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.

[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.

Multicountry study of SARS-CoV-2 and associated risk factors among healthcare workers in Côte d'Ivoire, Burkina Faso and South Africa.

BACKGROUND: Reports on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread across Africa have varied, including among healthcare workers (HCWs). This study assessed the comparative SARS-CoV-2 burden and associated risk factors among HCWs in three African countries. METHODS: A multicentre study was conducted at regional healthcare facilities in Côte d'Ivoire (CIV), Burkina Faso (BF) and South Africa (SA) from February to May 2021. HCWs provided blood samples for SARS-CoV-2 serology and nasopharyngeal/oropharyngeal swabs for testing of acute infection by polymerase chain reaction and completed a questionnaire. Factors associated with seropositivity were assessed with logistic regression. RESULTS: Among 719 HCWs, SARS-CoV-2 seroprevalence was 34.6% (95% confidence interval 31.2 to 38.2), ranging from 19.2% in CIV to 45.7% in BF. A total of 20 of 523 (3.8%) were positive for acute SARS-CoV-2 infection. Female HCWs had higher odds of SARS-CoV-2 seropositivity compared with males, and nursing staff, allied health professionals, non-caregiver personnel and administration had higher odds compared with physicians. HCWs also reported infection prevention and control (IPC) gaps, including 38.7% and 29% having access to respirators and IPC training, respectively, in the last year. CONCLUSIONS: This study was a unique comparative HCW SARS-CoV-2 investigation in Africa. Seroprevalence estimates varied, highlighting distinctive population/facility-level factors affecting COVID-19 burden and the importance of established IPC programmes to protect HCWs and patients.

Alten- und Pflegeheime – die COVID-19-Pandemie als Mahnung: Infektionshygienische Maßnahmen und Einflussfaktoren auf die Gesundheit der Bewohnenden Long-term care facilities—the COVID-19 pandemic as an urgent call: infection prevention, control measures, and factors influencing the health of residents

Die COVID-19-Pandemie hat die Vulnerabilität der Alten- und Pflegeheimbewohnenden aufgrund ihres erhöhten Risikos für einen schwerwiegenden oder tödlichen COVID-19-Verlauf verdeutlicht. Um die Bewohnenden in den Einrichtungen in Anbetracht hoher Inzidenzen von severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) in der Gesamtbevölkerung zu schützen, wurde eine Reihe von Infektionsschutzmaßnahmen empfohlen, die im Verlauf der Pandemie zu einem Rückgang der COVID-19-Fälle und -Todesfälle in den Einrichtungen geführt haben. Gleichzeitig hat sich jedoch gezeigt, dass in Alten- und Pflegeheimen häufig einige Faktoren existieren, welche die Umsetzung von Infektionsschutzmaßnahmen erschweren und einen erheblichen Einfluss auf die Gesundheit der Bewohnenden ausüben. Herausforderungen ergeben sich vor allem durch die Arbeitsbedingungen (Mangel an Personal grundsätzlich und mit entsprechenden Qualifikationen, arbeitsbedingte Belastungen), durch die Versorgung der Bewohnenden (medizinisch und psychosozial) sowie durch strukturelle und einrichtungsspezifische Faktoren (u. a. Größe von Heimen). Lösungskonzepte für diese Probleme zeigen, dass die Umsetzung von Infektionsschutzmaßnahmen nicht für sich alleine steht, sondern als Teil eines Konzeptes zur Neugestaltung der Arbeits‑, Wohn- und Lebensbereiche der Beschäftigten und der Bewohnenden der Einrichtungen betrachtet werden sollte. Dabei gilt es, den Infektionsschutz in Alten- und Pflegeheimen nicht ausschließlich in Hinblick auf zukünftige Pandemien zu planen, sondern dessen Relevanz auch für bereits jetzt bestehende Gesundheitsgefahren, wie nosokomiale Infektionen, Antibiotikaresistenzen oder Influenza, zu beachten.

[Long-term care facilities-the COVID-19 pandemic as an urgent call: infection prevention, control measures, and factors influencing the health of residents]. / Alten- und Pflegeheime ­ die COVID-19-Pandemie als Mahnung: Infektionshygienische Maßnahmen und Einflussfaktoren auf die Gesundheit der Bewohnenden.

The COVID-19 pandemic once again highlighted the vulnerability of residents of long-term care facilities due to their increased risk of a severe or fatal course of COVID-19. To protect the residents in the face of high incidences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV­2) in the general population, a number of measures for infection protection were recommended, which led to a decrease of COVID-19 case numbers and deaths in the facilities during the pandemic. However, factors in the facilities that hampered the implementation of these measures and represented a significant impact on the health of the residents also became visible.The challenges concern working conditions (e.g., lack of staff, both in general and with corresponding competencies, and work-related stress), the care of residents (e.g., medical and psychosocial), and structural as well as facility-related factors (e.g., facility size).Approaches to these problems indicate that a successful implementation of infection control measures should be part of a concept for redesigning the work and living conditions of the staff and residents of the facilities. It is important to note that infection control should not be planned exclusively with regard to future pandemics, but is of relevance for health risks that already exist in the facilities, such as healthcare-associated infections, antibiotic resistances, or influenza.

Effectiveness and sustainability of the WHO multimodal hand hygiene improvement strategy in the University Hospital Bouaké, Republic of Côte d'Ivoire in the context of the COVID-19 pandemic.

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 < 0.001) upon first and decreased to 13/25 in second follow-up. Compliance showed a significant increase from 12.7% to 36.8% (p < 0.001) in first and remained at 36.4% in second follow-up. Alcohol-based hand-rub production and consumption almost doubled after first confirmed COVID-19 case in Côte d'Ivoire. CONCLUSION: The WHO HH improvement strategy is an effective and pandemic-adaptable method to increase long-term HH compliance. This study emphasizes that the implementation of the strategy to build a robust system is of utmost importance.

Longitudinal SARS-CoV-2 seroepidemiological investigation among healthcare workers at a tertiary care hospital in Germany.

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.

SARS-CoV-2 outbreaks in hospitals and long-term care facilities in Germany: a national observational study.

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.

Impact of the COVID-19 pandemic on the surveillance, prevention and control of antimicrobial resistance: a global survey.

OBJECTIVES: The COVID-19 pandemic has had a substantial impact on health systems. The WHO Antimicrobial Resistance (AMR) Surveillance and Quality Assessment Collaborating Centres Network conducted a survey to assess the effects of COVID-19 on AMR surveillance, prevention and control. METHODS: From October to December 2020, WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) national focal points completed a questionnaire, including Likert scales and open-ended questions. Data were descriptively analysed, income/regional differences were assessed and free-text questions were thematically analysed. RESULTS: Seventy-three countries across income levels participated. During the COVID-19 pandemic, 67% reported limited ability to work with AMR partnerships; decreases in funding were frequently reported by low- and middle-income countries (LMICs; P < 0.01). Reduced availability of nursing, medical and public health staff for AMR was reported by 71%, 69% and 64%, respectively, whereas 67% reported stable cleaning staff availability. The majority (58%) reported reduced reagents/consumables, particularly LMICs (P < 0.01). Decreased numbers of cultures, elective procedures, chronically ill admissions and outpatients and increased ICU admissions reported could bias AMR data. Reported overall infection prevention and control (IPC) improvement could decrease AMR rates, whereas increases in selected inappropriate IPC practices and antimicrobial prescribing could increase rates. Most did not yet have complete data on changing AMR rates due to COVID-19. CONCLUSIONS: This was the first survey to explore the global impact of COVID-19 on AMR among GLASS countries. Responses highlight important actions to help ensure that AMR remains a global health priority, including engaging with GLASS to facilitate reliable AMR surveillance data, seizing the opportunity to develop more sustainable IPC programmes, promoting integrated antibiotic stewardship guidance, leveraging increased laboratory capabilities and other system-strengthening efforts.

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.

The Containment Scouts: First Insights into an Initiative to Increase the Public Health Workforce for Contact Tracing during the COVID-19 Pandemic in Germany.

The COVID-19 pandemic in Germany has demanded a substantially larger public health workforce to perform contact tracing and contact management of COVID-19 cases, in line with recommendations of the World Health Organization (WHO). In response, the Robert Koch Institute (RKI) established the national "Containment Scout Initiative" (CSI) to support the local health authorities with a short-term workforce solution. It is part of a range of measures for strengthening the public health system in order to limit the spread of SARS-CoV-2 in Germany. The CSI is an example of how solutions to address critical health system capacity issues can be implemented quickly. It also demonstrates that medical or health-related backgrounds may not be necessary to support health authorities with pandemic-specific tasks and fulfil accurate contact tracing. However, it is a short-term solution and cannot compensate for the lack of existing qualified staff as well as other deficits that exist within the public health sector in Germany. This article describes the structure and process of the first phase of this initiative in order to support health policymakers, public health practitioners, and researchers considering innovative and flexible approaches for addressing urgent workforce capacity issues.

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents.

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.

[Recording of SARS-CoV-2 laboratory tests in Germany]. / Erfassung der Labortestungen auf SARS-CoV-2 in Deutschland.

The collection of data on SARS-CoV­2 tests is central to the assessment of the infection rate in the context of the COVID-19 pandemic. At the Robert Koch Institute (RKI), data collected from various laboratory data recording systems are consolidated. First, this article aims to exemplify significant aspects regarding test procedures. Subsequently the different systems for recording laboratory tests are described and test numbers from the RKI test laboratory query and the laboratory-based SARS-CoV­2 surveillance as well as accounting data from the Association of Statutory Health Insurance Physicians for SARS-CoV­2 laboratory tests are shown.Early in the pandemic, the RKI test laboratory query and the laboratory-based SARS-CoV­2 surveillance became available and able to evaluate data on performed tests and test capacities. By recording the positive and negative test results, statements about the total number of tests and the proportion of positive test rates can be made. While the aggregate test numbers are largely representative nationwide, they are not always representative at the state and district level. The billing data of the Association of Statutory Health Insurance Physicians can complement the laboratory data afterwards. In addition, it can provide a retrospective assessment of the total number of SARS-CoV­2 numbers in Germany, because the services provided by statutory health insurers (around 85% of the population in Germany) are included. The various laboratory data recording systems complement one another and the evaluations flow into the recommended measures for the pandemic response.

[Measures to cope with the COVID-19 pandemic in Germany: nonpharmaceutical and pharmaceutical interventions]. / Maßnahmen zur Bewältigung der COVID-19-Pandemie in Deutschland: nichtpharmakologische und pharmakologische Ansätze.

When the emerging novel SARS-CoV­2 virus first appeared in December 2019, neither specific therapeutic options nor vaccinations were available. The role of nonpharmaceutical interventions (NPIs) became of central importance. At the Robert Koch Institute, a multilayer strategy consisting of population-based and individual preventive measures to control the pandemic was developed, which built upon existing influenza pandemic plans as well as generic plans. This paper explains the recommended NPIs and illustrates the pharmaceutical approaches developed in parallel.Among others, general contact bans, providing material for infection prevention and control, ban of events, closing educational institutions, and restricting travel are counted among population-based measures. Additional individual preventive measures are necessary, e.g., keeping a minimum distance, reducing contacts, and wearing a mouth-nose covering as well as quarantine and isolation. Measures within the health system are based on recommendations of the Commission on Hospital Hygiene and Infection Protection (Kommission für Krankenhaushygiene und Infektionsprävention (KRINKO)) and specified and implemented by professional societies. Since November 2020, an antiviral therapy with remdesivir and treatment with the glucocorticoid dexamethasone have been available as pharmaceutical interventions. Monoclonal antibodies are at this time not approved. Therapeutic anticoagulation is recommended.Recommendations are constantly adapted to the increasing knowledge on the pathogen and its means of transmission. A challenge is to strengthen the trust of the population. Many measures have to be applied on an individual basis in order to work together.

High impact of COVID-19 in long-term care facilities, suggestion for monitoring in the EU/EEA, May 2020.

Residents in long-term care facilities (LTCF) are a vulnerable population group. Coronavirus disease (COVID-19)-related deaths in LTCF residents represent 30-60% of all COVID-19 deaths in many European countries. This situation demands that countries implement local and national testing, infection prevention and control, and monitoring programmes for COVID-19 in LTCF in order to identify clusters early, decrease the spread within and between facilities and reduce the size and severity of outbreaks.