Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia.

Introduction: Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum ß-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. Methods: 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 10 (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1-V2 gene sequencing. Results: We included 48 samples in the SSG (n = 16 horses), 45 in the 5DG (n = 15), and 20 in the CG (for t0 and t1, n = 10). Two samples of equine patients receiving antibiotic prophylaxis (6.5%) were positive for ESBL-producing Enterobacterales at t0, while this rate increased to 67% at t1 and decreased only slightly at t2 (61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing there was no significant difference between horses suffering from acute colic (5DG, SDImean of 5.90, SSG, SDImean of 6.17) when compared to the CG (SDImean of 6.53) at t0. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2 the onset of microbiome recovery was noticed. Although we did not identify a significant SDImean difference 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 of Enterobacteriaceae, especially Escherichia, was noted for both study groups at t1. Conclusion: Colic surgery and PAP drive the equine gut microbiome towards dysbiosis and reduced biodiversity that is accompanied by an increase of samples positive for ESBL-producing Enterobacterales. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.

Three years into the pandemic: results of the longitudinal German COPSY study on youth mental health and health-related quality of life.

Purpose: For the past three years, the German longitudinal COPSY (COVID-19 and PSYchological Health) study has monitored changes in health-related quality of life (HRQoL) and the mental health of children and adolescents during the COVID-19 pandemic. Methods: A nationwide, population-based survey was conducted in May-June 2020 (W1), December 2020-January 2021 (W2), September-October 2021 (W3), February 2022 (W4), and September-October 2022 (W5). In total, n = 2,471 children and adolescents aged 7-17 years (n = 1,673 aged 11-17 years with self-reports) were assessed using internationally established and validated measures of HRQoL (KIDSCREEN-10), mental health problems (SDQ), anxiety (SCARED), depressive symptoms (CES-DC, PHQ-2), psychosomatic complaints (HBSC-SCL), and fear about the future (DFS-K). Findings were compared to prepandemic population-based data. Results: While the prevalence of low HRQoL increased from 15% prepandemic to 48% at W2, it improved to 27% at W5. Similarly, overall mental health problems rose from 18% prepandemic to W1 through W2 (30-31%), and since then slowly declined (W3: 27%, W4: 29%, W5: 23%). Anxiety doubled from 15% prepandemic to 30% in W2 and declined to 25% (W5) since then. Depressive symptoms increased from 15%/10% (CES-DC/PHQ-2) prepandemic to 24%/15% in W2, and slowly decreased to 14%/9% in W5. Psychosomatic complaints are across all waves still on the rise. 32-44% of the youth expressed fears related to other current crises. Conclusion: Mental health of the youth improved in year 3 of the pandemic, but is still lower than before the pandemic.

Establishing Infodemic Management in Germany: A Framework for Social Listening and Integrated Analysis to Report Infodemic Insights at the National Public Health Institute.

BACKGROUND: To respond to the need to establish infodemic management functions at the national public health institute in Germany (Robert Koch Institute, RKI), we explored and assessed available data sources, developed a social listening and integrated analysis framework, and defined when infodemic management functions should be activated during emergencies. OBJECTIVE: We aimed to establish a framework for social listening and integrated analysis for public health in the German context using international examples and technical guidance documents for infodemic management. METHODS: This study completed the following objectives: identified (potentially) available data sources for social listening and integrated analysis; assessed these data sources for their suitability and usefulness for integrated analysis in addition to an assessment of their risk using the RKI's standardized data protection requirements; developed a framework and workflow to combine social listening and integrated analysis to report back actionable infodemic insights for public health communications by the RKI and stakeholders; and defined criteria for activating integrated analysis structures in the context of a specific health event or health emergency. RESULTS: We included and classified 38% (16/42) of the identified and assessed data sources for social listening and integrated analysis at the RKI into 3 categories: social media and web-based listening data, RKI-specific data, and infodemic insights. Most data sources can be analyzed weekly to detect current trends and narratives and to inform a timely response by reporting insights that include a risk assessment and scalar judgments of different narratives and themes. CONCLUSIONS: This study identified, assessed, and prioritized a wide range of data sources for social listening and integrated analysis to report actionable infodemic insights, ensuring a valuable first step in establishing and operationalizing infodemic management at the RKI. This case study also serves as a roadmap for others. Ultimately, once operational, these activities will inform better and targeted public health communication at the RKI and beyond.

An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective.

The SARS-CoV-2 pandemic has highlighted the importance of viable infection surveillance and the relevant infrastructure. From a German perspective, an integral part of this infrastructure, genomic pathogen sequencing, was at best fragmentary and stretched to its limits due to the lack or inefficient use of equipment, human resources, data management and coordination. The experience in other countries has shown that the rate of sequenced positive samples and linkage of genomic and epidemiological data (person, place, time) represent important factors for a successful application of genomic pathogen surveillance. Planning, establishing and consistently supporting adequate structures for genomic pathogen surveillance will be crucial to identify and combat future pandemics as well as other challenges in infectious diseases such as multi-drug resistant bacteria and healthcare-associated infections. Therefore, the authors propose a multifaceted and coordinated process for the definition of procedural, legal and technical standards for comprehensive genomic pathogen surveillance in Germany, covering the areas of genomic sequencing, data collection and data linkage, as well as target pathogens. A comparative analysis of the structures established in Germany and in other countries is applied. This proposal aims to better tackle epi- and pandemics to come and take action from the "lessons learned" from the SARS-CoV-2 pandemic.

[Application areas of artificial intelligence in the context of One Health with a focus on antimicrobial resistance]. / Anwendungsbereiche von künstlicher Intelligenz im Kontext von One Health mit Fokus auf antimikrobielle Resistenzen.

Societal health is facing a number of new challenges, largely driven by ongoing climate change, demographic ageing, and globalization. The One Health approach links human, animal, and environmental sectors with the goal of achieving a holistic understanding of health in general. To implement this approach, diverse and heterogeneous data streams and types must be combined and analyzed. To this end, artificial intelligence (AI) techniques offer new opportunities for cross-sectoral assessment of current and future health threats. Using the example of antimicrobial resistance as a global threat in the One Health context, we demonstrate potential applications and challenges of AI techniques.This article provides an overview of different applications of AI techniques in the context of One Health and highlights their challenges. Using the spread of antimicrobial resistance (AMR), an increasing global threat, as an example, existing and future AI-based approaches to AMR containment and prevention are described. These range from novel drug development and personalized therapy, to targeted monitoring of antibiotic use in livestock and agriculture, to comprehensive environmental surveillance.

Genome-wide association reveals host-specific genomic traits in Escherichia coli.

BACKGROUND: Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. RESULTS: We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. CONCLUSIONS: This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.

SARS-CoV-2 infections in migrant populations in Germany: results from the COVID-19 snapshot monitoring survey.

OBJECTIVES: Research shows that there is an increased risk of SARS-CoV-2 infection in migrants and ethnic minorities. However, increasing evidence indicates that socio-economic factors, such as employment, education and income, contribute to the association between migrant status and SARS-CoV-2 infection. This study aimed to examine the association between migrant status and the risk of SARS-CoV-2 infection in Germany and to discuss potential explanations for these associations. STUDY DESIGN: This was a cross-sectional study. METHODS: Data from the German COVID-19 Snapshot Monitoring online survey were analysed, and hierarchical multiple linear regression models were used to calculate the probabilities of self-reported SARS-CoV-2 infection. Predictor variables were integrated in a stepwise method as follows: (1) migrant status (defined by own or parental country of birth other than Germany); (2) gender, age and education; (3) household size; (4) household language; and (5) occupation in the health sector, including an interaction term of migrant status (yes) and occupation in the health sector (yes). RESULTS: Of 45,858 participants, 3.5% reported a SARS-CoV-2 infection, and 16% were migrants. Migrants, participants in large households, those speaking a language other than German in their household and those working in the health sector were more likely to report SARS-CoV-2 infection. The probability of reporting SARS-CoV-2 infection was 3.95 percentage points higher for migrants than non-migrants; this probability decreased when integrating further predictor variables. The strongest association of reporting a SARS-CoV-2 infection was observed for migrants working in the health sector. CONCLUSIONS: Migrants and health sector employees, and especially migrant health workers, are at an increased risk of SARS-CoV-2 infection. The results show that the risk of SARS-CoV-2 infection is determined by living and working conditions rather than migrant status.

Migration and health: moving towards a diversity-oriented public health monitoring at the Robert Koch Institute.

Summarizing categories, such as migration background or history of migration, do not reflect the diversity and heterogeneity of the population living in Germany and their health. A differentiated description of the health situation of people with a history of migration should consider migration-related, social, and structural determinants of health as well as their interactions. The findings obtained in the 'Improving Health Monitoring in Migrant Populations (IMIRA)' projects will help to improve the inclusion of people with a history of migration in future studies as well as in the RKI panel. This will enable an adequate description of the health situation of people with a history of migration and therefore of the general population in Germany. In future studies, the health status of people who have not been well included in health surveys so far, such as people who are not listed at the registration office, should be monitored. For this purpose, continuous development of sampling and survey methods is necessary.

Monitoring the SARS-CoV-2 Pandemic: Prevalence of Antibodies in a Large, Repetitive Cross-Sectional Study of Blood Donors in Germany-Results from the SeBluCo Study 2020-2022.

SARS-CoV-2 serosurveillance is important to adapt infection control measures and estimate the degree of underreporting. Blood donor samples can be used as a proxy for the healthy adult population. In a repeated cross-sectional study from April 2020 to April 2021, September 2021, and April/May 2022, 13 blood establishments collected 134,510 anonymised specimens from blood donors in 28 study regions across Germany. These were tested for antibodies against the SARS-CoV-2 spike protein and nucleocapsid, including neutralising capacity. Seroprevalence was adjusted for test performance and sampling and weighted for demographic differences between the sample and the general population. Seroprevalence estimates were compared to notified COVID-19 cases. The overall adjusted SARS-CoV-2 seroprevalence remained below 2% until December 2020 and increased to 18.1% in April 2021, 89.4% in September 2021, and to 100% in April/May 2022. Neutralising capacity was found in 74% of all positive specimens until April 2021 and in 98% in April/May 2022. Our serosurveillance allowed for repeated estimations of underreporting from the early stage of the pandemic onwards. Underreporting ranged between factors 5.1 and 1.1 in the first two waves of the pandemic and remained well below 2 afterwards, indicating an adequate test strategy and notification system in Germany.

Estimating the share of SARS-CoV-2-immunologically naïve individuals in Germany up to June 2022.

After the winter of 2021/2022, the coronavirus disease 2019 (COVID-19) pandemic had reached a phase where a considerable number of people in Germany have been either infected with a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, vaccinated or both, the full extent of which was difficult to estimate, however, because infection counts suffer from under-reporting, and the overlap between the vaccinated and recovered subpopulations is unknown. Yet, reliable estimates regarding population-wide susceptibility were of considerable interest: Since both previous infection and vaccination reduce the risk of severe disease, a low share of immunologically naïve individuals lowers the probability of further severe outbreaks, given that emerging variants do not escape the acquired susceptibility reduction. Here, we estimate the share of immunologically naïve individuals by age group for each of the sixteen 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 5.6% of individuals in the German population have neither been in contact with vaccine nor any variant up to 31 May 2022 (quartile range [2.5%-8.5%]). For the adult population at higher risk of severe disease, this figure is reduced to 3.8% [1.6%-5.9%] for ages 18-59 and 2.1% [1.0%-3.4%] for ages 60 and above. However, estimates vary between German states mostly due to heterogeneous vaccine uptake. Excluding Omicron infections from the analysis, 16.3% [14.1%-17.9%] of the population in Germany, across all ages, are estimated to be immunologically naïve, highlighting the large impact the first two Omicron waves had until the beginning of summer in 2022. The method developed here might be useful for similar estimations in other countries or future outbreaks of other infectious diseases.

[Establishment of genomic pathogen surveillance to strengthen pandemic preparedness and infection prevention in Germany]. / Etablierung der Genomischen Erreger-Surveillance zur Stärkung des Pandemie- und Infektionsschutzes in Deutschland.

The SARS-CoV­2 pandemic has shown a deficit of essential epidemiological infrastructure, especially with regard to genomic pathogen surveillance in Germany. In order to prepare for future pandemics, the authors consider it urgently necessary to remedy this existing deficit by establishing an efficient infrastructure for genomic pathogen surveillance. Such a network can build on structures, processes, and interactions that have already been initiated regionally and further optimize them. It will be able to respond to current and future challenges with a high degree of adaptability.The aim of this paper is to address the urgency and to outline proposed measures for establishing an efficient, adaptable, and responsive genomic pathogen surveillance network, taking into account external framework conditions and internal standards. The proposed measures are based on global and country-specific best practices and strategy papers. Specific next steps to achieve an integrated genomic pathogen surveillance include linking epidemiological data with pathogen genomic data; sharing and coordinating existing resources; making surveillance data available to relevant decision-makers, the public health service, and the scientific community; and engaging all stakeholders. The establishment of a genomic pathogen surveillance network is essential for the continuous, stable, active surveillance of the infection situation in Germany, both during pandemic phases and beyond.

Secondary data for global health digitalisation.

Substantial opportunities for global health intelligence and research arise from the combined and optimised use of secondary data within data ecosystems. Secondary data are information being used for purposes other than those intended when they were collected. These data can be gathered from sources on the verge of widespread use such as the internet, wearables, mobile phone apps, electronic health records, or genome sequencing. To utilise their full potential, we offer guidance by outlining available sources and approaches for the processing of secondary data. Furthermore, in addition to indicators for the regulatory and ethical evaluation of strategies for the best use of secondary data, we also propose criteria for assessing reusability. This overview supports more precise and effective policy decision making leading to earlier detection and better prevention of emerging health threats than is currently the case.

Quality of life and mental health in children and adolescents during the first year of the COVID-19 pandemic: results of a two-wave nationwide population-based study.

BACKGROUND: The COVID-19 pandemic has disrupted the lives of children and adolescents worldwide. The German COPSY study is among the first population-based longitudinal studies to examine the mental health impact of the pandemic. The objective of the study was to assess changes in health-related quality of life (HRQoL) and mental health in children and adolescents and to identify the associated risk and resource factors during the pandemic. METHODS: A nationwide longitudinal survey was conducted with two waves during the pandemic (May/June 2020 and December 2020/January 2021). In total, n = 1923 children and adolescents aged 7 to 17 years and their parents participated (retention rate from wave 1 to wave 2: 85%). The self-report and parent-proxy surveys assessed HRQoL (KIDSCREEN-10), mental health problems (SDQ with the subscales emotional problems, conduct problems, hyperactivity, and peer problems), anxiety (SCARED), depressive symptoms (CES-DC, PHQ-2) and psychosomatic complaints (HBSC-SCL). Mixed model panel regression analyses were conducted to examine longitudinal changes in mental health and to identify risk and resource factors. RESULTS: The HRQoL of children and adolescents decreased during the pandemic, and emotional problems, peer-related mental health problems, anxiety, depressive and psychosomatic symptoms increased over time, however the change in global mental health problems from wave 1 to wave 2 was not significant, and some changes were negligible. Socially disadvantaged children and children of mentally burdened parents were at particular risk of impaired mental health, while female gender and older age were associated with fewer mental health problems. A positive family climate and social support supported the mental health of children and adolescents during the pandemic. DISCUSSION: Health promotion, prevention and intervention strategies could support children and adolescents in coping with the pandemic and protect and maintain their mental health.

[Attitudes Toward Influenza Vaccination in Fall/Winter 2021: Results of the COSMO Study]. / Einstellung zur Grippeimpfung im Herbst/Winter 2021: Ergebnisse der COSMO-Studie.

AIM OF THE STUDY: There is a lack of knowledge about attitudes to influenza vaccination in Germany in 2021/2022. Based on the COSMO survey ("COVID-19 Snapshot Monitoring"), the aim of this study was to shed some light on this topic. METHODS: Wave 49 (August 10 and 11, 2021) of the COSMO survey (n=967; Germany-wide non-probabilistic quota sample; 18 to 74 years). RESULTS: This year, about one-third of respondents (and health care workers) plan to get a flu shot, and among the at-risk group of people aged 60 and older (up to 74 years in our sample), more than half. Correlates (such as gender: women with a lower likelihood of a planned flu shot) were identified. CONCLUSION: Physicians should inform women in particular about the advantages of influenza vaccination, especially during the pandemic, and communicate data on the proven protective effect of influenza vaccination as convincingly as possible (e. g., using existing brochures).

How to survive pig farming: Mechanism of SCCmec element deletion and metabolic stress adaptation in livestock-associated MRSA.

Previous research on methicillin susceptible Staphylococcus aureus (MSSA) belonging to livestock-associated (LA-) sequence type (ST) 398, isolated from pigs and their local surroundings, indicated that differences between these MSSA and their methicillin resistant predecessors (MRSA) are often limited to the absence of the staphylococcal cassette chromosome mec (SCCmec) and few single nucleotide polymorphisms. So far, our understanding on how LA-MRSA endure the environmental conditions associated with pig-farming as well as the putative impact of this particular environment on the mobilisation of SCCmec elements is limited. Thus, we performed in-depth genomic and transcriptomic analyses using the LA-MRSA ST398 strain IMT38951 and its methicillin susceptible descendant. We identified a mosaic-structured SCCmec region including a putative replicative SCCmecVc which is absent from the MSSA chromosome through homologous recombination. Based on our data, such events occur between short repetitive sequences identified within and adjacent to two distinct alleles of the large cassette recombinase genes C (ccrC). We further evaluated the global transcriptomic response of MRSA ST398 to particular pig-farm associated conditions, i.e., contact with host proteins (porcine serum) and a high ammonia concentration. Differential expression of global regulators involved in stress response control were identified, i.e., ammonia-induced alternative sigma factor B-depending activation of genes for the alkaline shock protein 23, the heat shock response and the accessory gene regulator (agr)-controlled transcription of virulence factors. Exposure to serum transiently induced the transcription of distinct virulence factor encoding genes. Transcription of genes reported for mediating the loss of methicillin resistance, especially ccrC, was not significantly different compared to the unchallenged controls. We concluded that, from an evolutionary perspective, bacteria may save energy by incidentally dismissing a fully replicative SCCmec element in contrast to the induction of ccr genes on a population scale. Since the genomic SCCmec integration site is a hot-spot of recombination, occasional losses of elements of 16 kb size may restore capacities for the uptake of foreign genetic material. Subsequent spread of resistance, on the other hand, might depend on the autonomous replication machinery of the deleted SCCmec elements that probably enhance chances for reintegration of SCCmec into susceptible genomes by mere multiplication.