Intestinal Carriage of Two Distinct -Carrying Strains by a Child with Uncomplicated Diarrhea.

Two distinct -carrying () strains, isolated from a child with uncomplicated diarrhea fifteen weeks apart, were characterized by combining short- and long-read sequencing to compare their genetic relatedness. One strain was characterized as Shiga toxin-producing (STEC)/typical enteropathogenic (tEPEC) O63:H6 with a repertoire of virulence genes including , (α2-subtype), , and . The other STEC with serotype O157:H16, reported for the first time as -carrying in this study, possessed, in addition, (ε-subtype) and , amongst other virulence-related genes.

Multi-omics analyses of cancer-linked clinical salmonellae reveal bacterial-induced host metabolic shift and mTOR-dependent cell transformation.

Salmonellae are associated epidemiologically and experimentally with colon cancer. To understand how Salmonella induces cell transformation, we performed multi-omics and phenotypic analyses of Salmonella clinical strains isolated from patients later diagnosed with colon cancer (case strains) and control strains from patients without cancer. We show that high transformation efficiency is a frequent intrinsic feature of clinical (case and control) salmonellae, yet case strains showed higher transformation efficiency than control strains.

Virulence and antimicrobial resistance of Shiga toxin-producing Escherichia coli from dairy goat and sheep farms in The Netherlands.

Aims: The aim of our study was to investigate the virulence and resistance of STEC from small ruminants farms in The Netherlands. Moreover, the potential transmission of STEC between animals and humans on farms was evaluated.

Methods And Results: From 182 farms, in total, 287 unique STEC isolates were successfully recovered from animal samples.

New insights into the epidemiology of - A cross-sectoral retrospective genomic analysis in the Netherlands (2010-2020).

Introduction: Listeriosis, caused by infection with (), is a relatively rare but severe disease with one of the highest mortality rates among bacterial foodborne illnesses. A better understanding on the degree of clustering, the temporal distribution of the clusters, and their association with the various food sources is expected to lead to improved source tracing and risk-based sampling.

Methods: We investigated the genomic epidemiology of in the Netherlands between 2010 and 2020 by analyzing whole-genome-sequencing (WGS) data of isolates from listerioss patients and food sources from nationwide integrated surveillance and monitoring.

Genomic Characterization of hlyF-positive Shiga Toxin-Producing Escherichia coli, Italy and the Netherlands, 2000-2019.

Shiga toxin-producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E.

Sources and transmission routes of campylobacteriosis: A combined analysis of genome and exposure data.

Objectives: To determine the contributions of several animal and environmental sources of human campylobacteriosis and identify source-specific risk factors.

Methods: 1417 Campylobacter jejuni/coli isolates from the Netherlands in 2017-2019 were whole-genome sequenced, including isolates from human cases (n = 280), chickens/turkeys (n = 238), laying hens (n = 56), cattle (n = 158), veal calves (n = 49), sheep/goats (n = 111), pigs (n = 110), dogs/cats (n = 100), wild birds (n = 62), and surface water (n = 253). Questionnaire-based exposure data was collected.

Genomic epidemiology of emerging ESBL-producing Kentucky in Europe.

Global dissemination of ciprofloxacin-resistant Kentucky has been observed over the past decades. In recent years, there have been reports of extended-spectrum β-lactamase (ESBL) producing . Kentucky.

Transmission of ESBL-producing Escherichia coli between broilers and humans on broiler farms.

Background: ESBL and AmpC β-lactamases are an increasing concern for public health. Studies suggest that ESBL/pAmpC-producing Escherichia coli and their plasmids carrying antibiotic resistance genes can spread from broilers to humans working or living on broiler farms. These studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these isolates.

Do vegetarians less frequently carry ESBL/pAmpC-producing Escherichia coli/Klebsiella pneumoniae compared with non-vegetarians?

Background: ESBL and plasmid-mediated AmpC (pAmpC)-producing Enterobacteriaceae are frequently found on meat products in Dutch retail, especially on poultry.

Objectives: We investigated whether vegetarians are at lower risk of carrying ESBL/pAmpC-producing Escherichia coli/Klebsiella pneumoniae (ESBL-E/K) compared with persons who consume meat.

Methods: Vegetarians, pescatarians (vegetarians who eat fish) and non-vegetarians (persons who eat meat at least three times per week) were asked to send in a faecal sample and a questionnaire.

Comparative genomics reveals a lack of evidence for pigeons as a main source of stx-carrying Escherichia coli causing disease in humans and the common existence of hybrid Shiga toxin-producing and enteropathogenic E. coli pathotypes.

Background: Wild birds, in particular pigeons are considered a natural reservoir for stx-carrying E. coli. An extensive comparison of isolates from pigeons and humans from the same region is lacking, which hampers justifiable conclusions on the epidemiology of these pathogens.

Phenotypic Prediction: Linking Virulence to the Genomics of 59 Strains.

The increased availability of whole-genome-sequencing techniques generates a wealth of DNA data on numerous organisms, including foodborne pathogens such as . However, how these data can be used to improve microbial risk assessment and understanding of epidemiology remains a challenge. The aim of this study was to assess variability in virulence and genetic characteristics between and within different serovars.

Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7.

Background: Shiga toxin-producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.

Methods: We analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms.

Longitudinal study of ESBL Escherichia coli carriage on an organic broiler farm.

Objectives: To determine the molecular characteristics of ESBL-producing Escherichia coli (ESBL-E) collected during a longitudinal study on an organic broiler farm in order to investigate clonal expansion and horizontal gene transfer.

Methods: Isolates were obtained from a longitudinal study performed previously on an organic broiler fattening farm. Samples from individually followed-up broilers, the broiler house, the transport van and persons that took the samples, taken at several timepoints (days 1, 3, 4, 7, 10, 42 and 70) within a production round and during the consecutive one (days 1, 2, 3 and 70), had been investigated for the occurrence of ESBL-E.

Wild, insectivorous bats might be carriers of Campylobacter spp.

Background: The transmission cycles of the foodborne pathogens Campylobacter and Salmonella are not fully elucidated. Knowledge of these cycles may help reduce the transmission of these pathogens to humans.

Methodology/principal Findings: The presence of campylobacters and salmonellas was examined in 631 fresh fecal samples of wild insectivorous bats using a specially developed method for the simultaneous isolation of low numbers of these pathogens in small-sized fecal samples (≤ 0.

Prevalence and types of Campylobacter on poultry farms and in their direct environment.

To study whether broiler and layer farms contribute to the environmental Campylobacter load, environmental matrices at or close to farms, and caecal material from chickens, were examined. Similarity between Campylobacter from poultry and environment was tested based on species identification and Multilocus Sequence Typing. Campylobacter prevalence in caecal samples was 97% at layer farms (n = 5), and 93% at broiler farms with Campylobacter-positive flocks (n = 2/3).

Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis.

Background: In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.

Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.

Occurrence and molecular characteristics of ESBL/AmpC-producing Escherichia coli in faecal samples from horses in an equine clinic.

Objectives: To investigate the occurrence and characteristics of ESBL/AmpC-producing Escherichia coli in faecal samples from horses at one equine clinic in the Netherlands.

Methods: A total of 91 horses, including residents and patients, were sampled. ESBL/AmpC-producing E.

Transmission dynamics of extended-spectrum β-lactamase and AmpC β-lactamase-producing Escherichia coli in a broiler flock without antibiotic use.

Extended-spectrum and AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-EC) are found throughout the broiler production pyramid. Transmission of resistance between broilers and humans could occur at any point, representing a potential public health issue. Insight in farm transmission dynamics could provide a basis for control, leading to fewer contaminated broilers.

Comparative virulotyping of extended-spectrum cephalosporin-resistant E. coli isolated from broilers, humans on broiler farms and in the general population and UTI patients.

During the last decade extended-spectrum cephalosporin (ESC)-resistant Escherichia coli from food-producing animals, especially from broilers, have become a major public health concern because of the potential transmission of these resistant bacteria or their plasmid-encoded resistance genes to humans. The objective of this study was to compare ESC-resistant E. coli isolates from broilers (n=149), humans in contact with these broilers (n=44), humans in the general population (n=63), and patients with a urinary tract infection (UTI) (n=10) with respect to virulence determinants, phylogenetic groups and extended-spectrum β-lactamase (ESBL)/plasmidic-AmpC (pAmpC) genes.

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.

Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA.