillance and response
Putative authors: Amy Cawthorne1, Kirsty Hope2, Megge Miller3, Enrique Perez Gutierrez4 on behalf of the guidance writing group
Affiliations: 1. Food Safety, World Health Organization, Switzerland, 2. NSW Department of Health, Australia 3.Department for Health and Ageing, South Australia, Australia 4.Pan American Health Organization, United States of America
Abstract: Following the release of the World Health Organization’s (WHO) Estimates of the Global Burden of Foodborne Diseases, there has been increasing recognition of the true burden these diseases have on communities around the world. Foodborne diseases are largely preventable, through an effective food safety system which considers hazards across the food chain from production to consumption. Recent advances in whole genome sequencing are making the technology less expensive and more accessible. Sequencing is now being used to detect foodborne disease outbreaks and inform outbreak management. While sequencing offers benefits, there are also challenges for the implementation of the technology, especially in lower and middle income countries.
WHO is currently drafting a guidance document to assist lower and middle income countries wishing to use sequencing for strengthening foodborne disease surveillance and response systems. A meeting of technical experts was held in Washington DC in January 2017. The experts identified a vision for how sequencing could be used to strengthen the surveillance of and response to foodborne diseases. The barriers to using sequencing for foodborne diseases were also discussed and solutions were drafted. Authors were identified amongst the meeting participants and have been working with WHO to draft the technical content for the guidance document.
The guidance document examines the capacities that need to exist within a country’s surveillance and response system before that country can consider implementing sequencing. Four options for implementation are described and the minimum capacities that need to be in place for each option to be viable. Options include using sequencing for outbreak investigations, conducting a pilot project, using sequencing for one foodborne pathogen or using sequencing for all priority foodborne pathogens. The guidance addresses the key obstacles to implementation in each of the options. The obstacles have been grouped into four broad areas: social, technical, economic and political. Each obstacle is discussed and guidance provided to overcome them. As a country works through the guidance, a plan can be developed to help countries successfully implement sequencing within their surveillance and response system for foodborne diseases.
Tentative title: Whole Genome Sequence Analysis of Listeria monocytogenes Isolates Associated with Clinical Listeriosis in Ireland
Putative authors: Amber Hilliard, Dara Leong, Amy O’Callaghan, b, Eamonn P. Culligan, Ciara A. Morgan, Niall DeLappe, Colin Hill, Kieran Jordan, Martin Cormican, Cormac G.M. Gahan
Abstract: Listeria monocytogenes is a major human foodborne pathogen is prevalent in the natural environment and that has a high case fatality rate. . Whole genome sequencing (WGS) analysis has emerged as a valuable methodology for the surveillance and classification of L. monocytogenes isolates. In this study, WGS was used to provide an insight into 25 L. monocytogenes isolates from cases of clinical infection in Ireland between 2013 and 2015. Sequence analysis revealed that strains were either lineage I (14 isolates) or lineage II (11 isolates), with 12 clonal complexes represented, of which CC1 and CC101 were the most common. Single nucleotide polymorphism (SNP) analysis demonstrated that clinical isolates from mother-infant pairs were highly related and also identified similarities between otherwise distinct isolates. Clinical strains were positive for common virulence associated loci and 13 isolates harbour the LIPI-3 locus. Pulsed-field gel electrophoresis (PFGE) was used to compare strains to a database of Irish food and environmental isolates and determined that some clinical pulsotypes were previously encountered in the food processing environment. Six were identified as indistinguishable and sequencing of these 6 matching food and environmental strains demonstrated a correlation between pulsotype and genotype. Overall, the work provides insights into the nature of L. monocytogenes strains currently causing clinical disease in Ireland and indicates that similar isolates can be found in the food processing environment.
Tentative title: Regulation of Listeria monocytogenes listeriolysin O production by short chain fatty acids under aerobic or anaerobic conditions
Putative authors: Erica M. Rinehart, Nathan Wallace, Nicole Steinbicker, Katie Breitenbach, and Yvonne Sun
Affiliation: Department of Biology, University of Dayton, Dayton, OH, USA
Abstract: Listeria monocytogenes (LM) is gram positive, foodborne pathogen capable of secreting listeriolysin O (LLO), a pore-forming toxin encoded by the hly gene, to establish its intracellular life cycle inside mammalian host cells. The amount of LLO produced is influenced by multiple regulatory factors and environmental conditions. However, how the intestinal environment--devoid of oxygen and enriched in short chain fatty acids (SCFAs)--modulates LLO production has not been determined. To better understand LLO production in response to environmental conditions relevant to those found during LM transit through the intestinal lumen, a GUS reporter fusion strain as well as hemolytic assays were used to examine the effect of SCFAs on the transcription and the activity of LLO in the presence or absence of oxygen. Results demonstrated that LLO production was significantly affected by SCFAs and that the SCFA effect was strongly influenced by pH and oxygen. These results suggest that LM is capable of responding to the SCFA-rich environment during intestinal transmit and that SCFA abundance may contribute to individual susceptibility to LM infections.
Tentative title: Genomic diversity of Listeria monocytogenes from clinical and food samples in Chile
Putative authors: Viviana Toledo1, Henk den Bakker2, Marc Allard3, Helia Bello1, Gerardo González-Rocha1 and Andrea I. Moreno-Switt1.
Affiliations: 1Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile, 2 Center for Food Safety, College of Agricultural & Environmental Sciences, University of Georgia, USA, 3 Food and Drug Administration, College Park MD 20740 USA
Abstract: Listeria monocytogenes is the causative agent of listeriosis, a severe infection associated with high mortality rates in humans, especially, in risk groups as the elderly, pregnant woman and newborns. L. monocytogenes is able to proliferate in low temperatures and it can survive a variety of stress conditions, as high osmolality and low pH, which allows to colonize different niches like food processing environments. Genomics have shown, a considerable heterogeneity in their pathogenic potential in L monocytogenes lineages. In Chile, two listeriosis outbreaks and a sustained increase on listeriosis in the later years, have been reported. In this study, a total of 38 genomes of L monocytogenes isolated from listeriosis cases and different food matrices in Chile were sequenced and characterized. Using a maximum likelihood phylogenetic tree based on core genome SNPs, L. monocytogenes were clustered in the two main lineages (I and II). MLST showed the presence of 12 sequence type (ST), along with presence of the worldwide distributed clonal complexes (CC), CC-1 and CC-9. Different genomic elements associated with virulence were identified, including one novel inlA PMSC. Comparative analysis of strains circulating in Chile revealed differences among them at genomic level, specifically associated to virulence and stress survival. This study makes available baseline data on the genomic diversity of Listeria in Chile and further supports global distribution of key human disease associated L. monocytogenes clonal groups.
Tentative title: Association of virulence factors and resistance genes in feedlot cattle
Putative authors: M. D. Weinroth, N. R. Noyes, P. Rovira, P. S. Morley, and K. E. Belk
Affiliation: Center for Meat Safety & Quality, Department of Animal Sciences, Campus Delivery 1171, Colorado State University, Fort Collins, CO 80523-1171, USA
Abstract: The objective of this study is to assess the associations between virulence factor genes and antibiotic resistance genes in the microbiome of feedlot cattle. Feces from pens of cattle (N = 40) throughout North America were sampled. Total DNA was extracted from these samples and shotgun metagenomics libraries were constructed. Libraries were sequenced on an Illuminia platform. Raw sequences went through quality control and trimmed reads were aligned to the Virulence Factor Database for virulence factor gene assignment and MEGARes for antibiotic resistance gene assignment. Reads from both assignments were compared for possible associations.
4 Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
Tentative title: Pathogenicity islands genes distribution in Shiga toxin-producing Escherichia coli (STEC) from Argentina
Putative authors: Jimena S. Cadona, Juliana González, Ana V. Bustamante, A. Mariel Sanso
Affiliation: Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CIC-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7000 Tandil, Argentina
Abstract: Shiga toxin-producing Escherichia coli (STEC) are heterogeneous foodborne pathogens associated with outbreaks and hemolytic-uremic syndrome (HUS). Cattle are the main reservoir of STEC and human infections are acquired mainly by ingesting food or water contaminated directly or indirectly with cattle feces. E. coli O157:H7 is the serotype most associated to diseases, however, recent studies have shown that the number of non-O157 STEC infections sometimes surpasses the number of STEC O157 infections.
Pathogenicity islands (PAIs) play an important role in STEC pathogenicity. Since PAIs are normally absent in nonpathogenic strains, they may serve as useful markers to distinguish highly virulent strains from less-virulent or harmless strains. In addition, PAIs can be used to identify new and emerging pathogenic bacteria. Non-LEE effector (nle) genes are present on PAIs and encode translocated substrates of the type III secretion system. A molecular risk assessment (MRA) approach based on the evaluation of the nle gene content has been used to predict which STEC strains pose a significant risk to human health.
The goal of this study was to investigate the distribution of OI-36, OI-57, OI-71 and OI-122 among clinical, food and animal STEC isolates from Argentina. More specific, the research aimed at identifying associations of the PAIs and individual virulence genes with STEC seropathotypes (SPTs), isolation sources, serogroups, intimin presence/absence and type of Shiga toxin.
A total of 202 STEC strains belonging to 48 non-O157:H7 serotypes were screened by the presence of 20 markers virulence genes encoded by genomic O-islands OI-36 (nleB2, nleC, nleH1-1, nleD), OI-57 (nleG2-3, nleG5-2, nleG6-2), OI-71 (nleA, nleF, nleG, nleG2-1, nleG9, nleH1-2) and OI-122 (ent/espL2, nleB, nleE, Z4321, Z4326, Z4332, Z4333).
We found a full spectrum of nle gene markers and differences in frequencies of genetic markers and PAI virulence genes profiles. The gene nleB encoded on the OI-122 was found as the most conserved marker.
Tentative title: Genome-wide profiling and novel applications of enterotoxigenic Staphylococcus aureus strains
Putative authors: Guerrino Macori1,*, Alberto Bellio1, Angelo Romano1, Silvia Gallina1, Jacques-Antoine Hennekinne2 and Lucia Decastelli1
1 National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.
2 European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for food safety, ANSES, Université Paris-Est, Maisons-Alfort F-94700, France.
Abstract: Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with superantigenic activity can be produced by specific strains responsible of staphylococcal food poisoning, one of the most common food-borne diseases. In order to investigate enterotoxigenic S. aureus, the application of Whole Genome Sequencing provides the comprehensive view of the genome structure and gene content that is now being applied in outbreak investigations. In this study, six enterotoxigenic S.aureus strains have been genome-sequenced and analyzed with novel computational approaches, revealing the opportunity for the production of naturally contaminated materials and a database for genomic feature of this set of staphylococcal enterotoxins producers.