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Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum β-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited. Therefore, we collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and ten (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1– V2 gene sequencing.We included 48 samples in the SSG (n=16 horses), 45 in the 5DG (n=15) and 20 in the CG (n=10). Two samples (6.5%) were positive for ESBL-producing Enterobacterales at t0while this rate increased to 67% at t1and decreased only slightly at t2(61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing that horses suffering from acute colic seemed to have a compromised fecal microbiota composition (5DG, SDImeanof 5.90; SSG, SDImeanof 6.17) when compared to the CG (SDImeanof 6.53) at t0, although the difference lacked significance. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2the onset of microbiome recovery was noticed. Although we did not identify a significant SDImeandifference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance ofEnterobacteriaceae,especiallyEscherichia, was noted for both study groups at t1. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.

After having affected the population for two years, the COVID-19 pandemic has reached a phase where a considerable number of people in Germany have been either infected with a SARS-CoV-2 variant, vaccinated, or both. Yet the full extent to which the population has been in contact with either virus or vaccine remains elusive, particularly on a regional level, because (a) infection counts suffer from under-reporting, and (b) the overlap between the vaccinated and recovered subpopulations is unknown. Since previous infection, vaccination, or especially a combination of both reduce the risk of severe disease, a high share of individuals with SARS-CoV-2 immunity lowers the probability of severe outbreaks that could potentially overburden the public health system once again, given that emerging variants do not escape this reduction in susceptibility. Here, we estimate the share of immunologically naïve individuals by age group for each of the 16 German federal states by integrating an infectious disease model based on weekly incidences of SARS-CoV-2 infections in the national surveillance system and vaccine uptake, as well as assumptions regarding under-ascertainment. We estimate a median share of 7.0% of individuals in the German population have neither been in contact with vaccine nor any variant as of March 31, 2022 (quartile range [3.6%– 9.8%]). For the adult population at higher risk of severe disease, this figure is reduced to 3.5% [1.3%–5.5%] for ages 18–59 and 4.3% [2.7%–5.8%] for ages 60 and above. However, estimates vary between German states mostly due to heterogeneous vaccine uptake. Excluding Omicron infections from the analysis, 16.1% [14.0%–17.8%] of the population in Germany, across all ages, are estimated to be immunologically naïve, highlighting the large impact the Omicron wave had until the beginning of spring in 2022.

ObjectiveThe emergence of coronavirus disease 2019 (COVID-19) required countries to establish COVID-19 surveillance by adapting existing systems, such as mandatory notification and syndromic surveillance systems. We estimated age-specific COVID-19 hospitalization and intensive care unit (ICU) burden from existing severe acute respiratory infections (SARI) surveillance and compared the results to COVID-19 notification data.MethodsUsing data on SARI cases with ICD-10 diagnosis codes for COVID-19 (COVID-SARI) from the ICD-10 based SARI sentinel, we estimated age-specific incidences for COVID-SARI hospitalization and ICU for the first five COVID-19 waves in Germany and compared these to incidences from notification data on COVID-19 cases using relative change Δrat the peak of each wave.FindingsThe COVID-SARI incidence from sentinel data matched the notified COVID-19 hospitalization incidence in the first wave with Δr=6% but was higher during second to fourth wave (Δr=20% to 39%). In the fifth wave, the COVID-SARI incidence was lower than the notified COVID-19 hospitalization incidence (Δr=-39%). For all waves and all age groups, the ICU incidence estimated from COVID-SARI was more than twice the estimation from notification data.ConclusionThe use of validated SARI sentinel data adds robust and important information for assessing the true disease burden of severe COVID-19. Mandatory notifications of COVID-19 for hospital and ICU admission may underestimate (work overload in local health authorities) or overestimate (hospital admission for other reasons than the laboratory-confirmed SARS-CoV-2 infection) disease burden. Syndromic ICD-10 based SARI surveillance enables sustainable cross-pathogen surveillance for seasonal epidemics and pandemic preparedness of respiratory viral diseases.

BackgroundWhereas the majority of children under 6 years of age attend daycare centers in Germany, evidence on the role of daycare centers in the transmission of SARS-CoV-2 is scarce.AimsThis study aims to investigate the transmission risk in daycare centers among children and staff and the spread of infections to associated households.Methods30 daycare groups with at least one recent laboratory-confirmed SARS-CoV-2 case (child or staff) were enrolled in the study (10/2020-06/2021). Close contacts within the daycare group and households were examined over a 12-day period (repeated SARS-CoV-2 PCR tests, genetic sequencing of viruses, documentation of symptoms). Households, local health authorities and daycare staff were interviewed to gain comprehensive information on each outbreak. We determined primary cases for all daycare groups.ResultsThe number of secondary cases varied considerably between daycare groups. The pooled secondary attack rate (SAR) across all 30 daycare centers was 9.6%. The SAR tended to be higher in daycare centers in which the Alpha variant of the virus was detected (15.9% vs. 5.1% with evidence of wild type). The SAR in households was 53.3%. Exposed children were less likely to get infected with SARS-CoV-2 in daycare centers, compared to adults (7.7% vs. 15.5%).ConclusionContainment measures in daycare programs are critical and become increasingly important with highly transmissible new variants to reduce SARS-CoV-2 transmission, especially to avoid spread to associated households. Virus variants may modify transmission dynamics in daycare programs.

The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species’ guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer-based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada.We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dnaE, rpoB, ftsX or pycB play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.