Unraveling the Modes of Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) During a Nursing Home Outbreak: Looking Beyond the Church Superspreading Event.

BACKGROUND: An outbreak of coronavirus disease 2019 (COVID-19) in a nursing home in the Netherlands, following an on-site church service held on 8 March 2020, triggered an investigation to unravel sources and chain(s) of transmission. METHODS: Epidemiological data were collected from registries and through a questionnaire among church attendees. Symptomatic residents and healthcare workers (HCWs) were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse-transcription polymerase chain reaction and subjected to whole genome sequencing (WGS). Sequences from a selection of people from the same area were included as community reference. RESULTS: After the church service, 30 of 39 attendees (77%) developed symptoms; 14 (11 residents and 3 nonresidents) were tested and were positive for COVID-19. In the following 5 weeks, 62 of 300 residents (21%) and 30 of 640 HCWs (5%) tested positive for COVID-19; 21 of 62 residents (34%) died. The outbreak was controlled through a cascade of measures. WGS of samples from residents and HCWs identified a diversity of sequence types, grouped into 8 clusters. Seven resident church attendees all were infected with distinct viruses, 4 of which belonged to 2 larger clusters in the nursing home. CONCLUSIONS: Although initial investigation suggested the church service as the source of the outbreak, detailed analysis showed a more complex picture, most consistent with widespread regional circulation of the virus in the weeks before the outbreak, and multiple introductions into the nursing home before the visitor ban. The findings underscore the importance of careful outbreak investigations to understand SARS-CoV-2 transmission to develop evidence-based mitigation measures.

Obtaining nasal and rectal swabs from general practice patients to assess carriage of antibiotic resistant microorganisms: a feasibility study.

PURPOSE: The aim of this study was to assess the feasibility of obtaining nasal and rectal swabs from general practice patients for measuring carriage of antibiotic resistant microorganisms in an area in Rotterdam (the Netherlands) with low socioeconomic status and a large immigrant population. METHODS: Data collection was from May to December 2017, in one general practice in Rotterdam. We asked adults (≥18 years) visiting the general practitioner (GP) with complaints not related to infections for one nasal and two rectal swabs and tested these for highly resistant microorganisms (HRMOs). Indicators for feasibility were recruitment rate, implementation and acceptation of data collection procedures by the participants. RESULTS: We obtained a nasal swab from all included 234 patients and 164 (70%) also gave rectal swabs. On average, 3 out of 30 invited patients (10%) were recruited per day. The GPs considered the workload high to inform and refer to eligible patients for the study and did this inconsistently. Most participants experienced the rectal swab procedure as burdensome and preferred assistance of a medical assistant above self-swabbing. A monetary incentive increased the willingness to provide rectal swabs. CONCLUSIONS: Obtaining (nasal and) rectal swabs from general practice patients for study purposes proved difficult. Lessons learnt from this feasibility study will help increase participation in HRMO prevalence studies among asymptomatic general practice patients.

Low antimicrobial resistance in general practice patients in Rotterdam, the city with the largest proportion of immigrants in the Netherlands.

Antimicrobial resistance (AMR) is an increasing problem. The prevalence of antimicrobial resistance in general practice patients is expected to be relatively high in Rotterdam, the Dutch city with the largest proportion non-Western immigrants. The aim of this study was to assess the prevalence of antibiotic-resistant uropathogens (Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis) in general practices in Rotterdam, and to find a possible association between the prevalence of antibiotic-resistant E. coli and age, gender, and socioeconomic status (SES). A retrospective analysis was performed of urine samples from general practice patients in 2016. The prevalence of AMR in uropathogens was compared with national resistance data, as was the prevalence of highly and multidrug resistant and extended spectrum ß-lactamase (ESBL) producing E. coli and K. pneumoniae. Univariate logistic regression was used to study associations between antibiotic-resistant E. coli and age, gender, and SES area score. No clinically relevant differences were observed in the prevalence of antibiotic-resistant uropathogens in Rotterdam compared with the national prevalence. For E. coli and K. pneumoniae, the prevalence was 3.6% for ESBL production (both pathogens together), while the prevalence ranged between 4.2%-5.0% for high resistance and between 1.2%-3.3% for multidrug resistance. Ciprofloxacin-resistant E. coli was significantly associated with higher age. Although Rotterdam has a high percentage of non-western immigrants and a low SES, AMR is low among general practice patients. This indicates that adherence to national guidelines in general practice enables maintenance of low AMR, even in high-risk populations.

Distribution of serotypes and patterns of antimicrobial resistance among commensal Streptococcus pneumoniae in nine European countries.

BACKGROUND: Streptococcus pneumoniae is a commensal of the human upper respiratory tract and a major cause of morbidity and mortality worldwide. This paper presents the distribution of serotypes and antimicrobial resistance in commensal S. pneumoniae strains cultured from healthy carriers older than four years of age in nine European countries. METHODS: Nasal swabs from healthy persons (age between 4 and 107 years old) were obtained by general practitioners from each country from November 2010 to August 2011. Swabs were cultured for S. pneumoniae using a standardized protocol. Antibiotic resistance was determined for isolated S. pneumoniae by broth microdilution. Capsular sequencing typing was used to identify serotypes, followed by serotype-specific PCR assays in case of ambiguous results. RESULTS: Thirty-two thousand one hundred sixty-one nasal swabs were collected from which 937 S. pneumoniae were isolated. A large variation in serotype distribution and antimicrobial resistant serotypes across the participating countries was observed. Pneumococcal vaccination was associated with a higher risk of pneumococcal colonization and antimicrobial resistance independently of country and vaccine used, either conjugate vaccine or PPV 23). CONCLUSIONS: Serotype 11A was the most common in carriage followed by serotypes 23A and 19A. The serotypes showing the highest resistance to penicillin were 14 followed by 19A. Serotype 15A showed the highest proportion of multidrug resistance.

Surveillance of antimicrobial use in Dutch long-term care facilities.

Objectives: : Residents living in a long-term care facility (LTCF) are more susceptible to infections. Treatment with antimicrobials is sometimes necessary; however, antibiotic use is considered one of the most important drivers of the development of antibiotic resistance. Surveillance data on antibiotic use in these LTCFs are necessary to get more insight into these patterns. The objective of this study was to describe antibiotic use in LTCFs in the Netherlands. Methods: : One hundred and seventy-seven LTCFs in the Netherlands were contacted and asked to participate in a study concerning antibiotic resistance and antibiotic use. Associated pharmacies were asked to provide data about systemic antibiotic use for each participating LTCF location over 1 year. Results on antibiotic use are reported here. Results: : Antibiotic use data from 96 LTCFs were collected from the pharmacies, and 68 of these LTCFs completed additional questionnaires on general characteristics of their location. Mean total use of systemic antimicrobials was 73 DDDs/1000 residents per day (range 2-197 DDDs/1000 residents per day). Co-amoxiclav (23 DDDs/1000 residents/day, range 0-70) was used the most, followed by nitrofurantoin derivatives (12 DDDs/1000 residents/day, range 0-38) and fluoroquinolones (12 DDDs/1000 residents/day, range 0-52). Statistical analysis revealed no significant correlations between the LTCF characteristics and the level of antibiotic use. Conclusions: There was a high use of broad-spectrum antimicrobials, with a large variation in total antibiotic use between individual locations. Further analysis of more in-depth data and possible influencing factors is needed.

Carriage of antimicrobial-resistant commensal bacteria in Dutch long-term-care facilities.

OBJECTIVES: The objective of this study was to assess carriage of antimicrobial-resistant commensal microorganisms, i.e. Escherichia coli and Staphylococcus aureus, and its predictors in long-term-care facilities (LTCFs). METHODS: Nasal swabs and/or urine or incontinence samples were collected from participating residents in 111 LTCFs and tested for the presence of S. aureus and/or E. coli, respectively. Antimicrobial resistance to eight antimicrobials was linked to antimicrobial usage in the year preceding sampling and to LTCF characteristics. Using multilevel logistic regression, predictors of carriage of ESBL-producing E. coli in LTCFs were identified. RESULTS: S. aureus was identified in 1269/4763 (26.6%) nasal swabs, including 13/4763 (0.3%) MRSA carriers in 9/107 (8%) LTCFs. Of the 5359 urine/incontinence samples, 2934 (55%) yielded E. coli, including 123 (4.2%) producing ESBL, which were found in 53/107 locations (range 1%-33%). For all but one antimicrobial (i.e. nitrofurantoin) >20% of isolated E. coli were resistant. Multilevel multivariable logistic regression identified two predictors of carriage of ESBL-producing E. coli: (i) antimicrobial usage (OR 1.8, 95% CI 1.1-3.0 for each extra 50 DDD/1000 residents/day); and (ii) presence of MRSA carriers in the LTCFs (OR 2.4, 95% CI 1.0-5.6). CONCLUSIONS: The low proportion of 4.2% ESBL-producing E. coli and the low prevalence of 0.3% MRSA carriage found in LTCF residents suggest that Dutch LTCFs are not yet an important reservoir of MDR potential pathogens. Nevertheless, the large variation between LTCFs warrants close monitoring of antimicrobial resistance in LTCFs. Integrated surveillance, i.e. linking data sources on antimicrobial usage, microbiological testing, clinical background data and epidemiological data, is needed.

Detection of the plasmid-mediated colistin-resistance gene mcr-1 in faecal metagenomes of Dutch travellers.

BACKGROUND: Recently, the first plasmid-mediated colistin-resistance gene, mcr-1, was reported. Colistin is increasingly used as an antibiotic of last resort for the treatment of infections caused by carbapenem-resistant bacteria, which have been rapidly disseminating worldwide in recent years. OBJECTIVES: The reported carriage rate of mcr-1 in humans remains sporadic thus far, except for those reported in Chinese populations. We aimed to determine its presence in the faecal metagenomes of healthy Dutch travellers between 2010 and 2012. METHODS: Faecal metagenomic DNA of pre- and post-travel samples from 122 healthy Dutch long-distance travellers was screened for the presence of mcr-1 using a TaqMan quantitative PCR assay, which was designed in this study. All positive samples were confirmed by sequencing of the amplicons. RESULTS: The mcr-1 gene was detected in 6 (4.9%, 95% CI = 2.1%-10.5%) of 122 healthy Dutch long-distance travellers after they had visited destinations in South(-east) Asia or southern Africa between 2011 and 2012. One of these participants was already found to be positive before travel. CONCLUSIONS: Our study highlights the potential of PCR-based targeted metagenomics as an unbiased and sensitive method to screen for the carriage of the mcr-1 gene and suggests that mcr-1 is widespread in various parts of the world. The observation that one participant was found to be positive before travel suggests that mcr-1 may already have disseminated to the microbiomes of Dutch residents at a low prevalence, warranting a more extensive investigation of its prevalence in the general population and possible sources.

Prevalence of chronic wounds and structural quality indicators of chronic wound care in Dutch nursing homes.

The aim of this study was to measure the prevalence of (infected) chronic wounds in Dutch nursing homes and to explore which signs and symptoms are used to diagnose infected chronic wounds. Moreover, it was to determine which structural quality indicators related to chronic wound care at ward and institutional levels were fulfilled. In April 2012, as part of the annual National Prevalence Measurement of Care Problems of Maastricht University [Landelijke Prevalentiemeting Zorgproblemen (LPZ)], a multi-center cross-sectional point-prevalence measurement was carried out together with an assessment of relevant care quality indicators. The prevalence was 4·2%; 16 of 72 (22%) chronic wounds were considered to be infected. Increase of exudate (81·3%; n = 13), erythema (68·8%; n = 11), pain (56·3%; n = 9) and wound recalcitrance (56·3%; n = 9) were considered to be diagnostic signs and symptoms of a chronic wound infection. Although at institutional level most quality indicators were fulfilled, at ward level this was not the case. Despite the relatively low number of residents, we consider our population as representative for the nursing home population. It may be an advantage to appoint specific ward nurses and to provide them specifically with knowledge and skills concerning chronic wounds.

High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands.

We investigated the effect of international travel on the gut resistome of 122 healthy travelers from the Netherlands by using a targeted metagenomic approach. Our results confirm high acquisition rates of the extended-spectrum ß-lactamase encoding gene blaCTX-M, documenting a rise in prevalence from 9.0% before travel to 33.6% after travel (p<0.001). The prevalence of quinolone resistance encoding genes qnrB and qnrS increased from 6.6% and 8.2% before travel to 36.9% and 55.7% after travel, respectively (both p<0.001). Travel to Southeast Asia and the Indian subcontinent was associated with the highest acquisition rates of qnrS and both blaCTX-M and qnrS, respectively. Investigation of the associations between the acquisitions of the blaCTX-M and qnr genes showed that acquisition of a blaCTX-M gene was not associated with that of a qnrB (p = 0.305) or qnrS (p = 0.080) gene. These findings support the increasing evidence that travelers contribute to the spread of antimicrobial drug resistance.

A systematic review and meta-analysis of the effects of antibiotic consumption on antibiotic resistance.

BACKGROUND: Greater use of antibiotics during the past 50 years has exerted selective pressure on susceptible bacteria and may have favoured the survival of resistant strains. Existing information on antibiotic resistance patterns from pathogens circulating among community-based patients is substantially less than from hospitalized patients on whom guidelines are often based. We therefore chose to assess the relationship between the antibiotic resistance pattern of bacteria circulating in the community and the consumption of antibiotics in the community. METHODS: Both gray literature and published scientific literature in English and other European languages was examined. Multiple regression analysis was used to analyse whether studies found a positive relationship between antibiotic consumption and resistance. A subsequent meta-analysis and meta-regression was conducted for studies for which a common effect size measure (odds ratio) could be calculated. RESULTS: Electronic searches identified 974 studies but only 243 studies were considered eligible for inclusion by the two independent reviewers who extracted the data. A binomial test revealed a positive relationship between antibiotic consumption and resistance (p < .001) but multiple regression modelling did not produce any significant predictors of study outcome. The meta-analysis generated a significant pooled odds ratio of 2.3 (95% confidence interval 2.2 to 2.5) with a meta-regression producing several significant predictors (F(10,77) = 5.82, p < .01). Countries in southern Europe produced a stronger link between consumption and resistance than other regions. CONCLUSIONS: Using a large set of studies we found that antibiotic consumption is associated with the development of antibiotic resistance. A subsequent meta-analysis, with a subsample of the studies, generated several significant predictors. Countries in southern Europe produced a stronger link between consumption and resistance than other regions so efforts at reducing antibiotic consumption may need to be strengthened in this area. Increased consumption of antibiotics may not only produce greater resistance at the individual patient level but may also produce greater resistance at the community, country, and regional levels, which can harm individual patients.

The Carriage Of Multiresistant Bacteria After Travel (COMBAT) prospective cohort study: methodology and design.

BACKGROUND: Antimicrobial resistance (AMR) is one of the major threats to public health around the world. Besides the intense use and misuse of antimicrobial agents as the major force behind the increase in antimicrobial resistance, the exponential increase of international travel may also substantially contribute to the emergence and spread of AMR. However, knowledge on the extent to which international travel contributes to this is still limited. The Carriage Of Multiresistant Bacteria After Travel (COMBAT) study aims to 1. determine the acquisition rate of multiresistant Enterobacteriaceae during foreign travel 2. ascertain the duration of carriage of these micro-organisms 3. determine the transmission rate within households 4. identify risk factors for acquisition, persistence of carriage and transmission of multiresistant Enterobacteriaceae. METHODS/DESIGN: The COMBAT-study is a large-scale multicenter longitudinal cohort study among travellers (n = 2001) and their non-travelling household members (n = 215). Faecal samples are collected before and immediately after travel and 1 month after return from all participants. Follow-up faecal samples are collected 3, 6 and 12 months after return from travellers (and their non-travelling household members) who acquired multiresistant Enterobacteriaceae. Questionnaires are collected from all participants at each time-point. Faecal samples are screened phenotypically for the presence of extended-spectrum beta-lactamase (ESBL) or carbapenemase-producing Enterobacteriaceae. Positive post-travel isolates from travellers with negative pre-travel samples are genotypically analysed for ESBL and carbapenemase genes with microarray and gene sequencing. DISCUSSION: The design and scale of the COMBAT-study will enable us to provide much needed detailed insights into the risks and dynamics of introduction and spread of ESBL- and carbapenemase-producing Enterobacteriaceae by healthy travellers and the potential need and measures to monitor or manage these risks. TRIAL REGISTRATION: The study is registered at clinicaltrials.gov under accession number NCT01676974.

Primary care treatment guidelines for skin infections in Europe: congruence with antimicrobial resistance found in commensal Staphylococcus aureus in the community.

BACKGROUND: Over 90% of antibiotics for human use in Europe are prescribed in primary care. We assessed the congruence between primary care treatment guidelines for skin infections and commensal Staphylococcus aureus (S. aureus) antimicrobial resistance levels in community-dwelling persons. METHODS: The prevalence of antimicrobial resistance in S. aureus was analysed by taking nose swabs from healthy primary care patients in nine European countries (total N = 32,032). Primary care treatment guidelines for bacterial skin infections were interpreted with respect to these antimicrobial resistance patterns. First- and second-choice recommendations were assessed and considered congruent if resistance to the antibiotic did not exceed 20%. RESULTS: We included primary care treatment guidelines for impetigo, cellulitis, folliculitis and furuncle. Treatment recommendations in all countries were consistent: most of the first-choice recommendations were beta-lactams, both for children and adults. Antimicrobial resistance levels were low, except for penicillin (on average 73% resistance). Considerable variation in antimicrobial resistance levels was found between countries, with Sweden displaying the lowest levels and Spain the highest. In some countries resistance to penicillin and azithromycin was significantly higher in children (4-17 years) compared with adults. CONCLUSIONS: Most of the first- and second-choice recommendations in the treatment guidelines for skin infections were congruent with commensal S. aureus antimicrobial resistance patterns in the community, except for two recommendations for penicillin. Given the variation in antimicrobial resistance levels between countries, age groups and health care settings, national data regarding antimicrobial resistance in the community should be taken into account when updating or developing primary care treatment guidelines.

Establishment of the intestinal microbiota and its role for atopic dermatitis in early childhood.

BACKGROUND: Perturbations in the intestinal microbiota may disrupt mechanisms involved in the development of immunologic tolerance. The present study aimed to examine the establishment of the infant microbiota and its association to the development of atopic dermatitis (AD). METHODS: Within a randomized, placebo-controlled trial on the prevention of AD by oral supplementation of a bacterial lysate between week 5 and the end of month 7, feces was collected at the ages of 5 weeks (n = 571), 13 weeks (n = 332), and 31 weeks (n = 499) and subjected to quantitative PCRs to detect bifidobacteria, bacteroides, lactobacilli, Escherichia coli, Clostridium difficile, and Clostridium cluster I. RESULTS: Birth mode, breast-feeding but also birth order had a strong effect on the microbiota composition. With increasing number of older siblings the colonization rates at age 5 weeks of lactobacilli (P < .001) and bacteroides (P = .02) increased, whereas rates of clostridia decreased (P < .001). Colonization with clostridia, at the age of 5 and 13 weeks was also associated with an increased risk of developing AD in the subsequent 6 months of life (odds ratioadjusted = 2.35; 95% CI, 1.36-3.94 and 2.51; 1.30-4.86, respectively). Mediation analyses demonstrated that there was a statistically significant indirect effect via Clostridium cluster I colonization for both birth mode and birth order in association to AD. CONCLUSION: The results of this study are supportive for a role of the microbiota in the development of AD. Moreover, the "beneficial" influence of older siblings on the microbiota composition suggests that this microbiota may be one of the biological mechanisms underlying the sibling effect.

Volatile organic compounds in headspace characterize isolated bacterial strains independent of growth medium or antibiotic sensitivity.

INTRODUCTION: Early and reliable determination of bacterial strain specificity and antibiotic resistance is critical to improve sepsis treatment. Previous research demonstrated the potential of headspace analysis of volatile organic compounds (VOCs) to differentiate between various microorganisms associated with pulmonary infections in vitro. This study evaluates whether VOC analysis can also discriminate antibiotic sensitive from resistant bacterial strains when cultured on varying growth media. METHODS: Both antibiotic-sensitive and -resistant strains of Pseudomonas aeruginosa, Staphylococcus aureus and Klebsiella pneumonia were cultured on 4 different growth media, i.e. Brain Heart Infusion, Marine Broth, Müller-Hinton and Trypticase Soy Agar. After overnight incubation at 37°C, the headspace air of the cultures was collected on stainless steel desorption tubes and analyzed by gas chromatography time-of-flight mass spectrometry (GC-tof-MS). Statistical analysis was performed using regularized multivariate analysis of variance and cross validation. RESULTS: The three bacterial species could be correctly recognized based on the differential presence of 14 VOCs (p<0.001). This discrimination was not influenced by the different growth media. Interestingly, a clear discrimination could be made between the antibiotic-resistant and -sensitive variant of Pseudomonas aeruginosa (p<0.001) based on their species-specific VOC signature. CONCLUSION: This study demonstrates that isolated microorganisms, including antibiotic-sensitive and -resistant strains of Pseudomonas aeruginosa, could be identified based on their excreted VOCs independent of the applied growth media. These findings suggest that the discriminating volatiles are associated with the microorganisms themselves rather than with their growth medium. This study exemplifies the potential of VOC analysis as diagnostic tool in medical microbiology. However, validation of our results in appropriate in vivo models is critical to improve translation of breath analysis to clinical applications.

Antimicrobial resistance among respiratory Haemophilus influenzae isolates from pulmonology services over a six-year period.

BACKGROUND: Respiratory tract infections (RTI) are frequently caused by Haemophilus influenzae. Widespread antibacterial resistance among respiratory microorganisms complicates empirical RTI treatment. Therefore, national data on antibiotic resistance for H. influenzae are important for guiding optimal antibiotic choice. METHODS: The antibiotic susceptibility of H. influenzae strains isolated from respiratory specimens of patients admitted to the pulmonology services between 2005 and 2010 was assessed. Isolates were collected annually from 13 hospitals in the Netherlands as part of the national intramural antimicrobial resistance surveillance performed by the Dutch Working Group on Antibiotic Policy (SWAB). Breakpoints for resistance were in accordance with the criteria of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Trend analysis was performed using logistic regression analysis. RESULTS: In total, 1606 H. influenzae strains were analyzed. The prevalence of antibiotic resistance to amoxicillin, co-amoxiclav, doxycycline, co-trimoxazole, and clarithromycin was stable over the 6-y period, and there was a trend towards a decrease in the prevalence of beta-lactamase-producing isolates. Regarding prevalences, no significant trends were observed. CONCLUSIONS: Our study showed no significant changes in antibiotic resistance for H. influenzae isolated at different hospitals in the Netherlands over a 6-y period. Regular surveillance remains important in controlling the prevalence of resistance, since actual resistance data should be taken into account when the choice of an empiric antibiotic is made.

Swab versus biopsy for the diagnosis of chronic infected wounds.

OBJECTIVE: The goal of this review was to investigate the usefulness of a wound swab (using the Levine or Z technique) in comparison with a biopsy as a reliable method for the diagnosis of a chronic wound infection. METHOD: A literature review using the electronic databases PubMed, CINAHL, and MEDLINE were searched by strategy. A total of 6 articles fulfilled the inclusion criteria. MAIN RESULTS: The Levine technique detects more organisms in acute wounds, as well as in chronic wounds, than the Z technique. Comparing both with the biopsy as criterion standard, the diagnostic accuracy to diagnose a chronic wound infection by the Levine technique was higher in comparison to the Z technique. At a threshold of 3.7 × 10(4) microorganisms per swab, the Levine technique had a sensitivity of 0.90, a specificity of 57%, and a positive predictive value and negative predictive value of 0.77 and 0.91, respectively. Description of the method of swab taking was diverse and not uniform. DISCUSSION: Only a few studies in the literature compare wound swabs with biopsies for the diagnosis of chronic infected wounds. Until now, the Levine technique has been considered as the most reliable and valid method, but there is an urgent need for a well-designed study with a sufficient number of patients to optimize the diagnostic accuracy of chronic infected wounds. CONCLUSION: The best sampling technique for taking a swab has not yet been identified and validated. Until then, the authors recommend the Levine technique.

Molecular characterisation of methicillin-susceptible and methicillin-resistant Staphylococcus aureus in inpatients and outpatients in Bosnia and Herzegovina.

The aim of this study was to investigate the genetic background of methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) obtained from clinical specimens of inpatients and outpatients. Methicillin resistance was confirmed by the presence of the mecA gene by PCR. The genetic characterisation was performed using spa typing and the algorithm based upon repeat pattern (BURP). Staphylococcus aureus was isolated from 68 and 79 inpatient and outpatient samples, 31 (46 %) and 14 (18 %) of which were MRSA, respectively. Among 37 inpatients and 65 outpatients with MSSA, 22 and 38 spa types were clustered into seven and eight spa-CCs, respectively. The main MSSA spa-CC of inpatients and outpatients was spa-CC015 (multilocus sequence typing (MLST) CC45). Most MRSA were associated with spa-CC355/595 (MLST CC152). MRSA-related background was found in 32 % of inpatients and 43 % of outpatients with MSSA, suggesting that MRSA did not arise from predominant MSSA clones.

Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy.

BACKGROUND: Both gastrointestinal microbiota composition and cesarean section have been linked to atopic manifestations. However, results are inconsistent, and the hypothesized intermediate role of the microbiota in the association between birth mode and atopic manifestations has not been studied yet. OBJECTIVES: We sought to investigate the relationship between microbiota composition, mode and place of delivery, and atopic manifestations. METHODS: The Child, Parent and Health: Lifestyle and Genetic Constitution Birth Cohort Study included data on birth characteristics, lifestyle factors, and atopic manifestations collected through repeated questionnaires from birth until age 7 years. Fecal samples were collected at age 1 month (n = 1176) to determine microbiota composition, and blood samples were collected at ages 1 (n = 921), 2 (n = 822), and 6 to 7 (n = 384) years to determine specific IgE levels. RESULTS: Colonization by Clostridium difficile at age 1 month was associated with wheeze and eczema throughout the first 6 to 7 years of life and with asthma at age 6 to 7 years. Vaginal home delivery compared with vaginal hospital delivery was associated with a decreased risk of eczema, sensitization to food allergens, and asthma. After stratification for parental history of atopy, the decreased risk of sensitization to food allergens (adjusted odds ratio, 0.52; 95% CI, 0.35-0.77) and asthma (adjusted odds ratio, 0.47; 95% CI, 0.29-0.77) among vaginally home-born infants was only found for children with atopic parents. Mediation analysis showed that the effects of mode and place of delivery on atopic outcomes were mediated by C difficile colonization. CONCLUSION: Mode and place of delivery affect the gastrointestinal microbiota composition, which subsequently influences the risk of atopic manifestations.

The appropriateness of prescribing antibiotics in the community in Europe: study design.

BACKGROUND: Over 90% of all antibiotics in Europe are prescribed in primary care. It is important that antibiotics are prescribed that are likely to be effective; however, information about antibiotic resistance in the community is incomplete. The aim of our study is to investigate the appropriateness of antibiotic prescribing in primary care in Europe by collecting and combining patterns of antibiotic resistance patterns and antibiotic prescription patterns in primary care. We will also evaluate the appropriateness of national antibiotic prescription guidelines in relation to resistance patterns. METHODS/DESIGN: Antibiotic resistance will be studied in an opportunistic sample from the community in nine European countries. Resistance data will be collected by taking a nose swab of persons (N = 4,000 per country) visiting a primary care practice for a non-infectious disease. Staphylococcus aureus and Streptococcus pneumoniae will be isolated and tested for resistance to a range of antibiotics in one central laboratory. Data on antibiotic prescriptions over the past 5 years will be extracted from the electronic medical records of General Practitioners (GPs). The results of the study will include the prevalence and resistance data of the two species and 5 years of antibiotic prescription data in nine European countries. The odds of receiving an effective antibiotic in each country will be calculated as a measure for the appropriateness of prescribing. Multilevel analysis will be used to assess the appropriateness of prescribing. Relevant treatment guidelines of the nine participating countries will be evaluated using a standardized instrument and related to the resistance patterns in that country. DISCUSSION: This study will provide valuable and unique data concerning resistance patterns and prescription behaviour in primary care in nine European countries. It will provide evidence-based recommendations for antibiotic treatment guidelines that take resistance patterns into account which will be useful for both clinicians and policy makers. By improving antibiotic use we can move towards controlling the resistance problem globally.

Host-microbial interactions in childhood atopy: toll-like receptor 4 (TLR4), CD14, and fecal Escherichia coli.

BACKGROUND: Perturbations in the gut microbiota have been linked to atopic diseases. However, the development of atopic diseases depends not only on environmental factors (like microbial stimulation) but also on genetic factors. It is likely that particularly gene-environmental interactions in early life determine the development of atopy. OBJECTIVE: We examine the interaction between detection of fecal Escherichia coli and genetic variations in the CD14 and Toll-like receptor 4 (TLR4) genes in relation to atopic manifestations. METHODS: Within the Child, Parent and Health: Lifestyle and Genetic Constitution (KOALA) Birth Cohort Study, fecal samples of 957 one-month-old infants were collected and quantitatively screened for E coli. Fourteen haplotype-tagging polymorphisms in the genes TLR4 and CD14 were genotyped in 681 of the 957 children. Atopic outcomes were parentally reported eczema in the first 2 years of life and clinically diagnosed eczema and allergic sensitization at age 2 years. Multiple logistic regression was used to evaluate a multiplicative model of interaction. RESULTS: Most of the single nucleotide polymorphisms (SNPs) showed no significant interaction with E coli exposure for both eczema and allergic sensitization. A borderline significant multiplicative interaction was found between E coli and the rs2569190 (CD14/-159) SNP regarding allergic sensitization. Furthermore, a statistically significant multiplicative interaction was found for the TLR4 SNP rs10759932 (P for interaction = .001). E coli colonization was associated with a decreased risk of sensitization only in children with the rs10759932 TT genotype (adjusted odds ratio, 0.31; 95% CI, 0.14-0.68) and not in children with the minor C allele. This interaction remained statistically significant after controlling for multiple testing. CONCLUSION: The current study is the first to address the potential effect-modifying role of genetic variations in the relationship between the intestinal microbiota and allergy development.