Category Archives: WGS

Research – Yersinia enterocolitica biovar 1A: An underappreciated potential pathogen in the food chain.

Posted on January 24, 2024 by | Leave a comment

Science Direct

Highlights
Y. enterocolitica was isolated from chicken (74%), pork (80%), salmon (80%) and leafy green (10%) samples

Up to five Y. enterocolitica sequence types (STs) were isolated from the same food sample

Isolates from the same sample and ST differed by 0-74 single nucleotide polymorphisms (SNPs)

Almost all (99%) food Y. enterocolitica isolates were biotype 1A

Around half (51%) of food samples contained an ST previously isolated from UK human sources.

Abstract

Yersinia enterocolitica is an underreported cause of foodborne gastroenteritis. Little is known of the diversity of Y. enterocolitica isolated from food and which food commodities contribute to human disease. In this study, Y. enterocolitica was isolated from 37/50 raw chicken, 8/10 pork, 8/10 salmon and 1/10 leafy green samples collected at retail in the UK. Up to 10 presumptive Y. enterocolitica isolates per positive sample underwent whole genome sequencing (WGS) and were compared with publicly available genomes. In total, 207 Y. enterocolitica isolates were analyzed and belonged to 38 sequence types (STs). Up to five STs of Y. enterocolitica were isolated from individual food samples and isolates belonging to the same sample and ST differed by 0–74 single nucleotide polymorphisms (SNPs). Biotype was predicted for 205 (99 %) genomes that all belonged to biotype 1A, previously described as non-pathogenic. However, around half (51 %) of food samples contained isolates belonging to the same ST as previously isolated from UK human cases. The closest human-derived isolates shared between 17 and 7978 single nucleotide polymorphisms (SNPs) with the food isolates. Extensive food surveillance is required to determine what food sources are responsible for Y. enterocolitica infections and to re-examine the role of biotype 1A as a human pathogen.

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Posted in Emerging Pathogen, Food Pathogen, Pathogen, pathogenic, WGS, Whole Genomic Sequencing, Yersinia, yersinia enterocolitica, Yersinia pseudotuberculosis

Research – Legal Regulation of Whole Genome Sequencing of Listeria monocytogenes in the Food Industry: Challenges, Attitudes, Possibilities

Posted on January 23, 2024 by | Leave a comment

SSRN

Abstract

This report presents the outcome of legal research conducted under the aegis of the project ‘Food Safety with High Precision—Pathogenomics for the Food Industry’ (short title: PathoSeq). A central objective of the PathoSeq project has been to prepare the Norwegian food industry for challenges accompanying the introduction of whole genome sequencing (WGS) of foodborne bacteria. The report elucidates the legal rules that may affect the implementation of WGS of bacterial pathogens in the food industry, using Listeria monocytogenes (Lm) as a case study. While the report focuses predominantly on the Norwegian context, account is also taken of the experiences and practices of certain other European states, particularly Austria, in light of EU food safety rules. Three key issues are canvassed: (i) the role of WGS data in assessing the safety of food; (ii) access by food safety authorities to WGS data, or to isolates on which to perform WGS, from the food industry; and (iii) food business operators’ ability to receive Lm isolates and sequences held by the authorities. A special feature of the report is that it builds on, and presents, an extensive mapping of stakeholder perspectives on these issues and, more generally, on potentials, hindrances and needs in respect of mitigating Lm-related risk through WGS technology.

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Posted in Food Microbiology Research, Listeria, Listeria monocytogenes, Research, WGS

Research – Salmonella in horses at slaughter and public health effects in Italy

Posted on January 14, 2024 by | Leave a comment

Science Direct

Abstract

The study assessed the role of equids at slaughter as faecal carriers of Salmonella enterica and the occurrence of contaminated equid carcasses during the slaughter process in Northern Italy (Emilia-Romagna Region). From June to November 2021, 152 equids (146 horses, 5 donkeys and 1 mule) were tested for Salmonella both in caecal contents and through carcass swabs. Antimicrobial resistance (AMR) of recovered strains was tested against 15 antimicrobials. Salmonella was detected in 3/152 of the caecal contents (2.0 %), while all carcass samples were negative. S. enterica serovars Enteriditis, Typhimurium and Stanleyville were identified. The only AMR isolate was S. Typhimurium with AMR profile AmCStxT.

Considering the consumption of raw horse meat (i.e., minced raw meat named “pesto di cavallo” and dried and smoked strips named “sfilacci di cavallo”) in different areas of Northern Italy, we also investigated the possible link between horse meat eating and salmonellosis cases in the human population in the same area. Specifically, we compared the Salmonella strains collected during the study with those routinely processed in the laboratory surveillance system for human salmonellosis in Emilia-Romagna (a region with about 4.5 million inhabitants). The comparison was based on whole genome sequencing data through core genome multi-locus sequence typing (cgMLST) used in routine surveillance. A genomic match in cgMLST was found between the strain of S. enterica serovar Enteritidis isolated from a horse caecal content and an enduring outbreak of 17 human cases in Emilia-Romagna during the study period. The consequent epidemiological investigation highlighted that a number of cases with known food history reported the consumption of horse meat and traced different batches of the consumed meat, released weeks apart from each other, to the slaughter investigated in the study. The results of the epidemiological investigation suggested the role of horses in the S. enterica serovar Enteritidis outbreak affecting raw horse meat consumers.

This study shows that, despite the low prevalence on equid carcasses, S. enterica in horse meat can represent a risk to consumers. From the perspective of the slaughter activities, this highlights the need to maintain a high level of hygiene during the entire process, starting from the hygiene at lairage up to the slaughtering phase and dressing of carcasses.

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Posted in Antibacterial, Antibiotic Resistance, antimicrobial resistance, food bourne outbreak, foodborne outbreak, foodbourne outbreak, MLST, outbreak, Salmonella, WGS, Whole Genomic Sequencing

Research – Scientists look into Listeria risk in Costa Rica and Ecuador

Posted on December 24, 2023 by | Leave a comment

Food Safety News

According to researchers, mandatory reporting of Listeria infections in Costa Rica would help improve knowledge of the pathogen in the country.

Listeriosis is not a notifiable disease in the country, so its prevalence is unknown, and the diversity of Listeria monocytogenes circulating is unclear.

Previous studies found Listeria monocytogenes in various foods in Costa Rica, with contamination levels between 5 and 20 percent in processed meat products and fresh cheeses.

Researchers used whole genome sequencing (WGS) to characterize 92 isolates recovered from 2009 to 2019 from 16 clinical, 67 food, and nine production environment samples.

Isolates were from urban areas, including the capital city, San José, and from rural zones where cheese production is prevalent, including Turrialba, which accounts for 70 percent of fresh cheese made in the country.

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Posted in Food Microbiology Research, Food Pathogen, Listeria, Listeria in Cheese, Listeria monocytogenes, Pathogen, pathogenic, Research, WGS

USA – Outbreak Investigation of Salmonella: Onions (October 2023) – CDC Outbreak is Over

Posted on December 14, 2023 by | Leave a comment

FDA

Sample Product Image from the Outbreak Investigation of Salmonella Related to Onions (October 2023)

Product

Recalled Gills Onions-brand diced yellow onions, diced onions & celery, diced mirepoix, and diced red onions with use-by dates in August 2023.

The US Food and Drug Administration’s (FDA) investigation is complete; the Centers for Disease Control and Prevention (CDC) declares the outbreak over.

Stores Affected

  • Recalled Gills Onions were sold to foodservice and institutions nationwide and in Canada. The firm has directly notified foodservice customers who received recalled product.
  • Recalled product was sold to retailers in Arizona, California, Idaho, Montana, Oregon, and Washington.

The FDA and CDC, in collaboration with state and local partners, investigated an outbreak of Salmonella infections linked to recalled diced onions under the Gills Onions brand name.

As part of this investigation, FDA collected multiple water, environmental, and product samples from the farm that supplied the contaminated onions to Gills Onions. Six of the samples, three water and three environmental, were positive for Salmonella spp. Whole Genome Sequencing (WGS) analysis confirmed that the strain of Salmonella found in isolates associated with three of the samples matched the same strain of Salmonella causing illnesses in this outbreak. Additional Salmonella isolates from the samples were detected, and CDC identified people who got sick with these strains of Salmonella. FDA and CDC partners reviewed the available data; however, there was not enough epidemiologic or traceback evidence to implicate a product or source of contamination for those illnesses.

As of December 4, 2023, CDC announced that the outbreak is over. CDC reports a total of 80 illnesses in 23 states. There has been a total of 18 hospitalizations and one death associated with this incident. The last illness onset was November 11, 2023. FDA’s investigation is complete.

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Posted in CDC, FDA, food bourne outbreak, Food Illness, Foodborne Illness, foodborne outbreak, foodbourne outbreak, Illness, outbreak, Salmonella, WGS

Research -High technology is the key to detecting foodborne outbreaks over space and time

Posted on December 12, 2023 by | Leave a comment

Lex Blog

Most people think of foodborne illness outbreaks as spanning a few days or weeks. But, with current technology, disease detectives can find patients of a single outbreak spread across several years and multiple states.

That is the case with an ongoing outbreak of Listeria illnesses linked to fresh peaches that began in 2018. So far, 11 patients have been identified, most recently found in August this year. One of the patients died. Recent recalls of peaches, nectarines, and plums have been initiated while public health officials continue investigating the outbreak.

The links between people sickened in the outbreak this year and the initial patient in 2018 were made possible using whole genome sequencing (WGS). Whole genome sequencing has been likened to fingerprinting used in criminal investigations, but WGS allows the Centers for Disease Control and Prevention to look at millions of pieces of data.

“WGS examines more than 4.5 million ‘letters’ of the genetic code in disease-causing bacteria such as Salmonella. Bacteria closely related by WGS are more likely to have originated from the same source than more distantly related bacteria,” said John Besser, who retired in 2019 as Deputy Chief of the Enteric Diseases Laboratory Branch at the CDC. He continues to work on CDC-related projects through the Association of Public Health Laboratories.

“Ill persons in a WGS cluster will likely have shared exposure, such as a contaminated food product. By focusing on WGS clusters, investigators can detect outbreaks when they are small, even if cases are dispersed over multiple states or widely separated in time.”

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Posted in CDC, food bourne outbreak, Food Illness, Food Microbiology Research, Food Technology, Foodborne Illness, foodborne outbreak, foodbourne outbreak, Illness, outbreak, Research, Technology, WGS

WHO unveils WGS guides to help tackle foodborne disease

Posted on November 9, 2023 by | Leave a comment

Food Safety News

The World Health Organization (WHO) has released a guide for use of whole genome sequencing (WGS) in food safety.

The guidance comes in three parts. The first explains the minimum capacity requirements in the foodborne disease surveillance and response system prior to considering implementation of WGS.

The second discusses how WGS can help to support outbreak investigations and the third describes the usage of WGS in routine surveillance of foodborne diseases.

A related webinar was organized in June 2023 where lessons learned, opportunities, challenges and national examples were highlighted. The event featured Dr. Eric Brown, from the Center for Food Safety and Applied Nutrition (CFSAN), at the U.S. Food and Drug Administration.

WGS is useful for understanding foodborne diseases through enhancing routine surveillance, outbreak detection and response and for source identification, said WHO. It is hoped the technology will help reduce the burden of foodborne illness.

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Posted in Food Microbiology Research, Food Safety, Food Safety Management, food safety training, Research, WGS, WHO, Whole Genomic Sequencing

Research – Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health

Posted on October 19, 2023 by | Leave a comment

Microbiology Research

ABSTRACT

For the last two decades, the human infection frequency of  O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3–33.7; <0.001] and humans [OR 2.2 (1.5–3.2); <0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27–33.3); =0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9–1161); <0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.

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Posted in E.coli O157, E.coli O157:H7, eae, Food Microbiology Research, Microbiological Risk Assessment, Microbiology Risk, Research, STEC, STEC E.coli, STX 1, STX 2, WGS, Whole Genomic Sequencing

Research – Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK

Posted on August 28, 2023 by | Leave a comment

Microbiology Research

ABSTRACT

Non-typhoidal  (NTS) is a major cause of bacterial gastroenteritis. Although many countries have implemented whole genome sequencing (WGS) of NTS, there is limited knowledge on NTS diversity on food and its contribution to human disease. In this study, the aim was to characterise the NTS genomes from retail foods in a particular region of the UK and assess the contribution to human NTS infections. Raw food samples were collected at retail in a repeated cross-sectional design in Norfolk, UK, including chicken (=311), leafy green (=311), pork (=311), prawn (=279) and salmon (=157) samples. Up to eight presumptive NTS isolates per positive sample underwent WGS and were compared to publicly available NTS genomes from UK human cases. NTS was isolated from chicken (9.6 %), prawn (2.9 %) and pork (1.3 %) samples and included 14 serovars, of which  Infantis and  Enteritidis were the most common. The . Enteritidis isolates were only isolated from imported chicken. No antimicrobial resistance determinants were found in prawn isolates, whilst 5.1 % of chicken and 0.64 % of pork samples contained multi-drug resistant NTS. The maximum number of pairwise core non-recombinant single nucleotide polymorphisms (SNPs) amongst isolates from the same sample was used to measure diversity and most samples had a median of two SNPs (range: 0–251). NTS isolates that were within five SNPs to clinical UK isolates belonged to specific serovars: . Enteritidis and . Infantis (chicken), and . I 4,[5],12:i- (pork and chicken). Most NTS isolates that were closely related to human-derived isolates were obtained from imported chicken, but further epidemiological data are required to assess definitively the probable source of the human cases. Continued WGS surveillance of  on retail food involving multiple isolates from each sample is necessary to capture the diversity of  and determine the relative importance of different sources of human disease.

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Posted in Decontamination Microbial, Food Micro Blog, Food Microbiology, Food Microbiology Blog, Food Microbiology Research, Food Microbiology Testing, gastroenteritis, Gastrointestinal Infection, microbial contamination, Microbial growth, Microbiological Risk Assessment, Microbiology, Microbiology Investigations, Microbiology Risk, Salmonella, WGS, Whole Genomic Sequencing

Research – Listeria monocytogenes Strains Persisting in a Meat Processing Plant in Central Italy: Use of Whole Genome Sequencing and In Vitro Adhesion and Invasion Assays to Decipher Their Virulence Potential

Posted on July 1, 2023 by | Leave a comment

MDPI

Abstract

In this study, we used both a WGS and an in vitro approach to study the virulence potential of nine Listeria monocytogenes (Lm) strains belonging to genetic clusters persisting in a meat processing plant in Central Italy. The studied clusters belonged to CC1-ST1, CC9-ST9, and CC218-ST2801. All the CC1 and CC218 strains presented the same accessory virulence genes (LIPI-3, gltA, gltB, and aut_IVb). CC1 and CC9 strains presented a gene profile similarity of 22.6% as well as CC9 and CC218 isolates. CC1 and CC218 showed a similarity of 45.2% of the same virulence profile. The hypervirulent strains of lineage I (CC1 and CC218) presented a greater ability to adhere and invade Caco-2 cells than hypovirulent ones (CC9). CC1 strains were significantly more adhesive and invasive compared with CC9 and CC218 strains, although these last CCs presented the same accessory virulence genes. No statistically significant difference was found comparing CC218 with CC9 strains. This study provided for the first time data on the in vitro adhesiveness and invasiveness of CC218-ST2801 and added more data on the virulence characteristics of CC1 and CC9. What we observed confirmed that the ability of Lm to adhere to and invade human cells in vitro is not always decipherable from its virulence gene profile.

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Posted in Decontamination Microbial, Food Micro Blog, Food Microbiology, Food Microbiology Blog, Food Microbiology Research, Food Microbiology Testing, Listeria, Listeria monocytogenes, microbial contamination, Microbial growth, Microbiological Risk Assessment, Microbiology, Microbiology Investigations, Microbiology Risk, WGS, Whole Genomic Sequencing