#Risk of #pneumonia among #residents living near #goat and #poultry #farms during 2014-2016 (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]


Risk of pneumonia among residents living near goat and poultry farms during 2014-2016

Pim M. Post , Lenny Hogerwerf, Anke Huss, Ronald Petie, Gert Jan Boender, Christos Baliatsas, Erik Lebret, Dick Heederik, Thomas J. Hagenaars, C. Joris IJzermans, Lidwien A. M. Smit

Published: October 14, 2019 / DOI: https://doi.org/10.1371/journal.pone.0223601



In the Netherlands, an association was found between the prevalence of pneumonia and living near goat and poultry farms in 2007–2013. This association then led to regulatory decisions to restrict the building of new goat farms and to reduce emissions of poultry farms. Confirmation of these results, however, is required because the period of previous analyses overlapped a Q-fever epidemic in 2007–2010. To confirm the association, we performed a population-based study during 2014–2016 based on general practitioner (GP) data. Electronic medical records of 90,183 persons were used to analyze the association between pneumonia and the population living in the proximity (within 500–2000 m distance) of goat and poultry farms. Data were analyzed with three types of logistic regression (with and without GP practice as a random intercept and with stratified analyses per GP practice) and a kernel model to discern the influence of different statistical methods on the outcomes. In all regression analyses involving adults, a statistically significant association between pneumonia and residence within 500 meters of goat farms was found (odds ratio [OR] range over all analyses types: 1.33–1.60), with a decreasing OR for increasing distances. In kernel analyses (including all ages), a population-attributable risk between 6.0 and 7.8% was found for a distance of 2000 meters in 2014–2016. The associations were consistent across all years and robust for mutual adjustment for proximity to other animals and for several other sensitivity analyses. However, associations with proximity to poultry farms are not supported by the present study. As the causes of the elevated pneumonia incidence in persons living close to goat farms remain unknown, further research into potential mechanisms is required for adequate prevention.


Citation: Post PM, Hogerwerf L, Huss A, Petie R, Boender GJ, Baliatsas C, et al. (2019) Risk of pneumonia among residents living near goat and poultry farms during 2014-2016. PLoS ONE 14(10): e0223601. https://doi.org/10.1371/journal.pone.0223601

Editor: Eric HY Lau, The University of Hong Kong, CHINA

Received: May 22, 2019; Accepted: September 24, 2019; Published: October 14, 2019

Copyright: © 2019 Post et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: In consultation with the Medical Ethical Committee of the University Medical Centre of Utrecht that approved the study protocol (number 13/533), data are not publicly available due to privacy protection of participants. Sharing an anonymized and de-identified dataset is not possible as it would still contain Electronic Health Records and address data of GP patients, which could potentially lead to the identification of subjects. The data for this study are derived from the NIVEL Primary Care Database. More information about the NIVEL Primary Care Database can be found at https://www.nivel.nl/en/nivel-primary-care-database. Requests for data can be sent to zorgregistraties@nivel.nl. Because of the granularity of the data and the requirements for data protection according to the Dutch Data Protection Act and the General Data Protection Regulation, access to the data is limited. The governance structure (data access committee) of the NIVEL Primary Care Database assesses data requests on data protection, scientific soundness of the request and public interest. Part of the governance structure is the privacy committee of the NIVEL Primary Care Database. For questions on data access, R. Coppen, member of this privacy committee and Data Protection Officer of NIVEL, may be contacted. He is registered as Data Protection Officer at the Dutch Data Protection Authority, see https://autoriteitpersoonsgegevens.nl/nl/onderwerpen/algemene-informatie-avg/functionaris-gegevensbescherming-fg

Funding: The work in this paper was commissioned to the Netherlands Institute for Health Services Research (NIVEL), in collaboration with the Institute for Risk Assessment Sciences (IRAS), Utrecht University, and Wageningen University and Research, The Netherlands. It was funded by the Ministry of Health, Welfare and Sport and the Ministry of Agriculture, Nature and Food Quality of The Netherlands [through grant number BO-43-013.01-007]. PMP analyzed the data as part of his PhD-project, which is supervised by Lenny Hogerwerf and funded by the Strategic Programme (SPR) of the National Institute for Public Health and the Environment (RIVM), The Netherlands. The funding sources had no role in the study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Goat; Poultry; Pneumonia; Human; Netherlands.



#Sequence-based #epidemiology of an #OXA-48 #plasmid during a #hospital #outbreak (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak

Laura Hidalgo, Mark de Been, Malbert R.C. Rogers, Anita C. Schürch, Jelle Scharringa, Anneke van der Zee, Marc J.M. Bonten, Ad C. Fluit

DOI: 10.1128/AAC.01204-19




A large OXA-48 outbreak in the Netherlands involved the spread of OXA-48producing Enterobacteriaceae among at least 118 patients, suggesting horizontal transfer of this resistance gene through one or more plasmids. Elucidating transmission dynamics of resistance plasmids is hampered by the low resolution of classic typing methods. This study aimed to investigate the molecular epidemiology of plasmids carrying OXA-48 carbapenemase using a next-generation sequencing approach.


A total of 68 OXA-48-producing Enterobacteriaceae isolated from the hospital outbreak, as well as 22 non-outbreak related OXA-48-producing Enterobacteriaceae from the Netherlands, Libya and Turkey were selected. Plasmids were sequenced using the Illumina Miseq platform, and read sets were assembled and analysed.


In all plasmids blaOXA-48 was embedded in transposon Tn1999.2 and located on a ca. 62 kb IncL/M conjugative plasmid in 14 different species. There were a maximum of 2 SNPs (single nucleotide polymorphisms) between the core sequence alignment of all plasmids. Closely related sequence variants of this plasmid were detected in non-outbreak isolates from the Netherlands and other countries. Thirty-one of 89 OXA-48-producing isolates also harboured blaCTX-M-15, which was not located on the blaOXA-48-carrying plasmid. Sequencing of four plasmids harbouring blaCTX-M15 revealed extensive plasmid heterogeneity.


A ca. 62 kb plasmid was responsible for the OXA-48 outbreak in a Dutch hospital. Our findings provide strong evidence for both within-host inter-species and between host dissemination of plasmid-based OXA-48 during a nosocomial outbreak. These findings exemplify the complex epidemiology of carbapenemase producing Enterobacteriaceae (CPE).

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Enterobacteriaceae; Nosocomial Outbreaks; Netherlands.


#Quantification of visits of #wild #fauna to a commercial free-range layer #farm in the #Netherlands located in an #avian #influenza hot-spot area assessed by video-camera monitoring (Transbound Emerg Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Transbound Emerg Dis. 2019 Oct 6. doi: 10.1111/tbed.13382. [Epub ahead of print]

Quantification of visits of wild fauna to a commercial free-range layer farm in the Netherlands located in an avian influenza hot-spot area assessed by video-camera monitoring.

Elbers ARW1, Gonzales JL1.

Author information: 1 Dept. of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 3848 BW, Lelystad, Netherlands.



Free-range poultry farms have a high risk of introduction of avian influenza viruses (AIV), and it is presumed that wild (water)birds are the source of introduction. There is very scarce quantitative data on wild fauna visiting free-range poultry farms. We quantified visits of wild fauna to a free-range area of a layer farm, situated in an AIV hot-spot area, assessed by video-camera monitoring. A total of 5,016 hours (209 days) of video recordings, covering all 12 months of a year, were analyzed. A total of 16 families of wild birds and five families of mammals visited the free-range area of the layer farm. Wild birds, except for the dabbling ducks, visited the free-range area almost exclusively in the period between sunrise and the moment the chickens entered the free-range area. Known carriers of AIV visited the outdoor facility regularly: species of gulls almost daily in the period January – August; dabbling ducks only in the night in the period November – May, with a distinct peak in the period December – February. Only a small fraction of visits of wild fauna had overlap with presence of chickens at the same time in the free-range area. No direct contact between chickens and wild birds was observed. It is hypothesized that AIV transmission to poultry on free-range poultry farms will predominantly take place via indirect contact: taking up AIV by chickens via wild-bird-faeces-contaminated water or soil in the free-range area. The free-range poultry farmer has several possibilities to potentially lower the attractiveness of the free-range area for wild (bird)fauna: daily inspection of the free-range area and removal of carcasses and eggs; prevention of forming of water pools in the free range facility. Furthermore, there are ways to scare-off wild birds e.g. use of laser equipment or trained dogs.

© 2019 Blackwell Verlag GmbH.

KEYWORDS: avian influenza; ducks; free-range poultry; gulls; water pools; wild fauna

PMID: 31587498 DOI: 10.1111/tbed.13382

Keywords: Avian Influenza; Wild Birds; Poultry; Wildlife; Netherlands.


Circulation of low pathogenic #avian #influenza (#LPAI) viruses in #wildbirds and #poultry in the #Netherlands, 2006-2016 (Sci Rep., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Sci Rep. 2019 Sep 23;9(1):13681. doi: 10.1038/s41598-019-50170-8.

Circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands, 2006-2016.

Bergervoet SA1,2, Pritz-Verschuren SBE1, Gonzales JL3, Bossers A4, Poen MJ2, Dutta J5, Khan Z5, Kriti D5, van Bakel H5,6, Bouwstra R7, Fouchier RAM2, Beerens N8.

Author information: 1 Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. 2 Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands. 3 Department of Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. 4 Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. 5 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA. 6 Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA. 7 GD Animal Health Service, Deventer, The Netherlands. 8 Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. nancy.beerens@wur.nl.



In this study, we explore the circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands. Surveillance data collected between 2006 and 2016 was used to evaluate subtype diversity, spatiotemporal distribution and genetic relationships between wild bird and poultry viruses. We observed close species-dependent associations among hemagglutinin and neuraminidase subtypes. Not all subtypes detected in wild birds were found in poultry, suggesting transmission to poultry is selective and likely depends on viral factors that determine host range restriction. Subtypes commonly detected in poultry were in wild birds most frequently detected in mallards and geese. Different temporal patterns in virus prevalence were observed between wild bird species. Virus detections in domestic ducks coincided with the prevalence peak in wild ducks, whereas virus detections in other poultry types were made throughout the year. Genetic analysis of the surface genes demonstrated that most poultry viruses were related to locally circulating wild bird viruses, but no direct spatiotemporal link was observed. Results indicate prolonged undetected virus circulation and frequent reassortment events with local and newly introduced viruses within the wild bird population. Increased knowledge on LPAI virus circulation can be used to improve surveillance strategies.

PMID: 31548582 DOI: 10.1038/s41598-019-50170-8

Keywords: Avian Influenza; Reassortant strains; Poultry; Wild Birds; Netherlands.


#Enterovirus D68 #serosurvey: evidence for #endemic circulation in the #Netherlands, 2006 to 2016 (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

Enterovirus D68 serosurvey: evidence for endemic circulation in the Netherlands, 2006 to 2016

Eveliina Karelehto1, Gerrit Koen1, Kimberley Benschop2, Fiona van der Klis2, Dasja Pajkrt3, Katja Wolthers1

Affiliations: 1 Department of Medical Microbiology, Laboratory of Clinical Virology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands; 2 National Institute for Public Health and the Environment, Bilthoven, the Netherlands; 3 Department of Pediatric Infectious Diseases, Emma Children’s Hospital, University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands

Correspondence:  Katja C Wolthers

Citation style for this article: Karelehto Eveliina, Koen Gerrit, Benschop Kimberley, van der Klis Fiona, Pajkrt Dasja, Wolthers Katja. Enterovirus D68 serosurvey: evidence for endemic circulation in the Netherlands, 2006 to 2016. Euro Surveill. 2019;24(35):pii=1800671. https://doi.org/10.2807/1560-7917.ES.2019.24.35.1800671

Received: 12 Dec 2018;   Accepted: 05 Jun 2019




Enterovirus D68 (EV-D68) has caused major outbreaks of severe respiratory illness worldwide since 2010.


Our aim was to evaluate EV-D68 circulation in the Netherlands by conducting a serosurvey of EV-D68 neutralising antibodies (nAb) among the Dutch general population.


We screened 280 sera from children and adults in the Netherlands and used two independent sets of samples collected in the years 2006 and 2007 and in the years 2015 and 2016, time points before and after the first EV-D68 upsurge in 2010. Neutralisation capacity of the sera was tested against the prototype Fermon EV-D68 strain isolated in 1962 and against a recent EV-D68 strain (genotype B3) isolated in France in 2016.


Regardless of the time of serum collection, we found remarkably high overall seropositivity (94.3–98.3%) for nAb against both EV-D68 strains. Geometric mean titres increased in an age-dependent manner.


Our data suggest that EV-D68 has been circulating in the Netherlands for decades and that the enterovirus surveillance does not accurately capture the prevalence of this clinically relevant pathogen.

©  This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: Enterovirus; EV-D68; Pediatrics; Netherlands; Seroprevalence.


#Contact #precautions in single-bed or multiple-bed rooms for #patients with #ESBL-producing #Enterobacteriaceae in #Dutch #hospitals:… (Lancet Infect Dis., abstract)

[Source: The Lancet Infectious Diseases, full page: (LINK). Abstract, edited.]

Contact precautions in single-bed or multiple-bed rooms for patients with extended-spectrum β-lactamase-producing Enterobacteriaceae in Dutch hospitals: a cluster-randomised, crossover, non-inferiority study

Marjolein F Q Kluytmans-van den Bergh, PhD, Patricia C J Bruijning-Verhagen, PhD, Prof Christina M J E Vandenbroucke-Grauls, PhD, Els I G B de Brauwer, PhD, Anton G M Buiting, PhD, Bram M Diederen, PhD, Erika P M van Elzakker, MD, Prof Alex W Friedrich, PhD, Joost Hopman, MD, Nashwan al Naiemi, PhD, Prof John W A Rossen, PhD, Gijs J H M Ruijs, PhD, Prof Paul H M Savelkoul, PhD, Carlo Verhulst, BASc, Prof Margreet C Vos, PhD, Prof Andreas Voss, PhD, Prof Marc J M Bonten, PhD, Prof Jan A J W Kluytmans, PhD, on behalf of theSoM Study Group †

Published: August 23, 2019 / DOI: https://doi.org/10.1016/S1473-3099(19)30262-2




Use of single-bed rooms for control of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is under debate; the added value when applying contact precautions has not been shown. We aimed to assess whether an isolation strategy of contact precautions in a multiple-bed room was non-inferior to a strategy of contact precautions in a single-bed room for preventing transmission of ESBL-producing Enterobacteriaceae.


We did a cluster-randomised, crossover, non-inferiority study on medical and surgical wards of 16 Dutch hospitals. During two consecutive study periods, either contact precautions in a single-bed room or contact precautions in a multiple-bed room were applied as the preferred isolation strategy for patients with ESBL-producing Enterobacteriaceae cultured from a routine clinical sample (index patients). Eligible index patients were aged 18 years or older, had no strict indication for barrier precautions in a single-bed room, had a culture result reported within 7 days of culture and before discharge, and had no wardmate known to be colonised or infected with an ESBL-producing Enterobacteriaceae isolate of the same bacterial species with a similar antibiogram. Hospitals were randomly assigned in a 1:1 ratio by computer to one of two sequences of isolation strategies, stratified by university or non-university hospital. Allocation was masked for laboratory technicians who assessed the outcomes but not for patients, treating doctors, and infection-control practitioners enrolling index patients. The primary outcome was transmission of ESBL-producing Enterobacteriaceae to wardmates, which was defined as rectal carriage of an ESBL-producing Enterobacteriaceae isolate that was clonally related to the index patient’s isolate in at least one wardmate. The primary analysis was done in the per-protocol population, which included patients who were adherent to the assigned room type. A 10% non-inferiority margin for the risk difference was used to assess non-inferiority. This study is registered with Nederlands Trialregister, NTR2799.


16 hospitals were randomised, eight to each sequence of isolation strategies. All hospitals randomised to the sequence single-bed room then multiple-bed room and five of eight hospitals randomised to the sequence multiple-bed room then single-bed room completed both study periods and were analysed. From April 24, 2011, to Feb 27, 2014, 1652 index patients and 12 875 wardmates were assessed for eligibility. Of those, 693 index patients and 9527 wardmates were enrolled and 463 index patients and 7093 wardmates were included in the per-protocol population. Transmission of ESBL-producing Enterobacteriaceae to at least one wardmate was identified for 11 (4%) of 275 index patients during the single-bed room strategy period and for 14 (7%) of 188 index patients during the multiple-bed room strategy period (crude risk difference 3·4%, 90% CI −0·3 to 7·1).


For patients with ESBL-producing Enterobacteriaceae cultured from a routine clinical sample, an isolation strategy of contact precautions in a multiple-bed room was non-inferior to a strategy of contact precautions in a single-bed room for preventing transmission of ESBL-producing Enterobacteriaceae. Non-inferiority of the multiple-bed room strategy might change the current single-bed room preference for isolation of patients with ESBL-producing Enterobacteriaceae and, thus, broaden infection-control options for ESBL-producing Enterobacteriaceae in daily clinical practice.


Netherlands Organisation for Health Research and Development.

Keywords: Antibiotics; Drugs Resistance; Beta-lactams; Enterobacteriaceae; Nosocomial outbreaks; Netherlands.


Monitoring #antimicrobial #resistance #trends in commensal #Escherichia coli from #livestock, the #Netherlands, 1998 to 2016 (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

Monitoring antimicrobial resistance trends in commensal Escherichia coli from livestock, the Netherlands, 1998 to 2016

Ayla Hesp1,2, Kees Veldman1, Jeanet van der Goot1, Dik Mevius1,2, Gerdien van Schaik3,4

Affiliations: 1 Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; 2 Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands; 3 GD Animal Health, Deventer, the Netherlands; 4 Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands

Correspondence:  Ayla Hesp

Citation style for this article: Hesp Ayla, Veldman Kees, van der Goot Jeanet, Mevius Dik, van Schaik Gerdien. Monitoring antimicrobial resistance trends in commensal Escherichia coli from livestock, the Netherlands, 1998 to 2016. Euro Surveill. 2019;24(25):pii=1800438. https://doi.org/10.2807/1560-7917.ES.2019.24.25.1800438

Received: 07 Aug 2018;   Accepted: 23 Apr 2019




Monitoring of antimicrobial resistance (AMR) in animals is essential for public health surveillance. To enhance interpretation of monitoring data, evaluation and optimisation of AMR trend analysis is needed.


To quantify and evaluate trends in AMR in commensal Escherichia coli, using data from the Dutch national AMR monitoring programme in livestock (1998–2016).


Faecal samples were collected at slaughter from broilers, pigs and veal calves. Minimum inhibitory concentration values were obtained by broth microdilution for E. coli for 15 antimicrobials of eight antimicrobial classes. A Poisson regression model was applied to resistant isolate counts, with explanatory variables representing time before and after 2009 (reference year); for veal calves, sampling changed from 2012 represented by an extra explanatory variable.


Resistant counts increased significantly from 1998-2009 in broilers and pigs, except for tetracyclines and sulfamethoxazole in broilers and chloramphenicol and aminoglycosides in pigs. Since 2009, resistant counts decreased for all antimicrobials in broilers and for all but the phenicols in pigs. In veal calves, for most antimicrobials no significant decrease in resistant counts could be determined for 2009–16, except for sulfamethoxazole and nalidixic acid. Within animal species, antimicrobial-specific trends were similar.


Using Dutch monitoring data from 1998-2016, this study quantified AMR trends in broilers and slaughter pigs and showed significant trend changes in the reference year 2009. We showed that monitoring in commensal E. coli is useful to quantify trends and detect trend changes in AMR. This model is applicable to similar data from other European countries.

©  This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: Antibiotics; Drugs Resistance; E. Coli; Pigs; Poultry; Netherlands.