Search

Assessment of vancomycin-resistant Enterococcus faecium (VREfm) prevalence upon hospital admission and analysis of risk factors for colonization.From 2014 to 2018, patients were recruited within 72 hours of admission to seven participating German university hospitals, screened for VREfm and questioned for potential risk factors (prior multidrug-resistant organism detection, current/prior antibiotic consumption, prior hospital, rehabilitation or long-term care facility stay, international travel, animal contact and proton pump inhibitor [PPI]/antacid therapy). Genotype analysis was done using cgMLST typing. Multivariable analysis was performed.In 5 years, 265 of 17,349 included patients were colonized with VREfm (a prevalence of 1.5%). Risk factors for VREfm colonization were age (adjusted OR [aOR], 1.02; 95% CI, 1.01-1.03), previous (aOR, 2.71; 95% CI, 1.87-3.92) or current (aOR, 2.91; 95% CI, 2.60-3.24) antibiotic treatment, prior multidrug-resistant organism detection (aOR, 2.83; 95% CI, 2.21-3.63), prior stay in a long-term care facility (aOR, 2.19; 95% CI, 1.62-2.97), prior stay in a hospital (aOR, 2.91; 95% CI, 2.05-4.13) and prior consumption of PPI/antacids (aOR, 1.29; 95% CI, 1.18-1.41). Overall, the VREfm admission prevalence increased by 33% each year and 2% each year of life. 250 of 265 isolates were genotyped and 141 (53.2%) of the VREfm were the emerging ST117. Multivariable analysis showed that ST117 and non-ST117 VREfm colonized patients differed with respect to admission year and prior multidrug-resistant organism detection.Age, healthcare contacts and antibiotic and PPI/antacid consumption increase the individual risk of VREfm colonization. The VREfm admission prevalence increase in Germany is mainly driven by the emergence of ST117.

Objectives: The aim of this study was to quantify the time delay between screening and initiation of contact isolation for carriers of extended-spectrum beta-lactamase (ESBL)–producing Enterobacterales (ESBL-E). Methods: This study was a secondary analysis of contact isolation periods in a cluster-randomized controlled trial that compared 2 strategies to control ESBL-E (trial no. ISRCTN57648070). Patients admitted to 20 non-ICU wards in Germany, the Netherlands, Spain, and Switzerland were screened for ESBL-E carriage on admission, weekly thereafter, and on discharge. Data collection included the day of sampling, the day the wards were notified of the result, and subsequent ESBL-E isolation days. Results: Between January 2014 and August 2016, 19,122 patients, with a length of stay ≥2 days were included. At least 1 culture was collected for 16,091 patients (84%), with a median duration between the admission day and the day of first sample collection of 2 days (interquartile range [IQR], 1–3). Moreover, 854 (41%) of all 2,078 ESBL-E carriers remained without isolation during their hospital stay. In total, 6,040 ESBL-E days (32% of all ESBL-E days) accrued for patients who were not isolated. Of 2,078 ESBL-E-carriers, 1,478 ESBL-E carriers (71%) had no previous history of ESBL-E carriage. Also, 697 (34%) were placed in contact isolation with a delay of 4 days (IQR, 2–5), accounting for 2,723 nonisolation days (15% of ESBL-E days). Conclusions: Even with extensive surveillance screening, almost one-third of all ESBL-E days were nonisolation days. Limitations in routine culture-based ESBL-E detection impeded timely and exhaustive implementation of targeted contact isolation.

Background: Serratia marcescens may cause severe nosocomial infections, mostly in very low birth weight infants. Since S. marcescens exhibits by far the highest adjusted incidence rate for horizontal transmission, it can cause complex outbreak situations in neonatal intensive care units. Objective: The aim of this study was to establish a fast and highly sensitive colonization screening for prompt cohorting and barrier nursing strategies. Methods: A probe-based duplex PCR assay targeting the 16S rRNA gene of S. marcescens was developed and validated by using 36 reference strains, 14 S. marcescens outbreak- and nonoutbreak isolates, defined by epidemiological linkage and molecular typing, and applied in 1,347 clinical specimens from 505 patients. Results and Conclusions: The novel PCR assay proved to be highly specific and had an in vitro sensitivity of 100 gene copies per reaction (∼15 bacteria). It showed a similar (in laryngeal/tracheal specimens) or even higher (in rectal/stoma swabs) in vivo sensitivity in comparison to routine microbial culture and was much quicker (S. marcescens strains. PCR inhibition was low (1.6%) and observed with rectal swabs only. Cohort analysis illustrated applicability of the PCR assay as a quick tool to prevent outbreak scenarios by allowing rapid decisions on cohorting and barrier nursing. In summary, this novel molecular screening for colonization by S. marcescens is specific, highly sensitive, and substantially accelerates detection.

Enterobacter cloacae complex (ECC) represent globally important nosocomial pathogens. A three-year study of ECC in Germany identified Enterobacter xiangfangensis as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (mcr)-9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal arnBCADTEF gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in phoPQ and mgrB, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating phoPQ chimeras and combining them with mgrB alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase phoQ dictate arnBCADTEF expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.

Objectives Infections as a result of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) are considered infections with a high public health burden. In this study, we aimed to identify incidences of and risk factors for healthcare-associated infections (HAIs) after rectal colonization with ESBL-producing Escherichia coli (ESBL-EC) or Klebsiella pneumoniae (ESBL-KP). Methods This prospective cohort study was performed in 2014 and 2015. Patients colonized with ESBL-EC or ESBL-KP were monitored for subsequent HAI with ESBL-E and other pathogens. In the case of an ESBL-E infection, rectal and clinical isolates were compared using pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing (WGS) for ESBL-KP isolates. Proportional hazard models were applied to identify risk factors for HAIs, and to analyse competing risks. Results Among all patients admitted to the hospital during the study period, 13.6% were rectally screened for third-generation cephalosporin-resistant Enterobacterales (3GCREB). A total of 2386 rectal carriers of ESBL-EC and 585 of ESBL-KP were included in the study. Incidence density (ID) for HAI with ESBL-E was 2.74 per 1000 patient days at risk (95% confidence interval (CI) 2.16–3.43) among carriers of ESBL-EC, while it was 4.44 per 1000 patient days at risk (95% CI 3.17–6.04) among carriers of ESBL-KP. In contrast, ID for HAI with other pathogens was 4.36 per 1000 patient days at risk (95% CI 3.62–5.21) among carriers of ESBL-EC, and 5.00 per 1000 patient days at risk (95% CI 3.64–6.69) among carriers of ESBL-KP. Cox proportional hazard regression analyses identified colonization with ESBL-KP (HR = 1.58, 95% CI 1.068–2.325) compared with ESBL-EC as independent risk factor for HAI with ESBL-E. The results were consistent over all competing risk analyses. Conclusions Clinicians should be aware of the increased risk of ESBL-E infections among patients colonized with ESBL-KP compared with ESBL-EC that might be caused by underlying diseases, higher pathogenicity of ESBL-KP and other factors.

ObjectivesTo analyse the rectal carriage rate and the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) recovered from patients upon hospital admission.MethodsAdult patients were screened at six German university hospitals from five different federal states upon hospital admission for rectal colonization with VREfm between 2014 and 2018. Molecular characterization of VREfm was performed by WGS followed by MLST and core-genome MLST analysis.ResultsOf 16350 patients recruited, 263 were colonized with VREfm, with increasing prevalence rates during the 5 year study period (from 0.8% to 2.6%). In total, 78.5% of the VREfm were vanB positive and 20.2% vanA positive, while 1.2% harboured both vanA and vanB. The predominant ST was ST117 (56.7%) followed by ST80 (15%), ST203 (10.9%), ST78 (5.7%) and ST17 (3.2%). ST117/vanB VREfm isolates formed a large cluster of 96 closely related isolates extending across all six study centres and four smaller clusters comprising 13, 5, 4 and 3 isolates each. In contrast, among the other STs inter-regional clonal relatedness was rarely observed.ConclusionsTo our knowledge, this is the largest admission prevalence and molecular epidemiology study of VREfm. These data provide insight into the epidemiology of VREfm at six German university hospitals and demonstrate the remarkable inter-regional clonal expansion of the ST117/vanB VREfm clone.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses., Nature Methods, 19 (8), ISSN:1548-7105, ISSN:1548-7091

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ∼1,700 novel and known microbial genomes, as well as ∼600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results.Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.

[Objectives] We aimed to evaluate different interventions to reduce multidrug-resistant Enterobacteriaceae (MDR-E) infection/colonization., [Methods] A systematic review and meta-analysis evaluating interventions for prevention of MDR-E infection/colonization among hospitalized adult patients. The co-primary outcomes were mortality and MDR-E infections. PubMed, Cochrane library, and LILACS databases were searched up till December 2019, as well as grey literature sources. We included randomized controlled trials and observational studies. Infection/colonization/acquisition outcomes were reported per patient-days as pooled incidence ratios (IRs) with 95% confidence intervals (CIs). Interrupted time series (ITS) analysis studies were reported separately., [Results] Sixty-three studies were included, 16 RCTs, 33 observational studies, and 14 ITS. For the intervention of antimicrobial stewardship program (ASP), 23 studies were included. No differences in mortality or MDR-E infections were observed with ASP, however, MDR-E colonization was significantly reduced (IR 0.69, 95% CI 0.57–0.82). Seventeen studies examined decolonization without significant difference in outcomes. Other interventions were scarcely represented. Among 14 ITS publications, most evaluating ASP, 11 showed benefit of the intervention., [Conclusions] ASP is an effective measure in preventing MDR-E colonization. Decolonization did not show significant benefit in reducing infection or colonization. Studies are needed to evaluate the cost effectiveness of ASP and assess bundles of interventions., This publication was made possible by grants from following national funding agencies: Germany BMBF 01KI1704A (Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Institute of Hygiene and Environmental Medicine); 01KI1704B (Helmholtz Center for Infection Research GmbH) and 01KI1704C (Martin-Luther-University Halle-Wittenberg, medical faculty, Institute of medical epidemiology, biostatistics and informatics); the Netherlands ZonMw grant number 547001005 (Julius centre, University Medical centre Utrecht); Israel CSO-MOH grant number 3000013820 (Rabin Medical Center, Beilinson Hospital / Department of Medicine), and Poland National Science centre Poland, Unisono: 2016/22/Z/ST1/00690 (University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Institute of Applied Mathematics and Mechanics and Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University); within the 3rd JPI ARM framework (Joint Programming Initiative on Antimicrobial Resistance) cofound grant no. 681055 for the consortium EMerGE-Net (Effectiveness of infection control strategies against intra- and inter-hospital transmission of Multidrug-resistant Enterobacteriaceae).

The aim of this study is to analyze patient movement patterns between hospital departments to derive the underlying intra-hospital movement network, and to assess if movement patterns differ between patients at high or low risk of colonization. For that purpose, we analyzed patient electronic medical record data from five hospitals to extract information on risk stratification and patient intra-hospital movements. Movement patterns were visualized as networks, and network centrality measures were calculated. Next, using an agent-based model where agents represent patients and intra-hospital patient movements were explicitly modeled, we simulated the spread of multidrug resistant enterobacteriacae (MDR-E) inside a hospital. Risk stratification of patients according to certain ICD-10 codes revealed that length of stay, patient age, and mean number of movements per admission were higher in the high-risk groups. Movement networks in all hospitals displayed a high variability among departments concerning their network centrality and connectedness with a few highly connected departments and many weakly connected peripheral departments. Simulating the spread of a pathogen in one hospital network showed positive correlation between department prevalence and network centrality measures. This study highlights the importance of intra-hospital patient movements and their possible impact on pathogen spread. Targeting interventions to departments of higher (weighted) degree may help to control the spread of MDR-E. Moreover, when the colonization status of patients coming from different departments is unknown, a ranking system based on department centralities may be used to design more effective interventions that mitigate pathogen spread., Author summary Pathogens including multidrug resistant enterobacteriacae (MDR-E) inside hospital settings are associated with higher morbidity, mortality, and healthcare costs. Better understanding of the transmission routes of these pathogens is required to develop targeted and efficient measures to contain the spread of MDR-E in a hospital. We analyzed datasets from five hospitals in different countries to explore patient movement patterns between departments of these hospitals (intra-hospital movements). We assessed whether movement patterns differ between patients at high or low risk of colonization. Our results show that in every intra-hospital network, there exist a few departments which are strongly connected and many peripheral departments which are loosely connected. High-risk patients stay on average longer in the hospital, and move more frequently between departments than low-risk patients. Targeting interventions to strongly connected departments may help to reduce pathogen spread inside the hospital. To explore this, we simulated the spread of MDR-E inside one hospital using an agent-based model that includes patient movements. In the simulations, we found positive correlations between departments’ prevalence and network characteristics such as degree and weighted degree, thus highlighting the importance of targeting interventions to departments of higher (weighted) degree to control the spread of MDR-E.

Limited therapy options due to antibiotic resistance underscore the need for optimization of current diagnostics. In some bacterial species, antimicrobial resistance can be unambiguously predicted based on their genome sequence. In this study, we sequenced the genomes and transcriptomes of 414 drug‐resistant clinical Pseudomonas aeruginosa isolates. By training machine learning classifiers on information about the presence or absence of genes, their sequence variation, and expression profiles, we generated predictive models and identified biomarkers of resistance to four commonly administered antimicrobial drugs. Using these data types alone or in combination resulted in high (0.8–0.9) or very high (> 0.9) sensitivity and predictive values. For all drugs except for ciprofloxacin, gene expression information improved diagnostic performance. Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. The implementation of a molecular susceptibility test system in routine microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections., The spread of antibiotic resistance complicates infection treatment, requiring an optimization of current diagnostics. In this study, a machine learning approach identified a set of biomarkers suitable for the development of a molecular test system to determine antibiotic resistance profiles.

Objectives To assess the admission prevalence of third-generation cephalosporin-resistant Enterobacterales (3GCREB) and to assess whether risk factors vary by β-lactamase genotype. Methods Adult patients were recruited within 72 h of admission to general wards of six university hospitals in 2014 and 2015. Rectal swabs were screened for 3GCREB and isolates were analysed phenotypically and genotypically. Patients were questioned on potential risk factors. Multivariable analyses were performed to identify risk factors for 3GCREB colonization and for specific β-lactamases. Results Of 8753 patients screened, 828 were 3GCREB positive (9.5%). Eight hundred and thirteen isolates were available for genotyping. CTX-M-15 was the most common ESBL (38.0%), followed by CTX-M-1 (22.5%), CTX-M-14 (8.7%), CTX-M-27 (7.5%) and SHV-ESBL (4.4%). AmpC was found in 11.9%. Interestingly, 18 Escherichia coli isolates were AmpC positive, 12 of which (67%) contained AmpC on a gene of plasmid origin [CMY (n = 10), DHA (n = 2)]. Risk factors for 3GCREB colonization varied by genotype. Recent antibiotic exposure and prior colonization by antibiotic-resistant bacteria were risk factors for all β-lactamases except CTX-M-14 and CTX-M-27. Travel outside Europe was a risk factor for CTX-M-15 and CTX-M-27 [adjusted OR (aOR) 3.49, 95% CI 2.88–4.24 and aOR 2.73, 95% CI 1.68–4.43]. A previous stay in a long-term care facility was associated with CTX-M-14 (aOR 3.01, 95% CI 1.98–4.59). A preceding hospital stay in Germany increased the risk of CTX-M-15 (aOR 1.27, 95% CI 1.14–1.41), while a prior hospital stay in other European countries increased the risk of SHV-ESBL colonization (aOR 3.85, 95% CI 1.67–8.92). Conclusions The detection of different ESBL types is associated with specific risk factor sets that might represent distinct sources of colonization and ESBL-specific dissemination routes.

Background In addition to an overall rise in vancomycin-resistant Enterococcus faecium (VREfm), an increase in certain strain types marked by sequence type (ST) and cluster type (CT) has been reported in Germany over the past few years. Outbreak analyses at Charité - Universitätsmedizin Berlin revealed the frequent occurrence of VREfm ST117 CT71 isolates in 2017 and 2018. To investigate whether ST117 CT71 have emerged in recent years or whether these strains have been circulating for a longer time, we retrospectively analyzed non-outbreak strains that occurred between 2008 and 2018 to identify frequent STs and CTs. Methods In total, 120 VREfm isolates obtained from clinical and surveillance cultures from the years 2008, 2013, 2015, and 2018 were analyzed. Thirty isolates per year comprising the first 7–8 non-outbreak isolates of each quarter of the respective year were sequenced using whole genome sequencing. MLST and cgMLST were determined as well as resistance genes and virulence factors. Risk factors for VREfm ST117 were analyzed in a multivariable analysis with patient characteristics as possible confounders. Results The percentage of VREfm of type ST117 increased from 17% in 2008 to 57% in 2018 (p = 0.012). In 2008, vanA genotype accounted for 80% of all ST117 isolates compared to 6% in 2018. VanB CT71 first appeared in 2018 and predominated over all other ST117 at 43% (p The set of resistance genes (msrC, efmA, erm(B), dfrG, aac(6′)-Ii, gyrA, parC and pbp5) and virulence factors (acm, esp, hylEfm, ecbA and sgrA) in CT71 was also found in other ST117 non-CT71 strains, mainly in CT36. The study population did not differ among the different calendar years analyzed in terms of age, gender, length of stay, or ward type (each p > 0.2). Conclusion This study revealed an increase in ST117 strains from 2008 to 2018, accompanied by a shift toward CT71 strains with the vanB genotype in 2018. We did not detect resistance or virulence traits in CT71 that could confer survival advantage compared to other CTs among ST117 strains. To date, it is not clear why ST117 and in particular strain type ST117 CT71 predominates over other strains.

The growing importance of antibiotic resistance on clinical outcomes and cost of care underscores the need for optimization of current diagnostics. For a number of bacterial species antimicrobial resistance can be unambiguously predicted based on their genome sequence. In this study, we sequenced the genomes and transcriptomes of 414 drug-resistant clinical Pseudomonas aeruginosa isolates. By training machine learning classifiers on information about the presence or absence of genes, their sequence variation, and gene expression profiles, we generated predictive models and identified biomarkers of susceptibility or resistance to four commonly administered antimicrobial drugs. Using these data types alone or in combination resulted in high (0.8-0.9) or very high (>0.9) sensitivity and predictive values, where the relative contribution of the different categories of biomarkers strongly depended on the antibiotic. For all drugs except for ciprofloxacin, gene expression information substantially improved diagnostic performance. Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. The implementation of a molecular susceptibility test system in routine clinical microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections.

Background: The monitoring of antimicrobial resistance (AMR) in microorganisms that circulate in the environment is an important topic of scientific research and contributes to the development of action plans to combat the spread of multidrug-resistant (MDR) bacteria. As a synanthropic vector for multiple pathogens and a reservoir for AMR, flies can be used for surveillance. Methods: We collected 163 flies in the inner city of Berlin and examined them for extended-spectrum &beta, lactamase (ESBL)-producing Escherichia coli genotypically and phenotypically. Results: The prevalence of ESBL-producing E. coli in flies was 12.9%. Almost half (47.6%) of the ESBL-positive samples showed a co-resistance to ciprofloxacin. Resistance to carbapenems or colistin was not detected. The predominant ESBL-type was CTX-M-1, which is associated with wildlife, livestock, and companion animals as a potential major source of transmission of MDR E. coli to flies. Conclusions: This field study confirms the permanent presence of ESBL-producing E. coli in an urban fly population. For continuous monitoring of environmental contamination with multidrug-resistant (MDR) bacteria, flies can be used as indicators without much effort.

Introduction Skin and soft tissue infections (SSTI) caused by Panton-Valentine leukocidin (PVL)-producing strains of Staphylococcus aureus (PVL-SA) are associated with recurrent skin abscesses. Secondary prevention, in conjunction with primary treatment of the infection, focuses on topical decolonization. Topical decolonization is a standard procedure in cases of recurrent PVL-SA skin infections and is recommended in international guidelines. However, this outpatient treatment is often not fully reimbursed by health insurance providers, which may interfere with successful PVL-SA decolonization. Aim Our goal was to estimate the cost effectiveness of outpatient decolonization of patients with recurrent PVL-SA skin infections. We calculated the average cost of treatment for PVL-SA per outpatient decolonization procedure as well as per in-hospital stay. Methods The study was conducted between 2014 and 2018 at a German tertiary care university hospital. The cohort analyzed was obtained from the hospital’s microbiology laboratory database. Data on medical costs, DRG-based diagnoses, and ICD-10 patient data was obtained from the hospital’s financial controlling department. We calculated the average cost of treatment for patients admitted for treatment of PVL-SA induced skin infections. The cost of outpatient treatment is based on the German regulations of drug prices for prescription drugs. Results We analyzed a total of n = 466 swabs from n = 411 patients with recurrent skin infections suspected of carrying PVL-SA. PVL-SA was detected in 61.3% of all patients included in the study. Of those isolates, 80.6% were methicillin-susceptible, 19.4% methicillin-resistant. 89.8% of all patients were treated as outpatients. In 73.0% of inpatients colonized with PVL-SA the main diagnosis was SSTI. The median length of stay was 5.5 days for inpatients colonized with PVL-SA whose main diagnosis SSTI; the average cost was €2,283. The estimated costs per decolonization procedure in outpatients ranged from €50-€110, depending on the products used. Conclusion Our data shows that outpatient decolonization offers a highly cost-effective secondary prevention strategy, which may prevent costly inpatient treatments. Therefore, health insurance companies should consider providing coverage of outpatient treatment of recurrent PVL-SA skin and soft tissue infections.

Background: The ST131 Escherichia coli clone is associated with the global dissemination of ESBLs. It has been hypothesized that ST131 could take advantage of better colonizing abilities. However, the data on colonization prevalence of ESBL-ST131 in European hospitals are scarce. Objectives: To assess the prevalence of the ST131 clone and its microbiological characteristics among colonizing ESBL-producing E. coli (ESBL-Ec) from hospitalized patients in four European hospitals (Berlin, Geneva, Madrid and Utrecht) during the R-GNOSIS study. Methods: ESBL-Ec isolates (n = 688) were obtained from rectal swabs of hospitalized patients from March 2014 to February 2015 using selective media. The ST131 clone and its subclones were sought using PCR and positive isolates were further studied. blaESBL genes were characterized (PCR and sequencing), antibiotic susceptibility testing was performed, clonal relationships were studied by PFGE and fimH allele and O type (PCR) were assessed. Results: ST131 prevalence was 20.5% (141/688); C1/H30R1 isolates were significantly more prevalent in Geneva (49%) and C2/H30Rx in Madrid (67%). C1/H30R1 isolates showed less resistance to amikacin than C2/H30Rx (4% versus 35%) and all were susceptible to penicillin/inhibitor combinations. CTX-M-15 was the most common enzyme (49%) followed by CTX-M-27 (27%). C1/H30R1 isolates were significantly associated with CTX-M-27 (72%) and all of these isolates belonged to the C1-M27 clade. Moreover, C2/H30Rx isolates and CTX-M-15 were also significantly related (88%). Conclusions: The predominance of C2/H30Rx-CTX-M-15 in Madrid and C1/H30R1-CTX-M-27 in Geneva demonstrates a changing epidemiology of ESBLs in Europe caused by ST131 subclones; in particular, the emergence of the C1-M27 clade in Europe.

Health-care-associated infections by multi-drug-resistant bacteria constitute one of the greatest challenges to modern medicine. Bacterial pathogens devise various mechanisms to withstand the activity of a wide range of antimicrobial compounds, among which the acquisition of carbapenemases is one of the most concerning. In Klebsiella pneumoniae, the dissemination of the K. pneumoniae carbapenemase is tightly connected to the global spread of certain clonal lineages. Although antibiotic resistance is a key driver for the global distribution of epidemic high-risk clones, there seem to be other adaptive traits that may explain their success. Here, we exploited the power of deep transcriptome profiling (RNA-seq) to shed light on the transcriptomic landscape of 37 clinical K. pneumoniae isolates of diverse phylogenetic origins. We identified a large set of 3346 genes which was expressed in all isolates. While the core-transcriptome profiles varied substantially between groups of different sequence types, they were more homogenous among isolates of the same sequence type. We furthermore linked the detailed information on differentially expressed genes with the clinically relevant phenotypes of biofilm formation and bacterial virulence. This allowed for the identification of a diminished expression of biofilm-specific genes within the low biofilm producing ST258 isolates as a sequence type-specific trait.

Objectives We report on an outbreak of skin and soft tissue infections (SSTI) among kindergarten families. We analyzed the transmission route and aimed to control the outbreak. Methods The transmission route was investigated by nasal screening for Panton-Valentine leukocidin (PVL)-producing Staphylococcus aureus (PVL-SA), subsequent microbiological investigation including whole genome sequencing and a questionnaire-based analysis of epidemiological information. The control measures included distribution of outbreak information to all individuals at risk and implementation of a Staphylococcus aureus decontamination protocol. Results Individuals from 7 of 19 families were either colonized or showed signs of SSTI such as massive abscesses or eye lid infections. We found 10 PVL-SA isolates in 9 individuals. In the WGS-analysis all isolates were found identical with a maximum of 17 allele difference. The clones were methicillin-susceptible but cotrimoxazole resistant. In comparison to PVL-SAs from an international strain collection, the outbreak clone showed close genetical relatedness to PVL-SAs from a non-European country. The questionnaire results showed frequent travels of one family to this area. The results also demonstrated likely transmission via direct contact between families. After initiation of Staphylococcus aureus decontamination no further case was detected. Conclusions Our outbreak investigation showed the introduction of a PVL-SA strain into a kindergarten likely as a result of international travel and further transmission by direct contact. The implementation of a Staphylococcus aureus decontamination protocol was able to control the outbreak.

OBJECTIVES This study aimed to determine the prevalence of and risk factors for colonization with extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) and methicillin-resistant Staphylococcus aureus (MRSA) in very low birth weight (VLBW

Objectives: To discern the relevance of ST648 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli as a putative new group of multiresistant and extraintestinal pathogenic strains in animals, its frequency, ESBL types, antimicrobial resistance patterns and virulence gene (VG) profiles should be determined and compared with ST131 strains from the same collection of strains. Methods: ESBL-producing E. coli isolates (n=1152), consecutively sampled from predominantly dogs, cats and horses between 2008 and 2011, were assigned to a phylogenetic group by PCR. Partial multilocus sequence typingwas performed for group D and B2 strains and strains presumed to be D-ST648 and B2-ST131 were fully typed. ESBL genes and extraintestinal pathogenic E. coli (ExPEC)-like VGs were characterized by PCR and sequence analysis and antimicrobial resistance was determined by broth dilution. Clonal analysis was done by PFGE. Results: Forty (3.5%) ESBL-producing E. coli were determined as D-ST648, whereas B2-ST131 isolates occurred less frequently (2.8%). Although the predominant ESBL type in both groups was CTX-M-15 (72.5% versus 46.9%), ST648 strains from companion animals and horses displayed a lower variety of ESBL types (CTX-M-1,-3,-14,-15 and-61 versus CTX-M-1,-2,-14,-15,-27 and-55 and SHV-12). In contrast to ST131 strains, a higher proportion of ST648 strains showed resistance to most non-b-lactam antibiotics. Overall, VGs were less abundant in ST648 strains, although some strains had VG profiles comparable to those of ST131 strains. ExPEC-associated serotype O1:H6 was predominant (46.8%) among the ST648 strains. Some PFGE clusters comprised ST648 isolates from pets, horses and wild birds and humans included from previous studies. Conclusions: Our findings demonstrate that certain subgroups of E. coli D-ST648-CTX-M may represent a novel genotype that combines multiresistance, extraintestinal virulence and zoonotic potential. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved.

As part of the multicentre Antibiotic Therapy Optimisation Study (ATHOS), minimum inhibitory concentrations (MICs) were determined for cephalosporins alone and in combination with the β-lactamase inhibitors tazobactam, clavulanic acid and avibactam against third-generation cephalosporin-resistant Escherichia coli, Klebsiella spp. and Enterobacter spp. isolates collected in German hospitals. MIC50/90 values were 0.25–4 mg/L for cefepime/tazobactam, 0.25–2 mg/L for ceftazidime/avibactam, 0.125–0.5 mg/L for ceftaroline/avibactam, 0.5–4 mg/L for cefpodoxime/clavulanic acid and 0.25–1 mg/L for aztreonam/avibactam, depending on the underlying resistance mechanism and organism. Based on in vitro testing, β-lactam antibiotics play an important role in the treatment of infections due to β-lactamase-producing organisms.

Introduction Since 2000, a considerable increase in the number of Clostridium difficile infections (CDIs) leading to substantial morbidity, mortality and attributable costs has been observed, at least in North America and Europe [1]. Changes in the epidemiology of CDI have been mainly attributed to the emergence of a new hypervirulent strain called PCR ribotype 027, causing numerous outbreaks in North America and Europe [2,3] and, to a lesser extent, PCR ribotype 078 [1,4,5]. In addition, patients not previously considered to be at risk for the disease (e.g., without recent antibiotic therapy or hospitalisation) have also been described [1,6-8]. The European CDI study (ECDIS), initiated and funded by the European Centre for Disease Prevention and Control (ECDC), showed that the incidence of CDI varied from hospital to hospital [9]. In 2008, a weighted mean incidence of 4.1 cases (range: 0.0–36.3) per 10,000 patient-days per hospital reported by the ECDIS study was almost 70% higher than that reported in a previous European surveillance study in 2005 (2.45 cases per 10,000 patient-days per hospital, range: 0.13–7.1) [9,10]. ECDIS also revealed the contribution of strains other than PCR ribotype 027 and that some of these strains, notably PCR ribotypes 015, 018 and 056, could cause severe CDI. In response to the emerging problems associated with C. difficile, an ECDC working group published background information about the changing epidemiology of CDI, CDI case definitions and surveillance recommendations [2]. To support European Union (EU)/European Economic Area (EEA) Member States in increasing their capacity for CDI surveillance, ECDC also initiated and funded a new project – ECDIS-Net – to develop a European surveillance protocol and enhance laboratory capacity for diagnosis and typing of C. difficile in EU/EEA Member States. In 2011, a survey of existing CDI surveillance systems in European countries was performed as part of the ECDIS-Net project. The results of this survey, presented here, were later used to develop a standardised pan-European CDI surveillance protocol, which was tested in a three-month pilot study in 2013 [11]. Data collection in the ECDC-coordinated Europe-wide hospital-based CDI surveillance, using a finalised version of this piloted protocol, began on 1 January 2016 [12]. Methods National coordinators for this study were identified through the members of ECDC’s Healthcare-Associated Infections surveillance Network (HAI-Net) and via representatives for the ECDIS study [9]. A link to a web-based questionnaire was sent to these national coordinators to assess the characteristics of existing CDI surveillance systems in European countries. If the national coordinators indicated that CDI was under surveillance in their country, the surveillance protocols were requested and used to augment the information obtained via the questionnaire. Information on the national CDI surveillance systems was entered using a web- based electronic form designed for the purpose of this study. Results Between 6 June and 15 July 2011, 33 of the 35 national coordinators approached from 31 European countries responded to the web-based questionnaire (Iceland and Wales did not respond). Four surveillance systems were excluded from further analysis, as they were not ongoing, comprehensive nationwide surveillance systems, i.e. they were completed one-off studies (two studies from Spain), only regional (Switzerland) or focused only on outbreaks (one system of the Netherlands). In 14 countries, the national coordinators indicated that surveillance of CDI was in place. Of these, surveillance protocols were available from 10 surveillance systems. Thus, 18 CDI surveillance systems from 14 European countries (Austria, Belgium, Bulgaria, Denmark, Finland, France, Germany, Hungary, Ireland, the Netherlands, Sweden and three countries of the United Kingdom (UK), England, Northern Ireland and Scotland) remained available for analysis. Of the 18 surveillance systems, all but one reported national CDI rates annually.

Background We report on an outbreak in a surgical, interdisciplinary intensive care unit (ICU) of a tertiary care hospital. We detected a cluster of ICU patients colonized or infected with multidrug-resistant Pseudomonas aeruginosa. We established an outbreak investigation team, performed an exploratory epidemiological analysis and initiated an epidemiology-based intervention. Methods As part of the outbreak investigation, we performed microbiological examinations of the sinks in the patient rooms and a retrospective case-control study. All patients admitted to the outbreak ICU between January 2012 and February 2014 were included. Cases were patients colonized with the outbreak strain. Controls were patients with a different Pseudomonas aeruginosa strain. Risk factors were evaluated using multivariable conditional logistic regression analysis. Strain typing was performed using the repetitive element-based polymerase chain reaction (rep-PCR) DiversiLab system. Results The outbreak strain was found in the sinks of five (of 16) patient rooms. Altogether 21 cases and 21 (randomly selected) controls were included. In the univariate analysis, there was no significant difference in baseline data of the patients. In the multivariate analysis, stay in a room with a colonized sink (Odds Ratio[OR] 11.2, p = 0.007) and hemofiltration (OR 21.9, p = 0.020) were independently associated with an elevated risk for colonization or infection by the outbreak strain. In a subsequent evaluation of the work procedures associated with hemofiltration, we found that the ultra-filtrate bags had been on average five times per day emptied in the sinks of the patient rooms and were used multiple for the same patient. We exchanged the traps of the contaminated sinks and eliminated work procedures involving sinks in patient rooms by implementation of single use bags, which are emptied outside patient rooms to reduce splash water at the sinks. In the 20 month follow-up period, the outbreak strain was detected only once, which indicated that the outbreak had been ceased (incidence 0.75% vs. 0.04%, p

To determine the prevalence of extended-spectrum β-lactamase (ESBL) production in Enterobacteriaceae in retail chicken meat in Germany.A total of 399 chicken meat samples from nine supermarket chains, four organic food stores and one butcher's shop in two geographically distinct regions (Berlin and Greifswald) were screened for ESBL production using selective agar. Phenotypic ESBL isolates were tested for bla(TEM), bla(CTX-M) and bla(SHV) genes using PCR and DNA sequencing. Antibiotic coresistances were determined and strain typing was performed using PCR-based phylogenetic grouping and XbaI-PFGE.A total of 185 confirmed ESBL isolates were obtained from 175 samples (43.9%) from all tested sources. The majority of isolates were Escherichia coli producing ESBL types SHV-12 (n = 82), CTX-M-1 (n = 77) and TEM-52 (n = 16). No differences could be observed in the prevalence of ESBL producers between organic and conventional samples. 73.0% of the ESBL producers showed coresistance to tetracycline, 35.7% to co-trimoxazole and 7.6% to ciprofloxacin. Strain typing of selected E. coli isolates from Berlin revealed identical macrorestriction patterns for several isolates from samples taken from the same stores.This is the first comprehensive study from Germany showing a high prevalence of TEM-, CTX-M- and SHV-type ESBLs in Enterobacteriaceae isolated from retail chicken meat. The high rate of coresistance to different classes of antibiotics in the ESBL producers might reflect the common veterinary usage of these and related substances. There is an urgent need to further evaluate the role of poultry in the transmission of highly resistant ESBL-producing bacteria in humans.

Infection control personnel performing surveillance activities noticed a cluster of patients with isolates of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in the surgical intensive care unit (SICU) of a German University Hospital. An outbreak investigation including a descriptive analysis, a case-control study comparing 15 CRPA case patients with 18 patients with carbapenem-susceptible P. aeruginosa, environmental sampling and pulsed-field gel electrophoresis (PFGE) typing of P. aeruginosa isolates was carried out. Fifteen patients acquired CRPA in the SICU during the outbreak period between 1 July 2006 and 31 October 2006 and PFGE typing of 11 available patient isolates revealed two outbreak strains as well as sporadic CRPA isolates. Both outbreak strains were resistant to penicillins, cephalosporins, carbapenems, aminoglycosides and quinolones, and remained susceptible only to colistin. The most likely mode of transmission was cross-transmission between patients during postoperative wound care with abdominal and/or thoracic drains (odds ratio: 64.33; 95% confidence interval: 5.32-999) and therapy with quinolones (48.37; 3.71-999) being independent risk factors for acquisition of CRPA. No further clusters of CRPA cases were observed after implementation of contact isolation precautions and after healthcare workers were made aware of the likely mode of transmission. This study shows the complex epidemiology of CRPA in a SICU including cross-transmission of two CRPA strains related to postoperative wound care.

Surveillance data of nosocomial infection rates are increasingly used for public reporting and interhospital comparisons. Approximately 15% of nosocomial infections on intensive care units are the result of patient-to-patient transmissions of the causative organisms. These exogenous infections could be prevented by adherence to basic infection control measures. The association between bacterial cross transmissions and nosocomial infection rates was analyzed.Prospective cohort study during 24 months.Eleven intensive care units from two university hospitals.All inpatients.None.Primary isolates of six indicator organisms (Acinetobacter baumannii, Enterococcus faecalis and E. faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus) cultured from clinical samples or methicillin-resistant S. aureus surveillance testing of all inpatients were genotyped. Indistinguishable isolates inor =2 patients defined potential episodes of transmissions. Surveillance of nosocomial infection rates was performed according to the German nosocomial infection surveillance system, Krankenhaus Infektions Surveillance System. Transmission events and nosocomial infection rates were pooled by intensive care unit to calculate Spearman's rank-correlation test. During 100,781 patient days, 100,829 microbiological specimens from 24,362 patients were sampled (average investigation density: 1.0 sample per patient and day) and 3419 primary indicator organisms were cultured. Altogether, 462 transmissions (incidence density of 4.6 transmissions per 1000 patient days; range, 1.4-8.4 days) and 1216 nosocomial infections (incidence density of 12.1 per 1000 patient days; range, 6.2-16.6 days) were discerned. Correlation analysis was unable to reveal any association between the incidence of cross transmissions and nosocomial infections, duration of hospitalization, or device use.Differences in nosocomial infection rates between study intensive care units are not explained solely by cross transmissions. Other factors, like the severity of the patient's underlying diseases, the patient's endogenous flora, or invasive procedures, likely have a dominant effect on the magnitude of nosocomial infection rates.

Multi-drug-resistant gram-negative rods (MRGN) are associated with increased morbidity and mortality. Little is known about the epidemiology of this group of pathogens in endemic situations. The aim of this study was to determine the epidemiology of MRGN in our facility during a 3-year period. Prospective surveillance of any patient colonized or infected with a MRGN during hospital stay from 2002 to 2004 was performed. Patients proven to harbour extended beta-lactamase (ESBL)-producing bacteria as well as cystic fibrosis (CF) patients were excluded. After culture of MRGN, patients were considered positive until three consecutive samples from all previously affected locations had been tested negative. Five hundred and three case-patients were enrolled accounting for 8081 isolation days and an incidence of 0.43 per 1000 patient days with an average length of stay of 37.5 days (average duration of isolation: 22.6 days). Sixty-six percent of case-patients were known to be positive at the time of admission. Fifty-one percent of MRGN were acquired within the hospital. The most frequently detected species was Pseudomonas aeruginosa. There were 108 case-patients with pan-resistant pathogens. Eight of 169 (4.7%) screened contact patients were found to be MRGN positive. In our hospital cross-transmission of MRGN seems to occur less frequently than cross-transmission of MRSA (9.0%) or ESBL (11.1%). To prevent nosocomial transmission it is recommended to isolate patients colonized or infected with MRGN in our hospital in single rooms. Because there are many immunocompromised patients in our facility we will continue our current infection control management until more data concerning MRGN are available.

Several randomized controlled trials (RCTs) have examined the influence of oral chlorhexidine (CHX) in preventing nosocomial lower respiratory tract infection (LRTI). Most have failed to demonstrate a reduction in the incidence of LRTI. The present meta-analysis summarizes the effect of oral CHX on the development of LRTI. RCTs were identified through searching PubMed, MEDLINE and the Cochrane Central Register of Controlled Trials databases. Those describing the use of chlorhexidine for oral decontamination and reporting the incidence of LRTI as a study outcome were included in the meta-analysis. Seven RCTs met the inclusion criteria; pooling the results from these reveals a reduction in the relative risk (RR) of LRTI in the CHX group [RR(random): 0.58, 95% confidence interval (CI): 0.45-0.74; and RR(fixed): 0.56, CI95: 0.44-0.72, respectively]. Further analyses showed that this result applied only to patients ventilated for up to 48h (RR(random): 0.58, CI95: 0.45-0.74; and RR(fixed): 0.56, 95% CI: 0.44-0.72). Oral CHX should be included among preventive measures performed to reduce nosocomial LRTI. Whether it has an impact on the development of LRTI in patients requiring mechanical ventilation for a longer period of time remains unresolved.

The usefulness and applicability of isolation precautions were questioned for extended-spectrum beta-lactamase (ESBL)-producing strains of Enterobacteriaceae in the endemic setting. We performed a surveillance programme for ESBL-positive organisms and the infection control management of patients colonized or infected with these organisms. Between 1 January 2002 and 31 December 2004, a total of 147 cases of ESBL-producing strains of Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis from 123 patients were noted. The overall incidence of ESBL-producing-strain-positive cases was 0.12/1000 patient-days. The proportion of referred cases was 35% (N=51); 65% of cases (N=96) were acquired in our institution. Infections developed in 57 cases (38.8%), of which 36 (63.3%) were nosocomial. Contact isolation precautions were carried out for 79.6% of the cases, with a median duration of contact isolation precautions for 14 days (range: 0-144). The contact isolation precautions resulted in 2985 isolation days in total, i.e. 995 isolation days per year. Typing by pulsed-field gel electrophoresis showed clonal diversity in 94.2% of the isolates from patients. Seven patient-to-patient transmissions were noted. Only in 10 cases (6.8%) was colonization with ESBL-producing strains cleared. Considering the large number of immunocompromised patients treated in our institution (>1500 bone marrow or solid organ transplantations performed during 2002-2004), we will continue to isolate patients who are colonized or infected with ESBL-producing organisms.

The outcome of infections occurring at different anatomic sites caused by ESBL-producing E. coli or K. pneumoniae was retrospectively analysed for a 3-y period. 23 cases were compared to 46 controls with infections caused by third-generation cephalosporin-susceptible strains matched by age, severity of illness and duration of hospitalization before onset of infection. Only 27.8% of cases received appropriate empirical antimicrobial therapy compared with 79.6% of controls (OR(paired)=0.053, p=0.001). This did not result in higher costs of antibiotic therapy, a longer median post-infection hospital stay or higher mortality in cases of patients with urinary tract or wound infections. In cases of patients with respiratory tract and bloodstream infections (RTI/BSI), median costs of definitive antibiotic treatment were significantly higher than in controls (325 vs 58.9 Euros, p=0.002). Moreover, more case patients with RTI/BSI had a post-infection stay exceeding the 75th percentile of 15 d on ICU and of 18 d in hospital, respectively (50% vs 6.67%, p=0.034). There was no difference in in-hospital mortality between case and control patients with RTI/BSI (25% vs 20%, p=1.0).