Combination of and molecular techniques for discrimination and virulence characterization of marine and .

Introduction: Mammals are the main hosts for sp., agents of worldwide zoonosis. Marine cetaceans and pinnipeds can be infected by and , respectively.

Distribution of infectious and parasitic agents among three sentinel bee species across European agricultural landscapes.

Infectious and parasitic agents (IPAs) and their associated diseases are major environmental stressors that jeopardize bee health, both alone and in interaction with other stressors. Their impact on pollinator communities can be assessed by studying multiple sentinel bee species. Here, we analysed the field exposure of three sentinel managed bee species (Apis mellifera, Bombus terrestris and Osmia bicornis) to 11 IPAs (six RNA viruses, two bacteria, three microsporidia).

Phylogenetic relationship and virulence composition of O26:H11 cattle and human strain collections in Scotland; 2002-2020.

O26 is the commonest non-O157 Shiga toxin ()-producing serogroup reported in human infections worldwide. Ruminants, particularly cattle, are the primary reservoir source for human infection. In this study, we compared the whole genomes and virulence profiles of O26:H11 strains ( = 99) isolated from Scottish cattle with strains from human infections ( = 96) held by the Scottish O157/STEC Reference Laboratory, isolated between 2002 and 2020.

Deciphering the evolution of the temporal and geographic distribution of French Mycobacterium bovis genotypes using a high throughput SNP-targeted amplicon sequencing method.

Mycobacterium bovis, which belongs to the Mycobacterium tuberculosis complex, is a highly clonal pathogen. However, several lineages of M. bovis have been described worldwide and nine different clusters were identified in France.

Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing in Presence of Commensal .

The characterization of Shiga toxin-producing (STEC) is necessary to assess their pathogenic potential, but isolation of the strain from complex matrices such as milk remains challenging. In previous work, we have shown the potential of long-read metagenomics to characterize -positive STEC from artificially contaminated raw milk without isolating the strain. The presence of multiple strains in the sample was shown to potentially hinder the correct characterization of the STEC strain.

Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of -positive Shiga toxin-producing .

Introduction: The objective of this study was to develop, using a genome wide machine learning approach, an unambiguous model to predict the presence of highly pathogenic STEC in reads assemblies derived from complex samples containing potentially multiple strains. Our approach has taken into account the high genomic plasticity of and utilized the stratification of STEC and pathogroups classification based on the serotype and virulence factors to identify specific combinations of biomarkers for improved characterization of -positive STEC (also named EHEC for enterohemorrhagic ) which are associated with bloody diarrhea and hemolytic uremic syndrome (HUS) in human.

Methods: The Machine Learning (ML) approach was used in this study on a large curated dataset composed of 1,493 genome sequences and 1,178 Coding Sequences (CDS).

Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe.

Listeria monocytogenes is a ubiquitous bacterium that causes a foodborne illness, listeriosis. Most strains can be classified into major clonal complexes (CCs) that account for the majority of outbreaks and sporadic cases in Europe. In addition to the 20 CCs known to account for the majority of human and animal clinical cases, 10 CCs are frequently reported in food production, thereby posing a serious challenge for the agrifood industry.

A step forward for Shiga toxin-producing identification and characterization in raw milk using long-read metagenomics.

Shiga toxin-producing (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin ( genes), many additional factors have been reported, such as intimin ( gene), which is clearly an aggravating factor for developing HUS.

Hybrid Assembly from 75 E. coli Genomes Isolated from French Bovine Food Products between 1995 and 2016.

Here, we report the complete (or near-complete) genome sequences of 75 Escherichia coli isolates, including 71 -positive E. coli isolates, isolated in France between 1995 and 2016 from food of bovine origin. Genomes were assembled using a combination of long- and short-read sequencing.

Evaluation of high molecular weight DNA extraction methods for long-read sequencing of Shiga toxin-producing Escherichia coli.

Next generation sequencing has become essential for pathogen characterization and typing. The most popular second generation sequencing technique produces data of high quality with very low error rates and high depths. One major drawback of this technique is the short reads.

High Throughput Screening of Antimicrobial Resistance Genes in Gram-Negative Seafood Bacteria.

From a global view of antimicrobial resistance over different sectors, seafood and the marine environment are often considered as potential reservoirs of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs); however, there are few studies and sparse results on this sector. This study aims to provide new data and insights regarding the content of resistance markers in various seafood samples and sources, and therefore the potential exposure to humans in a global One Health approach. An innovative high throughput qPCR screening was developed and validated in order to simultaneously investigate the presence of 41 ARGs and 33 MGEs including plasmid replicons, integrons, and insertion sequences in Gram-negative bacteria.

Efficacy of passive immunization in broiler chicks via an inactivated autogenous vaccine administered to broiler breeder hens.

Avian pathogenic (APEC) cause extra-intestinal infections called colibacillosis, which is the dominant bacterial disease in broilers. To date, given the diversity of APEC strains and the need for an acceptable level of protection in day-old chicks, no satisfactory commercial vaccine is available. As part of a French nationwide project, we selected three representative strains among several hundred APEC that cause colibacillosis disease.

F74 plasmids are major vectors of virulence genes in bovine NTEC2.

Necrotoxigenic Escherichia coli 2 (NTEC2) are defined as E. coli producing the toxin known as cytotoxic necrotizing factor 2 (CNF2), a potent toxin primarily found in bovine but also in humans. NTEC2 are mostly associated with bovine, and cnf2 is known to be carried by pVir-like plasmids.

Insights into the assessment of highly pathogenic Shiga toxin-producing Escherichia coli in raw milk and raw milk cheeses by High Throughput Real-time PCR.

Current methods for screening Enterohemorrhagic Escherichia coli (EHEC) O157 and non-O157 serogroups in raw milk products typically rely on the molecular detection of stx, eae, and serogroup-specific wzx or wzy genes. As these genetic markers can also be carried by non-EHEC strains, a number of 'false positive' results are obtained during the screening step. The suitability of new EHEC markers (espK, espV, ureD, Z2098, and CRISPR) were tested as candidates for a more accurate screening of EHEC in dairy products.

Identification of Shiga-Toxin-Producing Shigella Infections in Travel and Non-Travel Related Cases in Alberta, Canada.

It has long been accepted that Shiga toxin (Stx) only exists in serotype 1. However, in recent decades, the presence of Shiga toxin genes () in other spp. have been reported.

Closed Genome Sequence of a Salmonella enterica Serovar Bovismorbificans Strain Isolated from Dried Pork Sausage Associated with an Outbreak in France.

We report here the closed genome sequence of one Salmonella enterica subsp. serovar Bovismorbificans strain isolated from dried pork sausage consumed by a patient suffering from salmonellosis.

Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov.

The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C.

A genetic variant of Burkholderia mallei detected in Kuwait: Consequences for the PCR diagnosis of glanders.

Glanders is a contagious zoonotic disease caused by Burkholderia mallei. Following the detection of glanders positive horses using the OIE complement fixation test, the tissues of two horses were analysed by PCR. While PCR systems targeting the Burkholderia pseudomallei complex gave positive signals, the species-specific PCR systems targeting B.

Prevalence of Enteropathogens and Virulence Traits in Brazilian Children With and Without Diarrhea.

The use of molecular diagnostics for pathogen detection in epidemiological studies have allowed us to get a wider view of the pathogens associated with diarrhea, but the presence of enteropathogens in asymptomatic individuals has raised several challenges in understanding the etiology of diarrhea, and the use of these platforms in clinical diagnosis as well. To characterize the presence of the most relevant bacterial enteropathogens in diarrheal episodes, we evaluated here the prevalence of diarrheagenic pathotypes, spp., and in stool samples of children with and without diarrhea using real-time quantitative PCR (qPCR).

Variations of the population in the digestive tract of broilers.

We explored the between-group and temporal variations in the intestinal populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) (2.