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). METHODS: Data on AMR and AMU between 2009 and 2020 from Dutch national surveillance programmes for humans and livestock were used. Associations between AMU in four major livestock sectors and AMR in humans were assessed for 10 antimicrobial classes and the ESBL resistance profile, using logistic regression analysis. Associations between AMU and AMR in livestock, between AMR in livestock and in humans, and between AMU and AMR in humans were also assessed. RESULTS: Statistical significance was reached for 16/31 of the tested associations between AMU in livestock and AMR in human E. coli UTIs. Of the significant associations, 11 were positive (OR 1.01-1.24), whereas 5 were negative (OR 0.96-0.99). All associations between human AMU and AMR in E. coli isolates from UTIs were positive and statistically significant. Weak but significant positive correlations were also observed between livestock AMR and human AMR. CONCLUSIONS: Although several significant associations between AMU in livestock and AMR in human UTIs caused by E. coli were observed, the associations between AMU and AMR were generally stronger within the human and animal populations. This indicates that potential zoonotic spread of AMR in E. coli causing human UTIs from livestock sources is limited.

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. Weekly pathogen incidence during lockdown weeks of 2020 and 2021 were compared with corresponding weeks in 2015-2019. The same analyses were performed to determine the effect of self-defined expected impact levels of measures (low, intermediate and high). Eight out of 9 diseases showed a significant decrease in case number in 2020, except for listeriosis, which remained unchanged. The largest decrease was observed for rotavirus gastronteritis A (-81%), norovirus gastroenteritis (-78%), hepatitis A (-75%) and shigellosis (-72). In 2021, lower case numbers were observed for 6 out of 9 diseases compared with 2015-2019, with the largest decrease for shigellosis (-5/%) and hepatitis E (-47%). No significant change was observed for listeriosis, STEC infection and rotavirus gastroenteritis. Overall, measures with increased expected impact level did not result in a larger decrease in number of cases, except for Campylobacter, and norovirus and rotavirus gastroenteritis. Disease transmitted via food significantly decreased during the COVID-19 pandemic, with a more pronounced effect during 2020 than 2021.

Effects of long-term exposure to outdoor air pollution on COVID-19 incidence: A population-based cohort study accounting for SARS-CoV-2 exposure levels in the Netherlands.

Several studies have linked air pollution to COVID-19 morbidity and severity. However, these studies do not account for exposure levels to SARS-CoV-2, nor for different sources of air pollution. We analyzed individual-level data for 8.3 million adults in the Netherlands to assess associations between long-term exposure to ambient air pollution and SARS-CoV-2 infection (i.e., positive test) and COVID-19 hospitalisation risks, accounting for spatiotemporal variation in SARS-CoV-2 exposure levels during the first two major epidemic waves (February 2020-February 2021). We estimated average annual concentrations of PM10, PM2.5 and NO2 at residential addresses, overall and by PM source (road traffic, industry, livestock, other agricultural sources, foreign sources, other Dutch sources), at 1 × 1 km resolution, and weekly SARS-CoV-2 exposure at municipal level. Using generalized additive models, we performed interval-censored survival analyses to assess associations between individuals' average exposure to PM10, PM2.5 and NO2 in the three years before the pandemic (2017-2019) and COVID-19-outcomes, adjusting for SARS-CoV-2 exposure, individual and area-specific confounders. In single-pollutant models, per interquartile (IQR) increase in exposure, PM10 was associated with 7% increased infection risk and 16% increased hospitalisation risk, PM2.5 with 8% increased infection risk and 18% increased hospitalisation risk, and NO2 with 3% increased infection risk and 11% increased hospitalisation risk. Bi-pollutant models suggested that effects were mainly driven by PM. Associations for PM were confirmed when stratifying by urbanization degree, epidemic wave and testing policy. All emission sources of PM, except industry, showed adverse effects on both outcomes. Livestock showed the most detrimental effects per unit exposure, whereas road traffic affected severity (hospitalisation) more than infection risk. This study shows that long-term exposure to air pollution increases both SARS-CoV-2 infection and COVID-19 hospitalisation risks, even after controlling for SARS-CoV-2 exposure levels, and that PM may have differential effects on these COVID-19 outcomes depending on the emission source.

Animal sources of antimicrobial-resistant bacterial infections in humans: a systematic review.

Bacterial antimicrobial resistance (AMR) is among the leading global health challenges of the century. Animals and their products are known contributors to the human AMR burden, but the extent of this contribution is not clear. This systematic literature review aimed to identify studies investigating the direct impact of animal sources, defined as livestock, aquaculture, pets, and animal-based food, on human AMR. We searched four scientific databases and identified 31 relevant publications, including 12 risk assessments, 16 source attribution studies, and three other studies. Most studies were published between 2012 and 2022, and most came from Europe and North America, but we also identified five articles from South and South-East Asia. The studies differed in their methodologies, conceptual approaches (bottom-up, top-down, and complex), definitions of the AMR hazard and outcome, the number and type of sources they addressed, and the outcome measures they reported. The most frequently addressed animal source was chicken, followed by cattle and pigs. Most studies investigated bacteria-resistance combinations. Overall, studies on the direct contribution of animal sources of AMR are rare but increasing. More recent publications tailor their methodologies increasingly towards the AMR hazard as a whole, providing grounds for future research to build on.

Risk of acquiring Ascaris lumbricoides infection in an endemically infected rural community in Venezuela.

Soil-transmitted helminths, such as Ascaris lumbricoides, are the most prevalent parasites globally. Optimal anthelmintic treatment for A. lumbricoides in endemically infected communities is challenged by several host-related and environmental factors influencing infection acquisition. We assessed the risk of A. lumbricoides (re)infection after treatment in a Venezuelan rural community. Individual merthiolate-iodine-formaldehyde-fixed faecal samples were collected from 224 persons before a single-dose pyrantel treatment and at 1, 3, 6, 9 and 15 months after treatment. Effects of age, sex and socioeconomic status (SES) on A. lumbricoides prevalence, eggs/gram faeces (EPG) and infection (re)acquisition were assessed using both generalised linear mixed-effects models and survival analysis. Pre-treatment A. lumbricoides prevalence was 39.7%. Higher prevalence was associated with younger age and lower SES. Higher EPG values were observed among young children. Median time to A. lumbricoides infection was six months after treatment: at 1, 3, 6, 9 and 15 months post-treatment, cumulative incidence was 6.7%, 18.9%, 34.6%, 42.2%, and 52.6%, respectively. Younger age, lower SES, and pre-treatment A. lumbricoides infection status showed significantly elevated hazard ratios. Mass drug administration protocols would benefit from considering these factors in selective treatment strategies and possibly more than just annual or biannual treatments in the target population.

Biosecurity and antimicrobial use in broiler farms across nine European countries: toward identifying farm-specific options for reducing antimicrobial usage.

Broiler chickens are among the main livestock sectors worldwide. With individual treatments being inapplicable, contrary to many other animal species, the need for antimicrobial use (AMU) is relatively high. AMU in animals is known to drive the emergence and spread of antimicrobial resistance (AMR). High farm biosecurity is a cornerstone for animal health and welfare, as well as food safety, as it protects animals from the introduction and spread of pathogens and therefore the need for AMU. The goal of this study was to identify the main biosecurity practices associated with AMU in broiler farms and to develop a statistical model that produces customised recommendations as to which biosecurity measures could be implemented on a farm to reduce its AMU, including a cost-effectiveness analysis of the recommended measures. AMU and biosecurity data were obtained cross-sectionally in 2014 from 181 broiler farms across nine European countries (Belgium, Bulgaria, Denmark, France, Germany, Italy, the Netherlands, Poland and Spain). Using mixed-effects random forest analysis (Mix-RF), recursive feature elimination was implemented to determine the biosecurity measures that best predicted AMU at the farm level. Subsequently, an algorithm was developed to generate AMU reduction scenarios based on the implementation of these measures. In the final Mix-RF model, 21 factors were present: 10 about internal biosecurity, 8 about external biosecurity and 3 about farm size and productivity, with the latter showing the largest (Gini) importance. Other AMU predictors, in order of importance, were the number of depopulation steps, compliance with a vaccination protocol for non-officially controlled diseases, and requiring visitors to check in before entering the farm. K-means clustering on the proximity matrix of the final Mix-RF model revealed that several measures interacted with each other, indicating that high AMU levels can arise for various reasons depending on the situation. The algorithm utilised the AMU predictive power of biosecurity measures while accounting also for their interactions, representing a first step toward aiding the decision-making process of veterinarians and farmers who are in need of implementing on-farm biosecurity measures to reduce their AMU.

Short-term and long-term effects of antimicrobial use on antimicrobial resistance in broiler and turkey farms.

RESEARCH HIGHLIGHTSSulfamethoxazole and ampicillin resistance are the highest in E. coli isolates of both broilers and turkeys.Short-term effects of antibiotic use on resistance are seen more often than long-term effects.Historical penicillin use is associated with penicillin resistance in broilers.There is an association between historical use and resistance to trimethoprim in turkeys.

The estimated disease burden of acute COVID-19 in the Netherlands in 2020, in disability-adjusted life-years.

The impact of COVID-19 on population health is recognised as being substantial, yet few studies have attempted to quantify to what extent infection causes mild or moderate symptoms only, requires hospital and/or ICU admission, results in prolonged and chronic illness, or leads to premature death. We aimed to quantify the total disease burden of acute COVID-19 in the Netherlands in 2020 using the disability-adjusted life-years (DALY) measure, and to investigate how burden varies between age-groups and occupations. Using standard methods and diverse data sources (mandatory notifications, population-level seroprevalence, hospital and ICU admissions, registered COVID-19 deaths, and the literature), we estimated years of life lost (YLL), years lived with disability, DALY and DALY per 100,000 population due to COVID-19, excluding post-acute sequelae, stratified by 5-year age-group and occupation category. The total disease burden due to acute COVID-19 was 286,100 (95% CI: 281,700-290,500) DALY, and the per-capita burden was 1640 (95% CI: 1620-1670) DALY/100,000, of which 99.4% consisted of YLL. The per-capita burden increased steeply with age, starting from 60 to 64 years, with relatively little burden estimated for persons under 50 years old. SARS-CoV-2 infection and associated premature mortality was responsible for a considerable direct health burden in the Netherlands, despite extensive public health measures. DALY were much higher than for other high-burden infectious diseases, but lower than estimated for coronary heart disease. These findings are valuable for informing public health decision-makers regarding the expected COVID-19 health burden among population subgroups, and the possible gains from targeted preventative interventions.

Changing epidemiology of Salmonella Enteritidis human infections in the Netherlands and Belgium, 2006 to 2019: a registry-based population study.

BackgroundSalmonellosis remains the second most common zoonosis in the European Union despite a long-term decreasing trend. However, this trend has been reported to have stagnated in recent years, particularly for Salmonella enterica serotype Enteritidis (SE).AimTo describe temporal changes in the incidence of SE human infections, and in its associated factors between 2006 and 2019. In addition, we aim to determine which factors influenced the stagnated trend seen in recent years.MethodsData on culture-confirmed SE human infections from national surveillance registries in the Netherlands and Belgium between 2006 and 2019 were analysed using multivariable negative-binomial regression models with restricted cubic splines.ResultsSE incidence was significantly higher in summer and autumn than winter, in persons aged 0-4 years and 5-14 years than in persons ≥ 60 years, and increased with increasing proportions of travel-related and resistant SE infections. SE incidence decreased significantly in both countries until 2015, followed by an increasing trend, which was particularly pronounced in the Netherlands. Potential SE outbreaks in both countries and invasive infections in the Netherlands also increased after 2015.ConclusionThe increase in potential outbreaks and invasive infections since 2015 may partially explain the observed reversal of the decreasing trend. While these results provide insights into the possible causes of this trend reversal, attention should also be given to factors known to influence SE epidemiology at primary (animal) production and pathogen genomic levels.

Impact of the COVID-19 pandemic on human salmonellosis in the Netherlands.

The public health measures implemented to control coronavirus disease 2019 (COVID-19) may influence also other infectious diseases. Using national laboratory surveillance data, we assessed the impact of the COVID-19 pandemic on human salmonellosis in the Netherlands until March 2021. Salmonellosis incidence decreased significantly after March 2020: in the second, third and fourth quarters of 2020, and in the first quarter of 2021, the incidence decreased by 55%, 57%, 47% and 37%, respectively, compared to the same quarters of 2016-2019. The decrease was strongest among travel-related cases (94%, 84%, 79% and 93% in the aforementioned quarters, respectively). Other significant changes were: increased proportion of cases among older adults and increased proportion of invasive infections, decreased proportion of trimethoprim resistance and increased proportion of serovar Typhimurium monophasic variant vs. Enteritidis. This led to decreased contributions of laying hens and increased contributions of pigs and cattle as sources of human infections. The observed changes probably reflect a combination of reduced exposure to Salmonella due to restrictions on international travels and gatherings, closure of dine-in restaurants, catering and hospitality sectors at large and changes in healthcare-seeking and diagnostic behaviours.

Association between Salmonella infection and colon cancer: a nationwide registry-based cohort study.

Laboratory data increasingly suggest that Salmonella infection may contribute to colon cancer (CC) development. Here, we examined epidemiologically the potential risk of CC associated with salmonellosis in the human population. We conducted a population-based cohort study using four health registries in Denmark. Person-level demographic data of all residents were linked to laboratory-confirmed non-typhoidal salmonellosis and to CC diagnoses in 1994-2016. Hazard ratios (HRs) for CC (overall/proximal/distal) associated with reported salmonellosis were estimated using Cox proportional hazard models. Potential effects of serovar, age, sex, inflammatory bowel disease and follow-up time post-infection were also assessed. We found no increased risk of CC ≥1 year post-infection (HR 0.99; 95% confidence interval (CI) 0.88-1.13). When stratifying by serovar, there was a significantly increased risk of proximal CC ≥1 year post-infection with serovars other than Enteritidis and Typhimurium (HR 1.40; 95% CI 1.03-1.90). CC risk was significantly increased in the first year post-infection (HR 2.08; 95% CI 1.48-2.93). The association between salmonellosis and CC in the first year post-infection can be explained by increased stool testing around the time of CC diagnosis. The association between proximal CC and non-Enteritidis/non-Typhimurium serovars is unclear and warrants further investigation. Overall, this study provides epidemiological evidence that notified Salmonella infections do not contribute significantly to CC risk in the studied population.

Specific staphylococcal cassette chromosome mec (SCCmec) types and clonal complexes are associated with low-level amoxicillin/clavulanic acid and cefalotin resistance in methicillin-resistant Staphylococcus pseudintermedius.

BACKGROUND: Staphylococcus pseudintermedius is a common pathogen in dogs and methicillin resistance has emerged over recent decades. According to the current guidelines, S. pseudintermedius displaying oxacillin resistance should be reported as resistant to all ß-lactams. OBJECTIVES: To identify possible associations between ß-lactam resistance levels and clonal complexes (CCs) and/or staphylococcal cassette chromosome mec (SCCmec) types in methicillin-resistant S. pseudintermedius (MRSP). METHODS: MICs of oxacillin, penicillin, ampicillin, amoxicillin/clavulanic acid and cefalotin were determined by broth microdilution for 86 clinical canine MRSP isolates from Denmark and the Netherlands. PCR and sequencing were used for SCCmec typing and MLST. RESULTS: Isolates belonged to CC71 (n = 36), CC258 (n = 33), CC45 (n = 11), CC68 (n = 1) and five singleton STs. SCCmecII-III was exclusively found in CC71 and SCCmecIV was significantly associated with CC258. SCCmecV and non-typeable SCCmec types occurred in 4 and 14 isolates, respectively. SCCmecIV was associated with lower MICs of oxacillin (<2 mg/L), ampicillin (<8 mg/L) and amoxicillin/clavulanic acid (<4 mg/L) and with susceptibility to cefalotin (<4 mg/L). All isolates harbouring SCCmecV were susceptible to cefalotin as well. CONCLUSIONS: SCCmec types were associated with different CCs and with either high- or low-level resistance to different ß-lactams. The finding of amoxicillin/clavulanic acid (20%) and cefalotin (70%) in vitro susceptibility across all CCs might have clinical implications, since amoxicillin/clavulanic acid and first-generation cephalosporins are first-choice antibiotics for treatment of S. pseudintermedius infections. Pharmacokinetic/pharmacodynamic and clinical outcome studies are warranted to evaluate the in vivo efficacy of these ß-lactams for treatment of MRSP infections.

Attribution of Listeria monocytogenes human infections to food and animal sources in Northern Italy.

Listeriosis is a foodborne illness characterized by a relatively low morbidity, but a large disease burden due to the severity of clinical manifestations and the high case fatality rate. Increased listeriosis notifications have been observed in Europe since the 2000s. However, the reasons for this increase are largely unknown, with the sources of sporadic human listerioris often remaining elusive. Here we inferred the relative contributions of several putative sources of Listeria monocytogenes strains from listerioris patients in Northern Italy (Piedmont and Lombardy regions), using two established source attribution models (i.e. 'Dutch' and 'STRUCTURE') in comparative fashion. We compared the Multi-Locus Sequence Typing and Multi-Virulence-Locus Sequence Typing profiles of strains collected from beef, dairy, fish, game, mixed foods, mixed meat, pork, and poultry. Overall, 634 L. monocytogenes isolates were collected from 2005 to 2016. In total, 40 clonal complexes and 51 virulence types were identified, with 36% of the isolates belonging to possible epidemic clones (i.e. genetically related strains from unrelated outbreaks). Source attribution analysis showed that 50% of human listerioris cases (95% Confidence Interval 44-55%) could be attributed to dairy products, followed by poultry and pork (15% each), and mixed foods (15%). Since the contamination of dairy, poultry and pork products are closely linked to primary production, expanding actions currently limited to ready-to-eat products to the reservoir level may help reducing the risk of cross-contamination at the consumer level.

Trends and correlates of antimicrobial use in broiler and turkey farms: a poultry company registry-based study in Italy.

BACKGROUND: Antimicrobial usage (AMU) in livestock plays a key role in the emergence and spread of antimicrobial resistance. Analysis of AMU data in livestock is therefore relevant for both animal and public health. OBJECTIVES: To assess AMU in 470 broiler and 252 turkey farms of one of Italy's largest poultry companies, accounting for around 30% of national poultry production, to identify trends and risk factors for AMU. METHODS: Antimicrobial treatments administered to 5827 broiler and 1264 turkey grow-out cycles in 2015-17 were expressed as DDDs for animals per population correction unit (DDDvet/PCU). A retrospective analysis was conducted to examine the effect of geographical area, season and prescribing veterinarian on AMU. Management and structural interventions implemented by the company were also assessed. RESULTS: AMU showed a 71% reduction in broilers (from 14 to 4 DDDvet/PCU) and a 56% reduction in turkeys (from 41 to 18 DDDvet/PCU) during the study period. Quinolones, macrolides and polymyxins decreased from 33% to 6% of total AMU in broilers, and from 56% to 32% in turkeys. Broiler cycles during spring and winter showed significantly higher AMU, as well as those in densely populated poultry areas. Different antimicrobial prescribing behaviour was identified among veterinarians. CONCLUSIONS: This study evidenced a decreasing trend in AMU and identified several correlates of AMU in broilers and turkeys. These factors will inform the design of interventions to further reduce AMU and therefore counteract antimicrobial resistance in these poultry sectors.

"Sickenin' in the rain" - increased risk of gastrointestinal and respiratory infections after urban pluvial flooding in a population-based cross-sectional study in the Netherlands.

BACKGROUND: Climate change is expected to increase the chance of extreme rainfall events in the Northern Hemisphere and herewith, there is an increased chance of urban pluvial flooding. Urban pluvial flooding often consists of street flooding and/or flooding of combined sewerage systems, leading to contamination of the floodwater with several gastrointestinal and/or respiratory pathogens. An increase in flooding events therefore pose a health risk to those exposed to urban floodwater. We studied the association between exposure to pluvial floodwater and acute gastroenteritis (AGE) and acute respiratory infection (ARI). METHODS: We performed a retrospective, cross-sectional survey during the summer of 2015 in 60 locations in the Netherlands with reported flooding. Two weeks after the flooding, questionnaires were sent to households in these locations, collecting data on self-reported AGE and ARI and information on floodwater exposure in the previous 2 weeks. Multivariable generalized estimating equations (GEE) regression models, accounting for the clustered data structure, were used to identify risk factors for AGE and ARI. RESULTS: In total, 699 households with 1,656 participants (response rate 21%) returned the questionnaire. Contact with floodwater was significantly associated with AGE (aOR 4.2, 95%CI 2.1-8.4) and ARI (aOR 3.3, 95%CI 2.0-5.4). Risk factors for AGE were skin contact with floodwater (aOR 4.0, 95%CI 1.8-9.0), performing post-flooding cleaning operations (aOR 8.6, 95%CI 3.5-20.9) and cycling through floodwater (aOR 2.3, 95%CI 1.0-5.0). Skin contact with floodwater (aOR 3.6, 95%CI 1.9-6.9) and performing post-flooding cleaning operations (aOR 5.5, 95%CI 3.0-10.3) were identified as risk factors for ARI. CONCLUSIONS: Results suggest an association between direct exposure to pluvial floodwater and AGE and ARI. As it is predicted that the frequency of pluvial flooding events will increase in the future, there is a need for flood-proof solutions in urban development and increased awareness among stakeholders and the public about the potential health risks. Future prospective studies are recommended to confirm our results.

Occupational risk of salmonellosis and campylobacteriosis: a nationwide population-based registry study.

OBJECTIVES: Occupational exposure to animals and foods thereof is a poorly characterised risk factor for salmonellosis and campylobacteriosis, the main causes of bacterial gastroenteritis in the Western world. We performed a population-based registry study in the Netherlands to assess whether differences exist in the incidence of reported salmonellosis and campylobacteriosis cases among occupational groups, and whether they can be explained by differences in the magnitude of exposure to these pathogens, as defined by serology. METHODS: Person-level occupational data for all Dutch residents were linked to lab-confirmed salmonellosis and campylobacteriosis data, and to serological data from a previous national serosurvey. SIRs for salmonellosis and campylobacteriosis among occupational sectors and specific high-risk occupations were calculated based on the total employed population. Moreover, Salmonella and Campylobacter seroincidence rates were compared among sectors and high-risk occupations. RESULTS: Occupational exposure to live animals or manure and working in the sale of animal-derived food products were associated with significantly increased risks of salmonellosis (SIR 1.55-1.82) and campylobacteriosis (SIR 1.36-1.65). Moreover, incidences were significantly higher in specific industrial sectors, as well as healthcare and social work sectors. Mean seroincidence rates ranged from 1.28 to 2.30 infections/person-year for Campylobacter, and from 0.36 to 0.99 for Salmonella, with only slightly higher rates for people in high-risk occupations. CONCLUSIONS: Significant differences in reported salmonellosis and campylobacteriosis incidence exist among occupational sectors, with the highest incidence in those persons occupationally exposed to live animals. These differences are only partially reflected in the serology.

Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016.

BackgroundThe epidemiology of carriage of extended-spectrum beta-lactamase-producing (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) in the general population is unknown.AimIn this observational study, the prevalence and risk factors for intestinal ESBL-E and CPE carriage in the Dutch general population were determined. ESBL-E were characterised.MethodsFrom 2014 to 2016, ca 2,000 residents were invited monthly to complete a questionnaire and provide a faecal sample, which was tested for ESBL-E. The first 1,758 samples were also tested for CPE. Risk factors for ESBL-E carriage were identified by multivariable logistic regression analysis. ESBL-E isolates underwent whole genome sequencing.ResultsOf 47,957 individuals invited, 4,177 (8.7%) completed the questionnaire and provided a faecal sample. ESBL-E were detected in 186 (4.5%) individuals, resulting in an adjusted prevalence of 5.0% (95% confidence interval (CI):3.4-6.6%). Risk factors were: born outside the Netherlands (odds ratio (OR): 1.99; 95% CI: 1.16-4.54), eating in restaurants > 20 times/year (OR: 1.70; 95% CI: 1.04-2.76), antibiotic use < 6 months ago (OR: 2.05; 95% CI: 1.05-4.03), swimming in sea/ocean < 12 months ago (OR: 1.63; 95% CI: 1.11-2.39), travelling to Africa (OR: 3.03; 95% CI: 1.23-7.46) or Asia (OR: 2.00; 95% CI: 1.02-3.90) < 12 months ago, and not changing kitchen towels daily (OR: 2.19; 95% CI: 1.24-3.87). The last had the largest population attributable risk (PAR) (47.5%). Eighty-four of 189 (44.4%) ESBL-E isolates carried bla CTX-M-15. Escherichia coli isolates belonged to 70 different sequence types (ST)s, of which ST131 (42/178 isolates; 23.6%) was most prevalent. Associations were observed between IncFIA plasmids and ST131 and bla CTX-M-27, and between IncI1 and ST88 and bla CTX-M-1. No CPE were detected.ConclusionsThe prevalence of ESBL-E carriage in the Netherlands' community-dwelling population is 5.0%. Identified risk factors were mostly travelling (particularly to Asia and Africa) and kitchen hygiene. CPE were not detected.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli to identify potential sources of colonization in commercial turkey farms.

Poultry are the main reservoir for thermophilic Campylobacter spp., which is the most common causative agent of human bacterial gastroenteritis. The epidemiology of Campylobacter in poultry, particularly in turkeys, is not completely understood. This study aimed at identifying potential sources and transmission routes of thermophilic Campylobacter spp. in commercial turkey farms. C. jejuni and C. coli isolates from breeders (n = 29, 20 C. jejuni and 9 C. coli) and their progeny (n = 51, 18 C. jejuni and 33 C. coli) reared in two different farms for three sequential production cycles were analysed by multilocus sequence typing (MLST). Strains (n = 88, 42 C. jejuni and 46 C. coli) isolated from environmental (i.e. anteroom and in-house overshoes), water (i.e. drinkers and water line), and pest (i.e. flies, Alphitobius diaperinus, and mice) sources were also examined. MLST of C. jejuni and C. coli isolates resulted in 13 and 12 different sequence types (STs) belonging to six and one previously-described clonal complexes (CCs), respectively. Three novel STs were identified. Genetic similarities were detected between isolates from fattening turkeys and the considered environmental, water, and pest sources, and with the breeders to a lesser extent. Source attribution analysis estimated that environmental and water sources accounted for most (∼75%) of fattening turkey isolates and were therefore identified as the most likely sources of flock colonization, followed by pests (∼20%) and breeders (∼5%). These sources may thus be targeted by control measures to mitigate the risk of Campylobacter colonization in commercial turkeys. RESEARCH HIGHLIGHTS High occurrence of C. jejuni and C. coli in commercial turkey flocks. High genetic diversity of C. jejuni and C. coli in commercial turkey flocks. Horizontal transmission responsible for Campylobacter colonization of commercial turkey flocks. Environmental and water sources involved in Campylobacter colonization of commercial turkey flocks. Strategies for prevention and control of Campylobacter colonization of commercial turkey flocks are needed.

New paradigms for Salmonella source attribution based on microbial subtyping.

Microbial subtyping is the most common approach for Salmonella source attribution. Typically, attributions are computed using frequency-matching models like the Dutch and Danish models based on phenotyping data (serotyping, phage-typing, and antimicrobial resistance profiling). Herewith, we critically review three major paradigms facing Salmonella source attribution today: (i) the use of genotyping data, particularly Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA), which is replacing traditional Salmonella phenotyping beyond serotyping; (ii) the integration of case-control data into source attribution to improve risk factor identification/characterization; (iii) the investigation of non-food sources, as attributions tend to focus on foods of animal origin only. Population genetics models or simplified MLVA schemes may provide feasible options for source attribution, although there is a strong need to explore novel modelling options as we move towards whole-genome sequencing as the standard. Classical case-control studies are enhanced by incorporating source attribution results, as individuals acquiring salmonellosis from different sources have different associated risk factors. Thus, the more such analyses are performed the better Salmonella epidemiology will be understood. Reparametrizing current models allows for inclusion of sources like reptiles, the study of which improves our understanding of Salmonella epidemiology beyond food to tackle the pathogen in a more holistic way.

Outbreak of Salmonella Bovismorbificans associated with the consumption of uncooked ham products, the Netherlands, 2016 to 2017.

In January 2017, an increase in reported Salmonellaenterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54 S. Bovismorbificans cases were identified. Sequencing indicated that all were infected with identical strains. Twenty-four cases and 37 controls participated in the study. Cases were more likely to have consumed ham products than controls (aOR = 13; 95% CI: 2.0-77) and to have shopped at a supermarket chain (aOR = 7; 95% CI: 1.3-38). Trace-back investigations led to a Belgian meat processor: one retail ham sample originating from this processor tested positive for S. Bovismorbificans and matched the outbreak strain by WGS. All ham products related to the same batch were removed from the market to prevent further cases. This investigation illustrates the importance of laboratory surveillance for all Salmonella serotypes and the usefulness of WGS in an outbreak investigation.