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.

Infection control strategies for healthcare workers during COVID-19 pandemic in German hospitals: A cross-sectional study in march–april 2021

Background Healthcare workers (HCW) are at risk of getting infected with COVID-19 at work. To prevent such incidents and provide a safe environment in hospitals, comprehensive infection control strategies are necessary. We aimed to collect information on COVID-19 infection control strategies regarding personal protective equipment (PPE), regulations during breaks for HCW and dissemination of pandemic-related information. Methods We invited infection control practitioners from 987 randomly selected German hospitals in March–April 2021 to participate in our cross-sectional online survey. We categorized the hospital based on bed capacity (≤499 beds = small;≥500 beds = large). Fisher's exact test was performed and p < 0.05 defined as statistically significant. Findings 100 participants completed the questionnaire. Small hospitals were more directive about requiring FFP2 respirators (63%), whereas larger hospitals more often gave their HCW a choice between these and medical masks (67%). For the care of COVID-19 and suspected COVID-19 cases, >90% of the participants recommended the use of gloves. Notably, gloves were recommended beyond COVID-19 in 30% of the hospitals. During meal breaks various strategies were followed. Conclusion Recommendations for PPE varied across hospital sizes, which could be due to different assessments of necessity and safety. Regulations during breaks varied strongly which illustrates the need for clear official guidelines.

Infection control strategies for healthcare workers during COVID-19 pandemic in German hospitals: A cross-sectional study in march-april 2021.

Background: Healthcare workers (HCW) are at risk of getting infected with COVID-19 at work. To prevent such incidents and provide a safe environment in hospitals, comprehensive infection control strategies are necessary. We aimed to collect information on COVID-19 infection control strategies regarding personal protective equipment (PPE), regulations during breaks for HCW and dissemination of pandemic-related information. Methods: We invited infection control practitioners from 987 randomly selected German hospitals in March-April 2021 to participate in our cross-sectional online survey. We categorized the hospital based on bed capacity (≤499 beds = small; ≥500 beds = large). Fisher's exact test was performed and p < 0.05 defined as statistically significant. Findings: 100 participants completed the questionnaire. Small hospitals were more directive about requiring FFP2 respirators (63%), whereas larger hospitals more often gave their HCW a choice between these and medical masks (67%). For the care of COVID-19 and suspected COVID-19 cases, >90% of the participants recommended the use of gloves. Notably, gloves were recommended beyond COVID-19 in 30% of the hospitals. During meal breaks various strategies were followed. Conclusion: Recommendations for PPE varied across hospital sizes, which could be due to different assessments of necessity and safety. Regulations during breaks varied strongly which illustrates the need for clear official guidelines.

[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.

Information Technology Systems for Infection Control in German University Hospitals-Results of a Structured Survey a Year into the Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic.

BACKGROUND: Digitalization is playing a major role in mastering the current coronavirus 2019 (COVID-19) pandemic. However, several outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in German hospitals last year have shown that many of the surveillance and warning mechanisms related to infection control (IC) in hospitals need to be updated. OBJECTIVES: The main objective of the following work was to assess the state of information technology (IT) systems supporting IC and surveillance in German university hospitals in March 2021, almost a year into the SARS-CoV-2 pandemic. METHODS: As part of the National Research Network for Applied Surveillance and Testing project within the Network University Medicine, a cross-sectional survey was conducted to assess the situation of IC IT systems in 36 university hospitals in Germany. RESULTS: Among the most prominent findings were the lack of standardization of IC IT systems and the predominant use of commercial IC IT systems, while the vast majority of hospitals reported inadequacies in the features their IC IT systems provide for their daily work. However, as the pandemic has shown that there is a need for systems that can help improve health care, several German university hospitals have already started this upgrade independently. CONCLUSIONS: The deep challenges faced by the German health care sector regarding the integration and interoperability of IT systems designed for IC and surveillance are unlikely to be solved through punctual interventions and require collaboration between educational, medical, and administrative institutions.

[COVID-19 vaccination strategy for employees of German hospitals: results of a survey of infection control practitioners within the B-FAST project]. / COVID-19-Impfstrategien für Beschäftigte deutscher Kliniken: Ergebnisse einer Befragung von Leitungen der (Krankenhaus­)Hygiene im Rahmen des B-FAST-Projektes.

BACKGROUND AND AIM: At the beginning of the COVID-19 vaccination campaign in Germany, employees in medical facilities were prioritised for vaccination against SARS-CoV­2 due to the high risk of exposure and contact with vulnerable groups. Hospitals were therefore encouraged to organise and implement the vaccination of their employees as soon as possible. The aim of the study was to record the practice regarding the vaccination strategy for employees in German hospitals. METHODS: In a self-developed cross-sectional study, infection control practitioners of all German university hospitals as well as non-university hospitals in Lower Saxony and Bavaria were surveyed in March 2021. The data were stratified according to the characteristics of university hospitals and non-university hospitals. RESULTS: Of 416 invitations sent out, 100 questionnaires (university hospitals: 33; non-university hospitals: 67) were completed. University hospitals reported greater vaccination capacity than non-university hospitals, but a limiting factor was uncertain vaccine supply. Vaccination information campaigns were planned or had already been conducted in 89% of clinics. About two-thirds of the respondents (70%) said they did not plan to conduct antibody tests on vaccinated employees. A follow-up of vaccinated employees to detect possible SARS-CoV­2 infections by PCR was planned by 41% of the respondents. In case of detection of SARS-CoV­2 infection, 72% of the respondents had planned further diagnostic procedures. DISCUSSION: All hospitals were able to achieve rapid implementation of COVID-19 vaccination of their employees. At the time of the survey, there was also much uncertainty regarding the management of breakthrough infections as well as the need for booster vaccinations.

Fallzahlen, Re-Identifikation und der technische Datenschutz

Die SARS-CoV-2-Pandemie hat viele sehr spezielle Fragen des Datenschutzes und der Datensicherheit aufgeworfen. Der vorliegende Beitrag widmet sich den mit der Veröffentlichung von Infiziertenzahlen verbundenen Re-Identifikationsrisiken. Er zeigt einen Weg auf, diese Risiken mit Mitteln des technischen Datenschutzes zu reduzieren, um sowohl das öffentliche Informationsbedürfnis zu befriedigen als auch das informelle Selbstbestimmungsrecht der Betroffenen zu wahren.

Experimental measurement of respiratory particles dispersed by wind instruments and analysis of the associated risk of infection transmission

Activities such as singing or playing a wind instrument release respiratory particles into the air that may contain pathogens and thus pose a risk for infection transmission. Here we report measurements of the size distribution, number, and volume concentration of exhaled particles from 31 healthy musicians playing 20 types of wind instruments using aerosol size spectrometry complemented with in-line holography in a strictly controlled cleanroom environment. We find that playing wind instruments carries a lower risk of airborne disease transmission than speaking or singing. We attribute this to the fact that the resonators of wind instruments act as filters for particles >10µm in diameter, which were found in high abundance right after a brass mouthpiece but very rarely at the instrument bell end. We have also measured the size-dependent filtering properties of different types of filters that can be used as instrument masks. Based on these measurements, we calculated the risk of airborne transmission of SARS-CoV-2 in different near- and far-field scenarios with and without masking and/or distancing. We conclude that in all cases where there is a possibility that the musician is infectious, the only safe measure to prevent airborne transmission of the disease is the use of well-fitting and well-filtering masks for the instrument and the susceptible person.

Clinical Post-SARS-CoV-2 Infection Scenarios in Vaccinated and Non-Vaccinated Cancer Patients in Three German Cancer Centers: A Retrospective Analysis.

COVID-19 vaccines have become an integral element in the protection of cancer patients against SARS-CoV-2. To date, there are no direct comparisons of the course of COVID-19 infection in cancer patients between the pre- and post-vaccine era. We analyzed SARS-CoV-2 infections and their impact on cancer in COVID-19 vaccinated and non-vaccinated patients from three German cancer centers. Overall, 133 patients with SARS-CoV-2 were enrolled in pre- and post-vaccine eras: 84 non-vaccinated and 49 vaccinated, respectively. A mild course of COVID-19 was documented more frequently in vaccinated patients (49% vs. 29%), while the frequency of severe and critical courses occurred in approximately one-half of the non-vaccinated patients (22% vs. 42%, p = 0.023). Particularly, patients with hematologic neoplasms benefited from vaccination in this context (p = 0.031). Admissions to intermediate- and intensive-care units and the necessity of non-invasive and invasive respiratory support were reduced by 71% and 50% among vaccinated patients, respectively. The median length of admission was 11 days for non-vaccinated and 5 days for vaccinated patients (p = 0.002). COVID-19 mortality was reduced by 83% in vaccinated patients (p = 0.046). Finally, the median time from SARS-CoV-2 infection to restarting cancer therapy was 12 and 26 days among vaccinated and non-vaccinated groups, respectively (p = 0.002). Although this study does not have enough power to perform multivariate analyses to account for confounders, it provides data on COVID-19 in non-vaccinated and vaccinated cancer patients and illustrates the potential benefits of COVID-19 vaccines for these patients.

Tracing COVID-19 Infection Chains Within Healthcare Institutions - Another Brick in the Wall Against SARS-CoV-2.

Early anticipation of COVID-19 infection chains within hospitals is of high importance for initiating suitable measures at the right time. Infection control specialists can be supported by application systems able of consolidating and analyzing heterogeneous, up-to-now non-standardized and distributed data needed for tracking COVID-19 infections and infected patients' hospital contacts. We developed a system, Co-Surv-SmICS, assisting in infection chain detection, in an open and standards-based way to ensure reusability of the system across institutions. Data is modelled in alignment to various national modelling initiatives and consensus data definitions, queried in a standardized way by the use of OpenEHR as information modelling standard and its associated model-based query language, analyzed and interactively visualized in the application. A first version has been published and will be enhanced with further features and evaluated in detail with regard to its potentials to support specialists during their work against SARS-CoV-2.

Fallzahlen, Re-Identifikation und der technische Datenschutz : Ein Aspekt der SARS-CoV-2-Pandemie

Die SARS-CoV-2-Pandemie hat viele sehr spezielle Fragen des Datenschutzes und der Datensicherheit aufgeworfen. Der vorliegende Beitrag widmet sich den mit der Veröffentlichung von Infiziertenzahlen verbundenen Re-Identifikationsrisiken. Er zeigt einen Weg auf, diese Risiken mit Mitteln des technischen Datenschutzes zu reduzieren, um sowohl das öffentliche Informationsbedürfnis zu befriedigen als auch das informelle Selbstbestimmungsrecht der Betroffenen zu wahren.

SARS-CoV-2 surveillance and testing: results of a survey from the Network of University Hospitals (NUM), B-FAST.

Background: The B-FAST project of the National University Network (NUM) examines and records applied surveillance strategies implemented in hospitals i.a., to protect patients and employees from SARS-CoV-2 infection. Methods: Infection control physicians in German university hospitals (UK), as well as non-university hospitals (NUK; Bavaria, Lower Saxony) were surveyed in March 2021 regarding SARS-CoV-2 testing/surveillance strategies in a cross-sectional study using a standardized online questionnaire. The focus was on screening strategies taking into account the "test" methods used (case history, PCR, antigen, antibody test). Results: The response rate was 91.7% (33/36) in UK and 11.3%-32.2% in NUK. Almost all hospitals (95.0%) performed a symptom and exposure check and/or testing upon inpatient admission. Non-cause-related testing (screening) of health care workers in COVID wards was preferably done by PCR in UK (69.7% PCR; 12.1% antigen), while NUK (29.9% PCR; 49.3% antigen) used antigen testing more frequently. Regardless of the type of facility, about half of the respondents rated the benefit of screening higher than the effort (patients: 49%; employees: 45%). Conclusion: Testing/surveillance strategies find a high level of acceptance at German hospitals and are generally carried out in accordance with the national testing strategy with differences depending on the level of care.

Infection surveillance measures during the COVID-19 pandemic in Germany.

Introduction: To address the question as to which infection surveillance measures are used during the ongoing COVID-19 pandemic in Germany and how they differ from pre-existing approaches. Methods: In accordance with the systematic approach of a scoping review, a literature search was conducted in national and international medical literature databases using a search string. The search in the databases was limited to the period from 01.01.2000 to 15.11.2020 and has been subsequently completed by hand search until 08.03.2021. A hand search, even beyond 15.11.2020, seemed necessary and reasonable, since due to the dynamics of the ongoing COVID-19 pandemic, a large number of articles and regulations are being published very quickly at short notice. Results: The literature search resulted in the following number of hits in the databases listed below: PubMed: 165 articlesCochrane: 1 review and 35 studiesWeb of Science: 217 articlesRobert Koch Institute: 49 articles Thus, a total of 467 hits were identified, with a total of 124 hits being duplicates. From these, 138 articles were considered relevant to the COVID-19 infection surveillance situation in Germany based on established criteria. After reading the full texts, 92 articles and websites were ultimately included in the scoping review. Discussion: Many of the lessons learned from previous outbreaks seem to have been implemented in the infection surveillance measures during the ongoing COVID-19 pandemic in Germany. Most of the changes compared with previous measures were based on technological streamlining of existing procedures and changes and more inclusion of the population in different infection surveillance measures.

COVID-19 Outbreaks in Settings With Precarious Housing Conditions in Germany: Challenges and Lessons Learned.

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.

COVID-19 Pandemic: Effect of Different Face Masks on Self-Perceived Dry Mouth and Halitosis.

Due to the COVID-19 pandemic, the use of face masks has increased, resulting in potential health-related side-effects. Therefore, the study aimed to analyse the effect of wearing face masks on self-perceived dry mouth and halitosis. A questionnaire addressing the daily wearing time of different face masks (community masks, surgical/medical masks and KN95-/N95-/FFP2-masks) and self-perceived dry mouth and halitosis was given to adults attending or working at a university hospital. Statistical analysis was performed using Wilcoxon signed-rank test and multiple linear regression analysis (p < 0.05). 3750 participants (age: 50.4 ± 15.5 years; 60.0% female) were included. During the pandemic, face masks were used for 4.7 ± 3.8 h per day: community masks: 0.9 ± 2.0 h, medical/surgical masks: 1.9 ± 2.8 h and KN95-/N95-/FFP2-masks: 1.9 ± 2.5 h per day. The use of face masks significantly increased self-perceived dry mouth and halitosis (both p < 0.001). Self-perceived dry mouth and halitosis increased with increasing wearing time (community masks: dry mouth: p < 0.001, halitosis: p = 0.014; medical/surgical masks: both: p < 0.001; KN95-/N95-/FFP2-masks: dry mouth: p < 0.001, halitosis: p = 0.011). The perception of dry mouth and halitosis was increased in females compared to males (both: p < 0.001). Participants used to wearing face masks prior to the pandemic perceived dry mouth to a higher extent (p = 0.043). Self-perceived halitosis was lower in older than in younger participants (p < 0.001). Due to the increased perception of dry mouth and halitosis, people might abstain from wearing face masks. Further studies need to analyse measurable changes in dry mouth or halitosis.

Validation of a Prospective Urinalysis-Based Prediction Model for ICU Resources and Outcome of COVID-19 Disease: A Multicenter Cohort Study.

In COVID-19, guidelines recommend a urinalysis on hospital admission as SARS-CoV-2 renal tropism, post-mortem, was associated with disease severity and mortality. Following the hypothesis from our pilot study, we now validate an algorithm harnessing urinalysis to predict the outcome and the need for ICU resources on admission to hospital. Patients were screened for urinalysis, serum albumin (SA) and antithrombin III activity (AT-III) obtained prospectively on admission. The risk for an unfavorable course was categorized as (1) "low", (2) "intermediate" or (3) "high", depending on (1) normal urinalysis, (2) abnormal urinalysis with SA ≥ 2 g/dL and AT-III ≥ 70%, or (3) abnormal urinalysis with SA or AT-III abnormality. Time to ICU admission or death served as the primary endpoint. Among 223 screened patients, 145 were eligible for enrollment, 43 falling into the low, 84 intermediate, and 18 into high-risk categories. An abnormal urinalysis significantly elevated the risk for ICU admission or death (63.7% vs. 27.9%; HR 2.6; 95%-CI 1.4 to 4.9; p = 0.0020) and was 100% in the high-risk group. Having an abnormal urinalysis was associated with mortality, a need for mechanical ventilation, extra-corporeal membrane oxygenation or renal replacement therapy. In conclusion, our data confirm that COVID-19-associated urine abnormalities on admission predict disease aggravation and the need for ICU (ClinicalTrials.gov number NCT04347824).

Diagnostic, Clinical and Post-SARS-CoV-2 Scenarios in Cancer Patients with SARS-CoV-2: Retrospective Analysis in Three German Cancer Centers.

Oncologists face challenges in the management of SARS-CoV-2 infections and post-SARS-CoV-2 cancer treatment. We analyzed diagnostic, clinical and post-SARS-CoV-2 scenarios in patients from three German cancer centers with RT-PCR confirmed SARS-CoV-2 infection. Sixty-three patients with SARS-CoV-2 and hematologic or solid neoplasms were included. Thirty patients were initially asymptomatic, 10 of whom developed COVID-19 symptoms subsequently. Altogether 20 (32%) patients were asymptomatic, 18 (29%) had mild, 12 (19%) severe and 13 (20%) critical courses. Lymphocytopenia increased risk of severe/critical COVID-19 three-fold (p = 0.015). Asymptomatic course was not associated with age, remission status, therapies or co-morbidities. Secondary bacterial infection accompanied more than one third of critical COVID-19 cases. Treatment was delayed post-SARS-CoV-2 in 46 patients, 9 of whom developed progressive disease (PD). Cancer therapy was modified in 8 SARS-CoV-2 survivors because of deteriorating performance or PD. At the last follow-up, 17 patients had died from COVID-19 (n = 8) or PD (n = 9) giving an estimated 73% four-month overall survival rate. SARS-CoV-2 infection has a heterogenous course in cancer patients. Lymphocytopenia carries a significant risk of severe/critical COVID-19. SARS-CoV-2 disruption of therapy is as serious as SARS-CoV-2 infection itself. Careful surveillance will allow early restart of the anti-cancer treatment.