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Abstract Background Campylobacter spp. is a significant etiological agent of bacterial gastroenteritis globally. In Burkina Faso (BFA), the actual impact of this pathogen on gastroenteritis is considerably underestimated, primarily due to inadequate surveillance systems. Objectives This study aimed to investigate the proportion of Campylobacter species responsible for acute gastroenteritis among patients of all ages in urban and rural areas of BFA, using molecular biology techniques. Study design & methods Between 2018 and 2021, faecal specimens were obtained from 1,295 individuals presenting with acute gastroenteritis. These samples underwent screening for the Campylobacter coli/jejuni/lari complex utilizing real-time polymerase chain reaction (PCR) assays. Subsequently, positive samples were subjected to species-level differentiation through the application of species-specific primers. Results Campylobacter spp. was detected in 25.0% (324/1,295) of the samples analysed. The majority of positive samples (95%, 308/324) were obtained from children under 5 years of age. Species identification was performed on a subset of 114 isolates, revealing 51 Campylobacter jejuni, 10 Campylobacter coli, and 53 Campylobacter isolates that remained unspeciated. Conclusions This study reveals a significant prevalence of Campylobacter species among patients with acute gastroenteritis, with a particularly high incidence observed in children under 5 years of age. Based on these findings, the implementation of routine Campylobacter surveillance in public health laboratories is strongly recommended to better monitor and address this health concern.

Abstract Background Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing. Results The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants. Conclusions Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.

Abstract Background Studies have shown that Omicron breakthrough infections can occur at higher SARS-CoV-2 antibody levels compared to previous variants. Estimating the magnitude of immunological protection induced from COVID-19 vaccination and previous infection remains important due to varying local pandemic dynamics and types of vaccination programmes, particularly among at-risk populations such as health care workers (HCWs). We analysed a follow-up SARS-CoV-2 serological survey of HCWs at a tertiary COVID-19 referral hospital in Germany following the onset of the Omicron variant. Methods The serological survey was conducted in January 2022, one year after previous surveys in 2020 and the availability of COVID-19 boosters including BNT162b2, ChAdOx1-S, and mRNA-1273. HCWs voluntarily provided blood for serology and completed a comprehensive questionnaire. SARS-CoV-2 serological analyses were performed using an Immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA). Antibody levels were reported according to HCW demographic and occupational characteristics, COVID-19 vaccination and SARS-CoV-2 infection history, and multivariate linear regression was used to evaluate these associations. Results In January 2022 (following the fourth COVID-19 wave in Germany including the onset of the Omicron variant), 1482/1517 (97.7%) HCWs tested SARS-CoV-2 seropositive, compared to 4.6% in December 2020 (second COVID-19 wave). Approximately 80% had received three COVID-19 vaccine doses and 15% reported a previous laboratory-confirmed SARS-CoV-2 infection. SARS-CoV-2 IgG geometric mean titres ranged from 335 (95% Confidence Intervals [CI]: 258–434) among those vaccinated twice and without previous infection to 2204 (95% CI: 1919–2531) among those vaccinated three times and with previous infection. Heterologous COVID-19 vaccination combinations including a mRNA-1273 booster were significantly associated with the highest IgG antibody levels compared to other schemes. There was an 8-to 10-fold increase in IgG antibody levels among 31 HCWs who reported a SARS-CoV-2 infection in May 2020 to January 2022 after COVID-19 booster vaccination. Conclusions Our findings demonstrate the importance of ongoing COVID-19 booster vaccination strategies in the context of variants such as Omicron and despite hybrid immunity from previous SARS-CoV-2 infections, particularly for at-risk populations such as HCWs. Where feasible, effective types of booster vaccination, such as mRNA vaccines, and the appropriate timing of administration should be carefully considered.

BackgroundViral gastrointestinal infections remain a major public health concern in developing countries. In Burkina Faso, there are very limited updated data on the circulating viruses and their genetic diversity.ObjectivesThis study investigates the detection rates and characteristics of rotavirus A (RVA), norovirus (NoV), sapovirus (SaV) and human astrovirus (HAstV) in patients of all ages with acute gastrointestinal infection in urban and rural areas.Study design & methodsFrom 2018 to 2021, stool samples from 1,295 patients with acute gastroenteritis were collected and screened for RVA, NoV, SaV and HAstV. Genotyping and phylogenetic analyses were performed on a subset of samples.ResultsAt least one virus was detected in 34.1% of samples. NoV and SaV were predominant with detection rates of respectively 10.5 and 8.8%. We identified rare genotypes of NoV GII, RVA and HAstV, recombinant HAstV strains and a potential zoonotic RVA transmission event.ConclusionsWe give an up-to-date epidemiological picture of enteric viruses in Burkina Faso, showing a decrease in prevalence but a high diversity of circulating strains. However, viral gastroenteritis remains a public health burden, particularly in pediatric settings. Our data advocate for the implementation of routine viral surveillance and updated management algorithms for diarrheal disease.

Abstract Background Exposure to antibiotics has been shown to be one of the drivers of antimicrobial resistance (AMR) and is critical to address when planning and implementing strategies for combatting AMR. However, data on antibiotic use in sub-Saharan Africa are still limited. Using hospital-based surveillance data from the African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA), we assessed self-reported antibiotic use in multiple sub-Saharan African countries. Methods ANDEMIA included 12 urban and rural health facilities in Côte d’Ivoire, Burkina Faso, Democratic Republic of the Congo, and Republic of South Africa. Patients with acute respiratory infection (RTI), acute gastrointestinal infection (GI) and acute febrile disease of unknown cause (AFDUC) were routinely enrolled, and clinical, demographic, socio-economic and behavioral data were collected using standardized questionnaires. An analysis of ANDEMIA data from February 2018 to May 2022 was conducted. Reported antibiotic use in the ten days prior to study enrolment were described by substance and by the WHO AWaRe classification (“Access”, “Watch”, “Reserve”, and “Not recommended” antibiotics). Frequency of antibiotic use was stratified by location, disease syndrome and individual patient factors. Results Among 19,700 ANDEMIA patients, 7,258 (36.8%) reported antibiotic use. A total of 9,695 antibiotics were reported, including 54.7% (n = 5,299) from the WHO Access antibiotic group and 44.7% (n = 4,330) from the WHO Watch antibiotic group. The Watch antibiotic ceftriaxone was the most commonly reported antibiotic (n = 3,071, 31.7%). Watch antibiotic use ranged from 17.4% (56/322) among RTI patients in Côte d’Ivoire urban facilities to 73.7% (630/855) among AFDUC patients in Burkina Faso urban facilities. Reported antibiotic use included WHO Not recommended antibiotics but no Reserve antibiotics. Conclusions Reported antibiotic use data from this multicenter study in sub-Saharan Africa revealed a high proportion of WHO Watch antibiotics. Differences in Watch antibiotic use were found by disease syndrome, country and health facility location, which calls for a more differentiated approach to antibiotic use interventions including further evaluation of accessibility and affordability of patient treatment.

IntroductionNon-communicable diseases (NCDs), the leading cause of death globally, are estimated to overtake communicable diseases in sub-Sahara Africa, where healthcare workers (HCWs) play a crucial role in prevention and treatment, but are in extreme shortage, thereby increasing the burden of NCDs among this specific population. To provide evidence for policy-making, we assessed the NCD burden, associated factors and treatment among HCWs in four sub-Saharan African countries.Materials and methodsWe conducted a cross-sectional study across four sub-Saharan African countries [Côte d'Ivoire (CIV), Democratic Republic of the Congo (DRC), Madagascar (MDG), and Nigeria (NIG)] between February and December 2022. In a standardized questionnaire, sociodemographic, chronic disease and treatment data were self-reported. We estimated the prevalence of (1) at least one chronic disease, (2) hypertension, and used backward elimination logistic regression model to identify risk factors.ResultsWe recruited a total of 6,848 HCWs. The prevalence of at least one chronic disease ranged between 9.7% in NIG and 20.6% in MDG, the prevalence of hypertension between 5.4% in CIV and 11.3% in MDG. At most, reported treatment rates reached 36.5%. The odds of each of both outcomes increased with age (at least one chronic disease adjusted odds ratio: CIV: 1.04; DRC: 1.09; MDG: 1.06; NIG: 1.10; hypertension: CIV: 1.10; DRC: 1.31; MDG: 1.11; NIG: 1.11) and with BMI (at least one chronic disease: CIV: 1.10; DRC: 1.07; MDG: 1.06; NIG: 1.08; hypertension: CIV: 1.10; DRC: 1.66; MDG: 1.13; NIG: 1.07). Odds of both outcomes were lower among males, except in CIV. In NIG, the odds of both outcomes were higher among medical doctors and odds of hypertension were higher among those working in secondary care. In MDG, working in secondary care increased and working as auxiliary staff decreased the odds of at least one chronic disease.ConclusionThe prevalence of self-reported chronic disease varied across the four sub-Saharan countries with potentially very low treatment rates. We identified several individual (age, sex, and BMI) and occupational (profession, level of healthcare) factors that influence the odds of NCDs. These factors should be taken into account when developing interventions addressing the burden and management of NCDs among HCWs.

The rapid increase of OXA-244-producing Escherichia coli, predominantly driven by genetically clustered isolates of sequence type (ST)38, has been observed in at least nine European countries, including Germany. However, the reasons for the spread of OXA-244-producing E. coli remain unclear. Here, we aim to evaluate the possibility of prolonged carriage. We identified a total of six different patients with repeated detection of OXA-244-producing E. coli isolates, which were subjected to both short and long-read whole-genome sequencing (WGS). Besides allelic differences using core genome multilocus sequence typing (cgMLST) analyses, we obtained numbers of single-nucleotide polymorphisms (SNPs) to calculate individual base-pair substitution (BPS) rates. To assess possible re-exposure and risk factors for prolonged carriage, case interviews were conducted. The time between detections ranged from eleven months to more than three years. Initial isolates originated in three+ out of six cases from clinical samples, whereas remaining samples were from screening, mostly in the inpatient setting. As expected, cgMLST analyses showed low numbers of allelic differences between isolates of each case ranging from 1 to 4, whereas numbers of SNPs were between 2 and 99 (mean = 36), thus clearly highlighting the discrepancy between these different bacterial typing approaches. For five out of six cases, observed BPS rates suggest that patients can be colonized with OXA-244-producing E. coli, including ST38 cluster isolates, for extensively long times. Thus, we may have previously missed the epidemiological link between cases because exposure to OXA-244-producing E. coli could have occurred in a time frame, which has not been evaluated in previous investigations. Our results may help to guide future epidemiological investigations as well as to support the interpretation of genetic diversity of OXA-244-producing E. coli, particularly among ST38 cluster isolates.

Abstract Objective: The present study aims to develop and discuss an extension of hospital-acquired severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections (HA-SIs) definition which goes beyond the use of time parameters alone. Design: A confirmatory factor analysis was carried out to test a suitable definition for HA-SI. Setting and Patients: A two-center cohort study was carried out at two tertiary public hospitals in the German state of lower Saxony. The study involved a population of 366 laboratory-confirmed SARS-CoV-2-infected inpatients enrolled between March 2020 and August 2023. Results: The proposed model shows adequate fit indices (CFI.scaled = 0.959, RMSEA = 0.049). A descriptive comparison with existing classifications revealed strong features of our model, particularly its adaptability to specific regional outbreaks. Conclusion: The use of the regional incidence as a proxy variable to better define HA-SI cases represents a pragmatic and novel approach. The model aligns well with the latest scientific results in the literature. This work successfully unifies, within a single model, variables which the recent literature described as significant for the onset of HA-SI. Further potential improvements and adaptations of the model and its applications, such as automating the categorization process (in terms of hospital acquisition) or employing a comparable model for hospital-acquired influenza classification, are subjects open for discussion.

Objectives Healthcare workers (HCWs) are on the frontline of combating COVID-19, hence are at elevated risk of contracting an infection with SARS-CoV-2. The present study aims to measure the impact of SARS-CoV-2 on HCWs in central sub-Saharan Africa.Setting A cross-sectional serological study was conducted at six urban and five rural hospitals during the first pandemic wave in the South Kivu province, Democratic Republic of the Congo (DRC).Participants Serum specimens from 1029 HCWs employed during the first pandemic wave were collected between August and October 2020, and data on demographics and work-related factors were recorded during structured interviews.Primary and secondary outcome measures The presence of IgG antibodies against SARS-CoV-2 was examined by ELISA. Positive specimens were further tested using a micro-neutralisation assay. Factors driving SARS-CoV-2 seropositivity were assessed by multivariable analysis.Results Overall SARS-CoV-2 seroprevalence was high among HCWs (33.1%), and significantly higher in urban (41.5%) compared with rural (19.8%) hospitals. Having had presented with COVID-19-like symptoms before was a strong predictor of seropositivity (31.5%). Personal protective equipment (PPE, 88.1% and 11.9%) and alcohol-based hand sanitizer (71.1% and 28.9%) were more often available, and hand hygiene was more often reported after patient contact (63.0% and 37.0%) in urban compared with rural hospitals, respectively. This may suggest that higher exposure during non-work times in high incidence urban areas counteracts higher work protection levels of HCWs.Conclusions High SARS-CoV-2 seropositivity indicates widespread transmission of the virus in this region of DRC. Given the absence of publicly reported cases during the same time period at the rural sites, serological studies are very relevant in revealing infection dynamics especially in regions with low diagnostic capacities. This, and discrepancies in the application of PPE between urban and rural sites, should be considered in future pandemic response programmes.

Background: Antimicrobial Resistance (AMR) is one of the top ten global public health threats facing humanity, alongside climate change. Here, we aim to summarise the effects of climate change (i.e. raise of temperature, change in humidity or precipitation) on spread of antibiotic resistance and on infections with antibiotic-resistant bacteria in Germany. Methods: We conducted a literature search with articles published between January 2012 and July 2022. Two authors screened titles, abstracts and full texts and extracted the data systematically. Results: From originally 2,389 titles, we identified six studies, which met our inclusion criteria. These studies show that an increase in temperature may lead to higher antibiotic resistance rates and an increased risk of colonisation as well as spread of pathogens. Furthermore, the number of healthcare-associated infections increases with increased temperature. Data indicate that higher antibiotic use is present in areas with warmer mean temperature. Conclusions: European data are scarce, but all studies identified point towards an increasing AMR burden due to climate change. However, further studies are needed to draw attention to the links between climatic factors and AMR and develop targeted preventive measures.

Background: Hospital-acquired infections are a common source of sepsis. Hospital onset of sepsis was found to be associated with higher acute mortality and hospital costs, yet its impact on long-term patient-relevant outcomes and costs is unknown. Objective: We aimed to assess the association between sepsis origin and acute and long-term outcomes based on a nationwide population-based cohort of sepsis patients in Germany. Methods: This retrospective cohort study used nationwide health claims data from 23 million health insurance beneficiaries. Sepsis patients with hospital-acquired infections (HAI) were identified by ICD-10-codes in a cohort of adult patients with hospital-treated sepsis between 2013 and 2014. Cases without these ICD-10-codes were considered as sepsis cases with community-acquired infection (CAI) and were matched with HAI sepsis patients by propensity score matching. Outcomes included in-hospital/12-month mortality and costs, as well as readmissions and nursing care dependency until 12 months postsepsis. Results: We matched 33,110 HAI sepsis patients with 28,614 CAI sepsis patients and 22,234 HAI sepsis hospital survivors with 19,364 CAI sepsis hospital survivors. HAI sepsis patients had a higher hospital mortality than CAI sepsis patients (32.8% vs. 25.4%, RR 1.3, p

Antimicrobial resistance (AMR) and hospital-acquired infections (HAIs) are global health challenges. The burden of antibiotic resistance in HAIs is still unclear in low- and lower-middle-income countries (L-LMICs). This study summarizes recent data on antibiotic resistance in priority HAIs (ESKAPE-E) in L-LMICs and compares them with data from high-income countries (HICs). EMBASE, Web of Science, and Global Index Medicus were searched for studies on AMR patterns in HAIs published from 01/2010 to 10/2020. Random-effects meta-analyses were performed to obtain pooled estimates. In total, 163 eligible studies were included in the review and meta-analysis. The pooled methicillin resistance proportion in Staphylococcus aureus was 48.4% (95% confidence interval [95%CI] 41·7-55·2, n = 80). Pooled carbapenem resistance proportions were high in Gram-negative pathogens: Escherichia coli: 16·6% (95%CI 10·7-23·4, n = 60); Klebsiella pneumoniae: 34·9% (95%CI 24·6-45·9, n = 50); Pseudomonas aeruginosa: 37.1% (95%CI 24·6-45·9, n = 56); Enterobacter spp.: 51·2% (95%CI 27·5-74·7, n = 7); and Acinetobacter baumannii (complex): 72·4% (95%CI 62·1-81·7%, n = 36). A higher resistance proportions were observed for third-generation cephalosporins: Klebsiella pneumoniae: 78·7% (95%CI 71·5-85·2, n = 46); Escherichia coli: 78·5% (95%CI 72·1-84·2%, n = 58); and Enterobacter spp.: 83·5% (95%CI 71·9-92·8, n = 8). We observed a high between-study heterogeneity (I2 > 80%), which could not be explained by our set of moderators. Pooled resistance proportions for Gram-negative pathogens were higher in L-LMICs than regional and national estimates from HICs. Patients in resource-constrained regions are particularly affected by AMR. To combat the high resistance to critical antibiotics in L-LMICs, and bridge disparities in health, it is crucial to strengthen local surveillance and the health systems in general.

Abstract Background Blood culture diagnostics are critical tools for sepsis management and antimicrobial resistance (AMR) surveillance. A baseline study was conducted to assess reported sepsis case finding, blood culture diagnostics, antimicrobial susceptibility testing (AST) and antimicrobial use at secondary health care facilities to inform the development of diagnostic stewardship improvement strategies in Nigeria. Methods A cross-sectional online survey was conducted among 25 public secondary health care facilities in Abuja, Federal Capital Territory (FCT) and Lagos State in Nigeria to evaluate the capacity for pathogen identification and AST. Data were then prospectively extracted on all patients with reported suspected sepsis from electronic medical records from selected departments at two facilities in the Federal Capital Territory from October 2020 to May 2021 to further assess practices concerning sepsis case-finding, clinical examination findings, samples requested, and laboratory test results. Data were descriptively analysed, and a multivariate logistic regression analysis was conducted to determine factors associated with blood culture requests. Results In the online survey, 32% (8/25) of facilities reported performing blood cultures. Only one had access to a clinical microbiologist, and 28% (7/25) and 4% (1/25) used standard bacterial organisms for quality control of media and quality control strains for AST, respectively. At the two facilities where data abstraction was performed, the incidence of suspected sepsis cases reported was 7.1% (2924/41066). A majority of these patients came from the paediatrics department and were outpatients, and the median age was two years. Most did not have vital signs and major foci of infection documented. Blood cultures were only requested for 2.7% (80/2924) of patients, of which twelve were positive for bacteria, mainly Staphylococcus aureus. No clinical breakpoints were used for AST. Inpatients (adjusted odds ratio [aOR]: 7.5, 95% CI: 4.6–12.3) and patients from the urban health care facility (aOR:16.9, 95% CI: 8.1–41.4) were significantly more likely to have a blood culture requested. Conclusion Low blood culture utilisation remains a key challenge in Nigeria. This has implications for patient care, AMR surveillance and antibiotic use. Diagnostic stewardship strategies should focus on improving access to clinical microbiology expertise, practical guidance on sepsis case finding and improving blood culture utilisation and diagnostics.

Urinary tract infections (UTIs) are among the most common reasons patients seeking health care and antibiotics to be prescribed in primary care. However, general practitioners’ (GPs) guideline adherence is low. The RedAres randomised controlled trial aims to increase guideline adherence by implementing a multimodal intervention consisting of four elements: information on current UTI guidelines (1) and regional resistance data (2); feedback regarding prescribing behaviour (3); and benchmarking compared to peers (4). The RedAres process evaluation assesses GPs’ perception of the multimodal intervention and the potential for implementation into routine care. We carried out 19 semi-structured interviews with GPs (intervention arm). All interviews were carried out online and audio recorded. For transcription and analysis, Mayring’s qualitative content analysis was used. Overall, GPs considered the interventions helpful for knowledge gain and confirmation when prescribing. Information material and resistance were used for patient communication and teaching purposes. Feedback was considered to enhance reflection by breaking routines of clinical workup. Implementation into routine practice could be enhanced by integrating feedback loops into patient management systems and conveying targeted information via trusted channels or institutions. The process evaluation of RedAres intervention was considered beneficial by GPs. It confirms the convenience of multimodal interventions to enhance guideline adherence.

Abstract Background Since May 2016, infection and colonisation with carbapenem non-susceptible Acinetobacter spp. (CRA) and Enterobacterales (CRE) have to be notified to health authorities in Germany. The aim of our study was to assess the epidemiology of CRA and CRE from 2017 to 2019 in Germany, to identify risk groups and to determine geographical differences of CRA and CRE notifications. Methods Cases were notified from laboratories to local public health authorities and forwarded to state and national level. Non-susceptibility was defined as intermediate or resistant to ertapenem, imipenem, or meropenem excluding intrinsic bacterial resistance or the detection of a carbapenemase gene. We analysed CRA and CRE notifications from 2017, 2018 and 2019 per 100,000 inhabitants (notification incidence), regarding their demographic, clinical and laboratory information. The effect of regional hospital-density on CRA and CRE notification incidence was estimated using negative binomial regression. Results From 2017 to 2019, 2278 CRA and 12,282 CRE cases were notified in Germany. CRA and CRE cases did not differ regarding demographic and clinical information, e.g. proportion infected. The notification incidence of CRA declined slightly from 0.95 in 2017 to 0.86 in 2019, whereas CRE increased from 4.23 in 2017 to 5.72 in 2019. The highest CRA and CRE notification incidences were found in the age groups above 70 years. Infants below 1 year showed a high CRE notification incidence, too. Notification incidences varied between 0.10 and 2.86 for CRA and between 1.49 and 9.99 for CRE by federal state. The notification incidence of CRA and CRE cases increased with each additional hospital per district. Conclusion The notification incidence of CRA and CRE varied geographically and was correlated with the number of hospitals.The results support the assumption that hospitals are the main driver for higher CRE and CRA incidence. Preventive strategies and early control measures should target older age groups and newborns and areas with a high incidence.

Abstract Introduction The most frequent adverse events in healthcare are healthcare-associated infections, whose burden is highest in resource-limited settings. In addition, low resource settings often lack Hand Hygiene (HH) knowledge and reliable supply to disinfectant, a necessity emphasized by the past West African Ebola Epidemic and the ongoing COVID-19 pandemic. PASQUALE aims to increase patient safety by introducing the WHO multimodal HH strategy in the University Hospital Bouaké, Côte d’Ivoire. Methods Assessment of HH knowledge, perception and compliance was performed 12 months before, right after the intervention and at a ten months interval using questionnaires for knowledge and perception and direct observation for compliance. The intervention consisted of a HH training and the introduction of local production of alcohol-based hand-rub. In the absence of a control group, the effectiveness of the intervention was assessed by a before-and-after study. Results Baseline knowledge score was 14/25, increased significantly to 17/25 (p

Abstract Background SARS-CoV-2 cases in Germany increased in early March 2020. By April 2020, cases among health care workers (HCW) were detected across departments at a tertiary care hospital in Berlin, prompting a longitudinal investigation to assess HCW SARS-CoV-2 serostatus with an improved testing strategy and associated risk factors. Methods In May/June and December 2020, HCWs voluntarily provided blood for serology and nasopharyngeal/oropharyngeal (NP/OP) samples for real-time polymerase chain reaction (PCR) and completed a questionnaire. A four-tiered SARS-CoV-2 serological testing strategy including two different enzyme-linked immunosorbent assays (ELISA) and biological neutralization test (NT) was used. ELISA-NT correlation was assessed using Pearson’s correlation coefficient. Sociodemographic and occupational factors associated with seropositivity were assessed with multivariate logistic regression. Results In May/June, 18/1477 (1.2%) HCWs were SARS-CoV-2 seropositive, followed by 56/1223 (4.6%) in December. Among those tested in both, all seropositive in May/June remained seropositive by ELISA and positive by NT after 6 months. ELISA ratios correlated well with NT titres in May/June (R = 0.79) but less so in December (R = 0.41). Those seropositive reporting a past SARS-CoV-2 positive PCR result increased from 44.4% in May/June to 85.7% in December. HCWs with higher occupational risk (based on profession and working site), nurses, males, and those self-reporting COVID-19-like symptoms had significantly higher odds of seropositivity. Conclusions This investigation provides insight into the burden of HCW infection in this local outbreak context and the antibody dynamics over time with an improved robust testing strategy. It also highlights the continued need for effective infection control measures particularly among HCWs with higher occupational risk.

Abstract Background Urinary tract infections (UTIs) are a common cause of prescribing antibiotics in family medicine. In Germany, about 40% of UTI-related prescriptions are second-line antibiotics, which contributes to emerging resistance rates. To achieve a change in the prescribing behaviour among family physicians (FPs), this trial aims to implement the guideline recommendations in German family medicine. Methods/design In a randomized controlled trial, a multimodal intervention will be developed and tested in family practices in four regions across Germany. The intervention will consist of three elements: information on guideline recommendations, information on regional resistance and feedback of prescribing behaviour for FPs on a quarterly basis. The effect of the intervention will be compared to usual practice. The primary endpoint is the absolute difference in the mean of prescribing rates of second-line antibiotics among the intervention and the control group after 12 months. To detect a 10% absolute difference in the prescribing rate after one year, with a significance level of 5% and a power of 86%, a sample size of 57 practices per group will be needed. Assuming a dropout rate of 10%, an overall number of 128 practices will be required. The accompanying process evaluation will provide information on feasibility and acceptance of the intervention. Discussion If proven effective and feasible, the components of the intervention can improve adherence to antibiotic prescribing guidelines and contribute to antimicrobial stewardship in ambulatory care. Trial registration DRKS, DRKS00020389, Registered 30 January 2020, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00020389 .

Abstract Background In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease 2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa. Methods ANDEMIA includes 12 urban and rural health care facilities in four African countries (Côte d’Ivoire, Burkina Faso, Democratic Republic of the Congo and Republic of South Africa). It was piloted in 2018 in Côte d’Ivoire and the initial phase will run from 2019 to 2021. Case definitions for ARI, GI and AFDUC were established, as well as syndrome-specific sampling algorithms including the collection of blood, naso- and oropharyngeal swabs and stool. Samples are tested using comprehensive diagnostic protocols, ranging from classic bacteriology and antimicrobial resistance screening to multiplex real-time polymerase chain reaction (PCR) systems and High Throughput Sequencing. In March 2020, PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and analysis of full genomic information was included in the study. Standardised questionnaires collect relevant clinical, demographic, socio-economic and behavioural data for epidemiologic analyses. Controls are enrolled over a 12-month period for a nested case-control study. Data will be assessed descriptively and aetiologies will be evaluated using a latent class analysis among cases. Among cases and controls, an integrated analytic approach using logistic regression and Bayesian estimation will be employed to improve the assessment of aetiology and associated risk factors. Discussion ANDEMIA aims to expand our understanding of ARI, GI and AFDUC aetiologies in sub-Saharan Africa using a comprehensive laboratory diagnostics strategy. It will foster early detection of emerging threats and continued monitoring of important common pathogens. The network collaboration will be strengthened and site diagnostic capacities will be reinforced to improve quality management and patient care.

A population-based seroepidemiological and molecular survey on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was performed to detect induced antibodies to prior exposure and active infection of children aged 14 years or less in Tehran between 19 September 2020 and 21 June 2021. Moreover, correlations between the children’s demographic data and coronavirus disease 2019 (COVID-19) symptoms with the infection status were investigated. Out of 1517 participants, cardinal symptoms of COVID-19 (fever > 38 °C and/or cough and/or diarrhea) were detected in 18%, and serological history of SARS-CoV-2 infection and polymerase chain reaction (PCR) positivity were confirmed in 33.2% and 10.7% of the weighted population, respectively. The prevalence of SARS-CoV-2 infection was significantly higher among 10–14-year-old children. Active infection was significantly higher in symptomatic children and during autumn 2020 and spring 2021. The quantitative reverse transcription real-time PCR (RT-qPCR) positivity was significantly higher among families with a lower socioeconomic status, whereas no association between RT-qPCR or seropositivity was determined with household size, underlying diseases, or gender. In conclusion, high SARS-CoV-2 infection prevalence and seroprevalence were detected in children in Tehran in different seasons. Infection prevalence was significantly higher in older children and in those with a positive history of close contact with infected cases and/or lower socioeconomic status.

Abstract Background Carbapenem-resistant Acinetobacter baumannii complex (CRABC) has globally emerged as a serious public health challenge. This study aimed to describe epidemiological trends and risk factors of carbapenem resistance in A. baumannii complex isolates in Germany between 2014 and 2018. Methods We analysed 43,948 clinical A. baumannii complex isolates using 2014 to 2018 data from the German Antimicrobial Resistance Surveillance system. We applied descriptive statistics and uni- and multivariable regression analyses to investigate carbapenem resistance in A. baumannii complex isolates. Results The proportion of carbapenem resistance in clinical A. baumannii complex isolates declined from 7.6% (95% confidence interval [95% CI] 4.4–12.7%) in 2014 to 3.5% (95% CI 2.5–4.7%) in 2018 (adjusted OR [aOR] 0.85 [95% CI 0.79–0.93, p ≤ 0.001]). Higher mean CRABC proportions for 2014 to 2018 were observed in secondary care hospitals (4.9% [95% CI 3.2–7.5%], aOR 3.6 [95% CI 2.4–5.3, p ≤ 0.001]) and tertiary care hospitals (5.9% [95% CI 3.0–11.2%], aOR 5.4 [95% CI 2.9–10.0, p ≤ 0.001) compared to outpatient clinics (1.3% [95% CI 1.1–1.6%]). CRABC proportions in hospitals varied between German regions and ranged between 2.4% (95% CI 1.6–3.5%) in the Southeast and 8.8% (95% CI 4.2–17.3%) in the Northwest. Lower CRABC proportions were observed in younger patients (

A joint comparative regional analysis of different resistance combinations across human and veterinary medicine has not been previously conducted in Germany. This study analyses 16 resistance combinations from four antibiotics in E. coli from different human and food-producing animal populations in three German regions: East, North West and South West. The E. coli data were collected from the three national surveillance and monitoring systems for antimicrobial resistance (AMR) bacteria in humans (ARS), food-safety (Zoonosis Monitoring) and animal pathogens (GERM-Vet) from January 2014 to December 2017. Analyses were performed using cluster analysis (hierarchical clustering, average linkage) in R. We included data from 537,215 E. coli isolates from human clinical isolates, from clinical as well as non-clinical isolates from food-producing animals and from food. The majority of the data originated from the North West region. There were two main clusters built on 54 different human and animal populations. We observed close similarities of resistance combinations in human isolates from the different regions within the same human populations from outpatient cares, general wards and ICUs. These resistance combinations clustered separately from non-clinical isolates from broilers, turkeys, cattle and pigs; except for some of clinical isolates from these populations which clustered closely to isolates from human populations. Frequently, the resistance combinations in E. coli isolates from farms clustered closely to the resistance combinations in isolates from slaughterhouses from broilers and turkeys over all regions. However, the resistance combinations in E. coli isolates from retail meat populations tended to cluster separately within their respective populations in between all regions.

Abstract Background Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk clonal lineages. The K. pneumoniae sequence type (ST) 307 lineage has appeared in several different parts of the world after first being described in Europe in 2008. From June to October 2019, we recorded an outbreak of an extensively drug-resistant ST307 lineage in four medical facilities in north-eastern Germany. Methods Here, we investigated these isolates and those from subsequent cases in the same facilities. We performed whole-genome sequencing to study phylogenetics, microevolution, and plasmid transmission, as well as phenotypic experiments including growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance for an in-depth characterization of this outbreak clone. Results Phylogenetics suggest a homogenous phylogram with several sub-clades containing either isolates from only one patient or isolates originating from different patients, suggesting inter-patient transmission. We identified three large resistance plasmids, carrying either NDM-1, CTX-M-15, or OXA-48, which K. pneumoniae ST307 likely donated to other K. pneumoniae isolates of different STs and even other bacterial species (e.g., Enterobacter cloacae) within the clinical settings. Several chromosomally and plasmid-encoded, hypervirulence-associated virulence factors (e.g., yersiniabactin, metabolite transporter, aerobactin, and heavy metal resistance genes) were identified in addition. While growth, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance were comparable to several control strains, results from siderophore secretion and hypermucoviscosity experiments revealed superiority of the ST307 clone, similar to an archetypical, hypervirulent K. pneumoniae strain (hvKP1). Conclusions The combination of extensive drug resistance and virulence, partly conferred through a “mosaic” plasmid carrying both antibiotic resistance and hypervirulence-associated features, demonstrates serious public health implications.

Abstract Background Due to limited therapeutic options and their association with high mortality and morbidity, carbapenem-non-susceptible Acinetobacter spp. (CNA) are of significant public health importance. This study aimed to describe current epidemiological trends of CNA proportions in Europe and to identify factors that are associated with carbapenem non-susceptibility of isolates from patients with invasive Acinetobacter spp. infections. Methods Data from routine carbapenem susceptibility testing of 18,412 invasive clinical Acinetobacter spp. isolates from 30 European countries in 2013–2017 were analysed using descriptive statistical analyses and uni- and multivariable regression analyses. These data were obtained from the European Antimicrobial Resistance Surveillance Network (EARS-Net). Results The population-weighted mean proportion of carbapenem-non-susceptible Acinetobacter spp. in Europe is 35.6% (95% confidence interval [CI] 29.7–42.0%). With CNA proportions of 75.5% (95% CI 71.2–79.4%) and 71.5% (95% CI 66.7–75.9%) the burden of CNA is particularly high in Southern and Eastern European regions. In contrast, Northern and Western European regions recorded CNA proportions of 2.8% (95% CI 1.2–6.0%) and 6.3% (95% CI 4.5–8.9%), respectively. Population-weighted mean CNA proportions are especially high in Acinetobacter spp. isolates from intensive care units (54.0% [95% CI 47.6–60.3%]). Male gender, age above 20 years and ICU admission were identified as independent factors associated with an increased likelihood of CNA. Conclusion The burden of carbapenem-non-susceptible Acinetobacter spp. is particularly high in Southern and Eastern Europe. There is a risk that resistance could spread to other parts of Europe. Therefore, increased efforts in infection control and antibiotic stewardship, particularly in Intensive Care Units, are necessary to combat the spread of CNA in Europe.

ABSTRACTVancomycin-resistant enterococci infections are of great public health significance due to limited therapeutic options. We investigated epidemiological trends and risk factors of vancomycin resistance in enterococci isolates from patients with bloodstream infections in the EU/EEA from 2012 to 2018. Routine vancomycin susceptibility data of clinical E. faecium (n = 67,022) and E. faecalis (n = 103,112) blood isolates from the European Antimicrobial Resistance Surveillance Network were analysed using descriptive statistics and multivariable regression analyses. In Europe, proportions of vancomycin-resistant E. faecium (VREFm) increased from 8.1% (95%CI 6.7–9.7%) in 2012 to 19.0% (95%CI 16.8–21.5%) in 2018. Rising VREFm proportions were observed across all European regions, both genders and all age groups except children and adolescents (1–19 years). Adults (20–59 years) and elderly (≥60 years) had an increased likelihood of VREFm compared to children and adolescents (1–19 years) (OR: 1.99 [95%CI 1.42–2.79, p

Summary: Background: Outbreaks of coronavirus disease (COVID-19) in hospitals and long-term care facilities (LTCFs) pose serious public health threats. We analysed how frequency and size of SARS-CoV-2 outbreaks in hospitals and LTCFs have altered since the beginning of the pandemic, in particular since the start of the vaccination campaign. Methods: We used mandatory notification data on SARS-CoV-2 cases in Germany and stratified by outbreak cases in hospitals and LTCFs. German vaccination coverage data were analysed. We studied the association of the occurrence of SARS-CoV-2 outbreaks and outbreak cases with SARS-CoV-2 cases in Germany throughout the four pandemic waves. We built also counterfactual scenarios with the first pandemic wave as the baseline. Findings: By 21 September 2021, there were 4,147,387 SARS-CoV-2 notified cases since March 2020. About 20% of these cases were reported as being related to an outbreak, with 1% of the cases in hospitals and 4% in LTCFs. The median number of outbreak cases in the different phases was smaller (≤5) in hospitals than in LTCFs (>10). In the first and second pandemic waves, we observed strong associations in both facility types between SARS-CoV-2 outbreak cases and total number of notified SARS-CoV-2 cases. However, during the third pandemic wave we observed a decline in outbreak cases in both facility types and only a weak association between outbreak cases and all cases. Interpretation: The vaccination campaign and non-pharmaceutical interventions have been able to protect vulnerable risk groups in hospitals and LTCFs. Funding: No specific funding

In Germany, there is an increasing amount of vancomycin-resistant Enterococcus faecium (VREfm) isolates in bloodstream infections (BSIs); however, estimates on recent incidences and disease burden are missing. We aim to estimate the incidence and calculate the annual disease burden in disease-adjusted life years (DALYs) for BSIs due to VREfm in Germany between 2015 and 2020 to support informed decision-making in the field of antimicrobial resistance (AMR). We used the Antibiotic Resistance Surveillance (ARS) system data to obtain incidence estimates. The estimated incidences were used in the Burden of Communicable Disease in Europe (BCoDE) toolkit to calculate the attributable DALYs. A total of 3417 VREfm blood culture-positive isolates were observed within ARS. The estimated incidence of VREfm-BSIs per 100,000 inhabitants increased from 1.4 (95% Uncertainty Interval [UI]: 0.8–1.9) in 2015 to 2.9 (95% UI: 2.4–3.3) in 2020. The estimated burden, expressed in DALYs per 100,000 inhabitants, increased from 8.5 (95% UI: 7.3–9.7; YLD = 0.9, YLL = 7.6) in 2015 to 15.6 (95% UI: 14.6–16.6; YLD = 1.6, YLL = 14) in 2020. The most affected groups within the observed period are the 65–69-year-old males with 262.9 DALYs per 100,000 inhabitants, and in the younger age groups (

Two COVID-19 outbreaks occurred in residential buildings with overcrowded housing conditions in the city of Göttingen in Germany during May and June 2020, when COVID-19 infection incidences were low across the rest of the country, with a national incidence of 2.6/100,000 population. The outbreaks increased the local incidence in the city of Göttingen to 123.5/100,000 in June 2020. Many of the affected residents were living in precarious conditions and experienced language barriers. The outbreaks were characterized by high case numbers and attack rates among the residents, many asymptomatic cases, a comparatively young population, and substantial outbreak control measures implemented by local authorities. We analyzed national and local surveillance data, calculated age-, and gender-specific attack rates and performed whole genome sequencing analysis to describe the outbreak and characteristics of the infected population. The authorities' infection control measures included voluntary and compulsory testing of all residents and mass quarantine. Public health measures, such as the general closure of schools and a public space as well as the prohibition of team sports at local level, were also implemented in the district to limit the outbreaks locally. The outbreaks were under control by the end of June 2020. We describe the measures to contain the outbreaks, the challenges experienced and lessons learned. We discuss how public health measures can be planned and implemented through consideration of the needs and vulnerabilities of affected populations. In order to avoid coercive measures, barrier-free communication, with language translation when needed, and consideration of socio-economic circumstances of affected populations are crucial for controlling infectious disease transmission in an outbreak effectively and in a timely way.

Abstract Background Due to limited therapeutic options, vancomycin-resistant Enterococcus faecium (VREF) is of great clinical significance. Recently, rising proportions of vancomycin resistance in enterococcal infections have been reported worldwide. This study aims to describe current epidemiological trends of VREF in German hospitals and to identify factors that are associated with an increased likelihood of vancomycin resistance in clinical E. faecium isolates. Methods 2012 to 2017 data from routine vancomycin susceptibility testing of 35,906 clinical E. faecium isolates from 148 hospitals were analysed using data from the German Antimicrobial Resistance Surveillance System. Descriptive statistical analyses and uni- and multivariable regression analyses were performed to investigate the impact of variables, such as year of sampling, age and region, on vancomycin resistance in clinical E. faecium isolates. Results From 2014 onwards the proportions of clinical E. faecium isolates exhibiting resistance to vancomycin increased from 11.2% (95% confidence interval [CI] 9.4–13.3%) to 26.1% (95% CI 23.1–29.4%) in 2017. The rise of VREF proportions is primarily observed in the southern regions of Germany, whereas northern regions do not show a major increase. In the Southwest and Southeast, VREF proportions increased from 10.8% (95% CI 6.9–16.5%) and 3.8% (95% CI 3.0–11.5%) in 2014 to 36.7% (95% CI 32.9–40.8%) and 36.8% (95% CI 29.2–44.7%) in 2017, respectively. VREF proportions were considerably higher in isolates from patients aged 40–59 years compared to younger patients. Further regression analyses show that in relation to secondary care hospitals, E. faecium samples collected in specialist care hospitals and prevention and rehabilitation care centres are more likely to be vancomycin-resistant (odds ratios: 2.4 [95% CI 1.2–4.6] and 2.4 [95% CI 1.9–3.0], respectively). No differences in VREF proportions were found between female and male patients as well as between different clinical specimens. Conclusion The proportion of VREF is increasing in German hospitals, particularly in southern regions in Germany. Increased efforts in infection control and antibiotic stewardship activities accounting for local resistance patterns are necessary to combat the spread of VREF in Germany.

ABSTRACTDue to therapeutic challenges, hospital-acquired infections (HAIs) caused by Acinetobacter baumannii (HA-AB), particularly carbapenem-resistant strains (HA-CRAB) pose a serious health threat to patients worldwide. This systematic review sought to summarize recent data on the incidence and prevalence of HA-AB and HA-CRAB infections in the WHO-defined regions of Europe (EUR), Eastern Mediterranean (EMR) and Africa (AFR). A comprehensive literature search was performed using MEDLINE, EMBASE and GMI databases (01/2014-02/2019). Random-effects meta-analyses were performed to determine the pooled incidence of HA-AB and HA-CRAB infections as well as the proportions of A. baumannii among all HAIs. 24 studies from 3,340 records were included in this review (EUR: 16, EMR: 6, AFR: 2). The pooled estimates of incidence and incidence density of HA-AB infection in intensive care units (ICUs) were 56.5 (95% CI 33.9-92.8) cases per 1,000 patients and 4.4 (95% CI 2.9-6.6) cases per 1,000 patient days, respectively. Five studies conducted at a hospital-wide level or in specialized clinical departments/wards (ICU + non-ICU patients) showed HA-AB incidences between 0.85 and 5.6 cases per 1,000 patients. For carbapenem-resistant A. baumannii infections in ICUs, the pooled incidence and incidence density were 41.7 (95% CI 21.6-78.7) cases per 1,000 patients and 2.1 (95% CI 1.2-3.7) cases per 1,000 patient days, respectively. In ICUs, A. baumannii and carbapenem-resistant A. baumannii strains accounted for 20.9% (95% CI 16.5-26.2%) and 13.6% (95% CI 9.7-18.7%) of all HAIs, respectively. Our study highlights the persistent clinical significance of hospital-acquired A. baumannii infections in the studied WHO regions, particularly in ICUs.

Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015–November 2019). We used descriptive epidemiology and whole-genome sequencing (WGS) for a detailed outbreak investigation. Of the 2905 cases, 2776 (95.3%) were colonized, whereas from 127 (3.7%), VRE could be isolated from otherwise sterile body fluids or sites unlikely for enterococci colonization. Cases had a median age of 78 years (IQR 68–84) and 1339/2905 (46%) were female. The majority of isolates sequenced belonged to the clonal lineage ST80/CT1013 (212/397, 53%). Nosocomial transmission was observed as well as the constant import of VRE into the hospital. Extensive IPC measures were implemented and terminated the outbreak in late 2019, eventually. Our study shows that the combination of epidemiological and genomic analyses is indispensable for comprehensive outbreak investigations. The adaptation of IPC measures to these findings, their timely implementation, and strict execution also allow containment of large VRE outbreaks in hospital settings.

Data on microbiological profiles in odontogenic infections are scarce. This study aimed to analyze the spectrum of pathogens and antimicrobial resistance in clinical isolates from dental and oral-maxillofacial clinical settings in Germany. We analyzed 20,645 clinical isolates (dental practices: n = 5,733; hospitals: n = 14,912) from patients with odontogenic infections using data (2012–2019) from the German Antimicrobial-Resistance-Surveillance (ARS) system. A total of 224 different species from 73 genera were found in clinical isolates from dental practices, and 329 different species from 97 genera were identified in isolates from hospital patients. In both hospitals and dental practices Streptococcus spp. (33 and 36%, respectively) and Staphylococcus spp. (21 and 12%, respectively) were the most frequently isolated microorganisms. In Streptococcus spp. isolates from hospitals, penicillin and aminopenicillin resistance proportions were 8.0% (95%CI 4.7–14.9%) and 6.9% (95%CI 4.7–9.9%), respectively. Substantially lower resistance proportions of penicillin and aminopenicillin were observed in dental practices [2.6% (95%CI 1.4–4.7%) and 2.1% (95%CI 1.1–4.0%), respectively]. Among Staphylococcus aureus isolates from hospital patients methicillin resistance proportions were 12.0% (95%CI 9.7–14.8%), which was higher than in isolates from dental practices (5.8% (95%CI 4.1–8.1%)]. High clindamycin and macrolide resistance proportions (>17%) were observed in Streptococcus spp. and Staphylococcus aureus isolates. In Klebsiella spp. isolates carbapenem resistance proportions were

Background: Blood cultures (BC) have a high clinical relevance and are a priority specimen for surveillance of antimicrobial resistance. Manual BC are still most frequently used in resource-limited settings. Data on automated BC performance in Africa are scarce. We implemented automated BC at a surveillance site of the African Network for improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA).Methods: Between June 2017 and January 2018, pairs of automated BC (BacT/ALERT®FA Plus) and manual BC (brain-heart infusion broth) were compared at a University hospital in Bouaké, Côte d'Ivoire. BC were inoculated each with a target blood volume of 10 ml from the same venipuncture. Automated BC were incubated for up to 5 days, manual BC for up to 10 days. Terminal subcultures were performed for manual BC only. The two systems were compared regarding yield, contamination, and turnaround time. For quality assurance, isolates were retested in a German routine microbiological laboratory.Results: BC sampling was increased from on average 24 BC to 63 BC per month. A total of 337 matched pairs of BC were included. Automated BC was positive in 36.5%, manual BC in 24.0% (p-value < 0.01), proportion of contamination was 47.9 and 43.8%, respectively (p-value = 1.0). Turnaround time of positive BC was shortened by 2.5 days with automated compared to manual BC (p < 0.01). Most common detected pathogens in both systems were Klebsiella spp. (26.0%) and Staphylococcus aureus (18.2%). Most contaminants were members of the skin flora. Retesting of 162 isolates was concordant in 79.6% on family level.Conclusions: Implementing automated BC in a resource-limited setting is possible and improves microbiological diagnostic performance. Automated BC increased yield and shortened turnaround times. Regular training and mentorship of clinicians has to be intensified to increase number and quality of BC. Pre-analytical training to improve diagnostic stewardship is essential when implementing a new microbiological method. Retesting highlighted that manual identification and antimicrobial susceptibility testing can be of good quality and sustainable. The implementation of automated tools should be decided individually according to economic considerations, number of samples, stable supply chain of consumables, and technical sustainability.

Vancomycin-resistant Enterococcus faecium (VREF) and methicillin-resistant Staphylococcus aureus (MRSA) are associated with significant health burden. We investigated linezolid and daptomycin resistance among VREF and MRSA in the EU/EEA between 2014 and 2018. Descriptive statistics and multivariable logistic regression were used to analyze 6,949 VREF and 35,131 MRSA blood isolates from patients with bloodstream infection. The population-weighted mean proportion of linezolid resistance in VREF and MRSA between 2014 and 2018 was 1.6% (95% CI 1.33–2.03%) and 0.28% (95% CI 0.32–0.38%), respectively. Daptomycin resistance in MRSA isolates was similarly low [1.1% (95% CI 0.75–1.6%)]. On the European level, there was no temporal change of daptomycin and linezolid resistance in MRSA and VREF. Multivariable regression analyses showed that there was a higher likelihood of linezolid and daptomycin resistance in MRSA (aOR: 2.74, p < 0.001; aOR: 2.25, p < 0.001) and linezolid in VREF (aOR: 1.99, p < 0.001) compared to their sensitive isolates. The low proportion of linezolid and daptomycin resistance in VREF and MRSA suggests that these last-resort antibiotics remain effective and will continue to play an important role in the clinical management of these infections in Europe. However, regional and national efforts to contain antimicrobial resistance should continue to monitor the trend through strengthened surveillance that includes genomic surveillance for early warning and action.

Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics-ampicillin, cefotaxime, ciprofloxacin and gentamicin-for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.

Abstract Objective This systematic review focusses on the prognostic accuracy of neonatal body surface screening during outbreaks caused by Gram-negative bacteria for prediction of sepsis. In a previous systematic review we reported that only limited evidence of very low quality exists regarding the predictive value of this screening under routine conditions. We aimed to investigate whether this is different in outbreak settings. Results We identified five studies performed during outbreaks in three countries, comprising a total of 316 infants. All studies were at high risk of bias. In outbreak settings, pooled sensitivity of body surface screening to predict sepsis was 98% (95 CI 60 to 100%), while pooled specificity was 26% (95% CI 0.5 to 96%). Evidence quality was low for all outcomes. Extending a previously published systematic review, we show here that in contrast to routine settings sensitivity of body surface screening for sepsis prediction is very high, while specificity is still insufficient. Surface screening appears to be a useful component of bundles of interventions used during outbreaks, but the evidence base is still limited. PROSPERO Registration Number: CRD42016036664.

Abstract Background Carbapenem resistance in Klebsiella pneumoniae is of significant public health concern and recently spread across several countries. We investigated the extent of carbapenem non-susceptibility in K. pneumoniae isolates in Germany. Methods We analysed 2011–2016 data from the German Antimicrobial Resistance Surveillance (ARS) System, which contains routine data of antimicrobial susceptibility testing from voluntarily participating German laboratories. Klebsiella pneumoniae isolates tested resistant or intermediate against an antibiotic were classified as non-susceptible. Results We included 154,734 isolates from 655 hospitals in the analysis. Carbapenem non-susceptibility in K. pneumoniae isolates was low in Germany 0.63% (95% CI 0.51–0.76%). However, in continuously participating hospitals the number of K. pneumoniae isolates almost doubled and we found evidence for a slowly increasing trend for non-susceptibility (OR = 1.20 per year, 95% CI 1.09–1.33, p

Antimicrobial resistance (AMR) data from humans are mostly collected from clinical isolates, whereas from livestock data also exist from colonizing pathogens. In Germany, livestock data are collected from clinical and nonclinical isolates. We compared resistance levels of clinical and nonclinical isolates of Escherichia coli from weaning and fattening pigs with clinical outpatient isolates of humans from urban and rural areas. We also studied the association of AMR with available antimicrobial use (AMU) data from humans and pigs. Differences between rural and urban isolates were minor and did not affect the comparison between human and pig isolates. We found higher resistance levels to most antimicrobials in human isolates compared to nonclinical isolates of fattening pigs. Resistance to ampicillin, however, was significantly more frequent in clinical isolates of fattening pigs and in clinical and nonclinical isolates of weaning pigs compared to isolates from humans. The opposite was observed for ciprofloxacin. Co-trimoxazole resistance proportions were higher in clinical isolates of weaning and fattening pigs as compared to isolates from humans. Resistance proportions were higher in clinical isolates than in nonclinical isolates from pigs of the same age group and were also higher in weaner than in fattening pigs. Significant associations of AMU and AMR were found for gentamicin resistance and aminoglycoside use in humans (borderline) and for ampicillin resistance in clinical isolates and penicillin use in fattening pigs. In summary, we found significant differences between isolates from all populations, requiring more detailed analyses supported by molecular data and better harmonized data on AMU and AMR.

Summary: The development of an educational concept of a training programme for infection prevention and control (IPC) was seen as a key issue to successfully address the complexity of change processes of professional IPC routines in clinical procedures. Therefore, the Nigeria Centre for Disease Control (NCDC), Nigeria, and the Robert Koch Institute (RKI), Germany established an interdisciplinary project framework, involving knowledge and competences from different disciplines and professions like health professionals, epidemiologists and educators (MAURICE project). A multi-module training programme for health care workers to improve IPC standards was developed and implemented based on the participatory approach and a systemic view for organizational change. Keywords: Nigeria, Infection prevention and control (IPC), Training programme, Participatory approach, Systemic view, Inter- and transdisciplinary approach

Data from surveillance networks show that men have a higher incidence rate of infections with anti-microbial-resistant (AMR) pathogens than women. We systematically analysed data of infections and colonisations with AMR pathogens under mandatory surveillance in Germany to quantify gender-specific differences. We calculated incidence-rates (IR) per 100,000 person–years for invasive infections with Methicillin-resistant Staphylococcus aureus (MRSA), and for infections or colonisations with carbapenem-non-susceptible Acinetobacter spp. (CRA), and Enterobacterales (CRE), using the entire German population as a denominator. We limited the study periods to years with complete notification data (MRSA: 2010–2019, CRA/CRE: 2017–2019). We used Poisson regression to adjust for gender, age group, federal state, and year of notification. In the study periods, IR for all notifications were 4.2 for MRSA, 0.90 for CRA, and 4.8 for CRE per 100,000 person-–years. The adjusted IR ratio for infections of men compared to women was 2.3 (95% confidence interval [CI]: 2.2–2.3) for MRSA, 2.2 (95%CI: 1.9–2.7) for CRA, and 1.7 (95%CI: 1.6–1.8) for CRE. Men in Germany show about double the risk for infection with AMR pathogens than women. This was also true for colonisations, where data were available. Screening procedures and associated hygiene measures may profit from a gender-stratified approach.