Cross-sectoral genomic surveillance reveals a lack of insight in sources of human infections with Shiga toxin-producing , the Netherlands, 2017 to 2023.

Shiga toxin-producing (STEC) is a zoonotic pathogen associated with illness ranging from mild diarrhoea to haemolytic uremic syndrome (HUS) or even death. Cross-sectoral data sharing provides an opportunity to gain insight in reservoirs and sources of human infections and starting points for pro-active measures. Nevertheless, phylogenetic clustering of STEC strains from animals, food and human cases is low in the Dutch surveillance system.

Reducing antimicrobial use in livestock alone may be not sufficient to reduce antimicrobial resistance among human infections: an ecological study in the Netherlands.

Reducing antimicrobial use (AMU) in livestock may be one of the keys to limit the emergence of antimicrobial resistance (AMR) in bacterial populations, including zoonotic pathogens. This study assessed the temporal association between AMU in livestock and AMR among isolates from human infections in the Netherlands between 2004 - 2020. Moreover, the associations between AMU and AMR in livestock and between AMR in livestock and AMR in human isolates were assessed.

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.

Impact of non-pharmaceutical interventions during the COVID-19 pandemic on pathogens transmitted via food in the Netherlands.

The COVID-19 pandemic impacted the transmission of many pathogens. The aim was to determine the effect of non-pharmaceutical interventions on the incidence of diseases transmitted via food. Weekly incidence rates for nine foodborne pathogens were collected from national surveillance registries.

Use of whole genome sequencing for surveillance and control of foodborne diseases: and .

Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state ("") and future directions ("") based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens.

Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands.

Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires.

Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan.

Our understanding of the normal variation in the upper respiratory tract (URT) microbiota across the human lifespan and how these relate to host, environment, and health is limited. We studied the microbiota of 3,104 saliva (<10 year-olds)/oropharynx (≥10 year-olds) and 2,485 nasopharynx samples of 3,160 Dutch individuals 0-87 years of age, participating in a cross-sectional population-wide study (PIENTER-3) using 16S-rRNA sequencing. The microbiota composition was strongly related to age, especially in the nasopharynx, with maturation occurring throughout childhood and adolescence.

Association between antimicrobial usage in livestock and antimicrobial resistance in Escherichia coli isolates from human urinary tract infections in the Netherlands, 2009-2020.

Background: In the last decade, veterinary antimicrobial usage (AMU) and antimicrobial resistance (AMR) among indicator bacteria in livestock have decreased substantially in the Netherlands. The extent to which this decrease has affected AMR levels among human infections remains unclear.

Objectives: To assess the association between AMU in livestock and AMR in Escherichia coli isolates from human urinary tract infections (UTIs).

Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark.

We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted clinical case of V. cholerae has been reported in Denmark for more than 100 years.

Livestock-associated spatial risk factors for human salmonellosis and campylobacteriosis.

Aims: Most human infections with non-typhoid Salmonella (NTS) or Campylobacter are zoonotic in nature and acquired though consumption of contaminated food of mainly animal origin. However, individuals may also acquire salmonellosis or campylobacteriosis through non-foodborne transmission pathways, such as those mediated by the environment. This emphasizes the need to consider both direct and indirect exposure to livestock sources as a possible transmission route for NTS and Campylobacter.

Utility of various genome lengths in diversity and evolution analyses of Hepatitis E virus.

The aim of this study was to investigate to what extent fragments of the HEV genome could be used for accurate diagnostics and inference of viral population-scale processes. For this, we selected all the published whole genome sequences from the NCBI GenBank and trimmed them to various fragment lengths (ORF1,2,3, ORF1, ORF2, ORF3, 493 nt in ORF2 and 148 nt in ORF2). Each of the fragment lengths was used to infer the richness and diversity of the viral sequence types, typing accuracy, and potential use in phylodynamics.

Lower prevalence of post-Covid-19 Condition following Omicron SARS-CoV-2 infection.

Objectives: Different SARS-CoV-2 variants can differentially affect the prevalence of Post Covid-19 Condition (PCC). This prospective study assesses prevalence and severity of symptoms three months after an Omicron infection, compared to Delta, test-negative and population controls. This study also assesses symptomology after reinfection and breakthrough infections.

New methodology to assess the excess burden of antibiotic resistance using country-specific parameters: a case study regarding urinary tract infections.

Objectives: Antimicrobial resistant (AMR) infections are a major public health problem and the burden on population level is not yet clear. We developed a method to calculate the burden of resistance which uses country-specific parameter estimates and surveillance data to compare the mortality and morbidity due to resistant infection against a counterfactual (the expected burden if infection was antimicrobial susceptible). We illustrate this approach by estimating the excess burden for AMR (defined as having tested positive for extended-spectrum beta-lactamases) urinary tract infections (UTIs) caused by in the Netherlands in 2018, which has a relatively low prevalence of AMR , and in Italy in 2016, which has a relatively high prevalence.

Combining Whole Genome Sequencing Data from Human and Non-Human Sources: Tackling Outbreaks.

() is ubiquitous in nature and known for its ability to contaminate foods during production processes. Near real-time monitoring of whole genome sequences from food and human isolates, complemented with epidemiological data, has been used in the Netherlands since 2019 to increase the speed and success rate of source finding in the case of (active) clusters. Nine clusters with 4 to 19 human cases investigated between January 2019 and May 2023 are described.

Seroprevalence of and associated risk factors for infection in the Netherlands: third cross-sectional national study.

A third nationally representative serosurvey was performed to study the changes in seroprevalence in the Netherlands over a 20-year time span and to identify and confirm risk factors for acquired toxoplasmosis. This cross-sectional study (conducted in 2016/2017) was designed similarly to the previous two studies (1995/1996 and 2006/2007) and included a questionnaire and serum sampling among Dutch residents. Factors associated with seropositivity for were determined using multivariable analysis of the questionnaire-derived data.

Assessing potential determinants of the stagnating trend in human infections in Europe and options for intervention: A multi-criteria decision analysis.

Background: After years of significant decline, the incidence of serotype Enteritidis (SE) human infections in Europe has started stagnating in recent years. The reasons for this stagnation remain largely unclear and are possibly multifactorial and interconnected in nature. We assessed and ranked several potential determinants of the stagnating SE trend in Europe, as well as different options for intervention at the level of poultry health and production, public health (infra)structure, and pathogen biology.

Epidemiology of Pathogens Listed as Potential Bioterrorism Agents, the Netherlands, 2009‒2019.

We provide incidences (cases/10 million persons) in the Netherlands during 2009-2019 for pathogens listed as potential bioterrorism agents. We included pathogens from the highest categories of the European Medicines Agency or the US Centers for Disease Control and Prevention. Notifiable diseases and recently published data were used to calculate the average annual incidence.

Increased antimicrobial resistance among non-typhoidal Salmonella infections in international travellers returning to the Netherlands.

Highlights: Increased fluoroquinolone resistance in the two most common non-typhoidal (NTS) serotypes among travellers returning to the Netherlands. Resistant infections are most likely to be acquired abroad, specifically outside Europe. This study highlights the importance of travel history when patients with NTS infections require empiric antimicrobial treatment.

Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance.

Despite high vaccination rates in the Netherlands, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate. Longitudinal sewage surveillance was implemented along with the notification of cases as two parts of the surveillance pyramid to validate the use of sewage for surveillance, as an early warning tool, and to measure the effect of interventions. Sewage samples were collected from nine neighborhoods between September 2020 and November 2021.

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.