Robert Koch Institut

Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown. We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression‐associated histone marks, and acclimatory response to nitrogen starvation. Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26–31‐nt‐long double‐stranded sRNAs originating mostly from transposons covered by repression‐associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression‐associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR‐KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress. Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species.

Background Salmonella enterica are important foodborne pathogens and the third leading cause of death among diarrheal infections worldwide. This cross-sectional study investigated the frequency of antibiotic-resistant Salmonella enterica in commercial and smallholder farm environments in the Ashanti Region of Ghana. A total of 1490 environmental samples, comprising 800 (53.7%) soil (from poultry, pigs, sheep, goats and cattle farms), 409 (27.4%) pooled poultry fecal and 281 (18.9%) dust (from poultry farms) samples, were collected from 30 commercial and 64 smallholder farms. All samples were processed using standard culture methods. Isolates were identified by biochemical methods and confirmed using the VITEK 2 System. Antibiotic susceptibility testing was carried out by disk diffusion following the EUCAST guidelines. Serotyping was performed using the Kauffman White Le Minor Scheme. Results The overall Salmonella frequency was 6.0% (n/N = 90/1490); the frequency varied according to the type of sample collected and included: 8.9% for dust (n/N = 25/281), 6.5% for soil (n/N = 52/800) and 3.2% for pooled poultry fecal samples (n/N = 13/409). Salmonella was also recovered from commercial farm environments (8.6%, n/N = 68/793) than from smallholder farms (3.2%, n/N = 22/697) (PR = 2.7, CI: 1.7 – 4.4). Thirty-four different Salmonella serovars were identified, the two most common being Rubislaw (27.8%, n/N = 25/90) and Tamale (12.2%, n/N = 11/90). Serovar diversity was highest in strains from soil samples (70.6%, n/N = 24/34) compared to those found in the dust (35.2%, n/N = 12/34) and in fecal samples (29.4%, n/N = 10/34). Salmonella frequency was much higher in the rainy season (8.4%, n/N = 85/1007) than in the dry season (1.0%, n/N = 5/483) (PR = 8.4, 95% CI: 3.3 – 20.0). Approximately 14.4% (n/N = 13/90) of the isolates were resistant to at least one of the tested antimicrobials, with 84.6% (n/N = 11/13) being resistant to multiple antibiotics. All Salmonella Kentucky (n = 5) were resistant to ciprofloxacin. Conclusion This study showed that farm environments represent an important reservoir for antibiotic-resistant Salmonella, which warrants monitoring and good husbandry practices, especially in commercial farms during the rainy season, to control the spread of this pathogen.

The cochlea forms a key element of the human auditory system in the temporal bone. Damage to the cochlea continues to produce significant impairment for sensory reception of environmental stimuli. To improve this impairment, the optical cochlear implant forms a new research approach. A prerequisite for this method is to understand how light propagation, as well as scattering, reflection and absorption, takes place within the cochlea. We offer a method to study the light distribution in the human cochlea through phantom materials which have the objective to mimic the optical behaviour of bone and Monte‐Carlo simulations. The calculation of an angular distribution after scattering requires a phase function. Often approximate functions like Henyey‐Greenstein, two‐term Henyey‐Greenstein or Legendre polynomial decompositions are used as phase function. An alternative is to exactly calculate a Mie distribution for each scattering event. This method provides a better fit to the data measured in this work. This article is protected by copyright. All rights reserved.

Zusammenfassung Die Erfahrungen aus der COVID-19-Pandemie können (und müssen) langfristig zu einer höheren Resilienz des Gesundheitswesens in Gesundheitskrisen beitragen. Erste Auswertungen und Empfehlungen liegen auf nationaler und internationaler Ebene vor, müssen aber durch weitere Prozesse auf allen Ebenen ergänzt werden, bevor die nationale Krisenplanung überarbeitet werden kann. Materialien von WHO, ECDC und RKI können genutzt werden, um Lessons-Learned-Prozesse strukturiert durchzuführen und Krisenpläne zu überarbeiten.

Zusammenfassung Für die Überwachung von Infektionskrankheiten, Eindämmung von Ausbrüchen und angewandte Forschung in der Infektionsepidemiologie ist eine spezielle Expertise erforderlich. Die Postgraduiertenausbildung für angewandte Epidemiologie (PAE) bildet als das deutsches Feldepidemiologie-Trainingsprogramm (FETP) seit 1996 hierfür Fachleute aus. Durch die Ausweitung der Ausbildung von der Bundesebene auf die Landesebene und kommunale Ebene und durch die Entwicklung kürzerer und skalierbarer Ausbildungsformate wird das öffentliche Gesundheitssystem weiter gestärkt.

Zusammenfassung Der Öffentliche Gesundheitsdienst in Deutschland benötigt für seine Arbeit eine breitere wissenschaftliche Basis. Der Beirat für den Pakt für den ÖGD empfiehlt eine Stärkung der wissenschaftlichen Kompetenzen und Vernetzung, stratifiziert anhand der Ebenen Bund, Länder und Kommunen. Ziele sind eine bessere Erhebung handlungsrelevanter Informationen, die Entwicklung und Anwendung evidenzbasierter Leitlinien sowie eine gesteigerte Qualitätssicherung.

In diesem Beitrag werden empirische Befunde zum Ausmaß und Erscheinungsbild der sozialen Unterschiede in der Gesundheit, Morbidität und Lebenserwartung in Deutschland dargestellt. Anschließend werden verschiedene Erklärungsansätze für diese Unterschiede inkl. einer integrativen Betrachtung dieser Ansätze beschrieben. Zum Abschluss werden mögliche Forschungsperspektiven aufgezeigt und Schlussfolgerungen für politische Bemühungen zur Verringerung der gesundheitlichen Ungleichheit formuliert.

Zusammenfassung Komplexe Gesundheitsherausforderungen erfordern agile Netzwerke. Das Konsortium ÖGD-FORTE zielt auf den Aufbau und die Etablierung neuer Strukturen und Prozesse zwischen Public-Health-Forschung und ÖGD-Praxis ab, um die nachhaltige Anwendung relevanter Forschungsmethoden zur Bearbeitung von Forschungsfragen zu ermöglichen und den Wissenstransfer zu befördern. Durch innovative und partizipative Prozesse entsteht ein überregionales Forschungsnetzwerk aus ÖGD-Partnern verschiedener föderaler Ebenen, was zu positiven Synergieeffekten führt, deren Nachhaltigkeit und Weiterentwicklung jedoch von strukturellen Verstetigungsoptionen abhängt.

Zusammenfassung Für die Analyse regionaler Unterschiede in der Gesundheit sind kleinräumig differenzierbare Daten wie die der Schuleingangsuntersuchungen (SEU) des Öffentlichen Gesundheitsdienstes bedeutsam. Im Pilotprojekt AdiRaum wurden die Adipositasprävalenzen aus den SEU von sechs Ländern zusammengeführt, mit räumlichen Informationen verknüpft und in einem Dashboard visualisiert. Damit können Unterschiede in der Adipositasverbreitung auf Kreisebene identifiziert und Zusammenhänge mit regionalen Einflussfaktoren untersucht werden.

Background Malaysia introduced the two dose measles-mumps-rubella (MMR) vaccine in 2004 as part of its measles elimination strategy. However, despite high historical coverage of MCV1 and MCV2, Malaysia continues to report high measles incidence. This study suggests a novel indicator for investigating population immunity against measles in the Malaysian population. Methods We define effective vaccine coverage (EVC) of measles as the proportion of a population vaccinated with measles-containing vaccine (MCV) and effectively protected against measles infection. A quantitative evaluation of EVC throughout the life course of Malaysian birth cohorts was conducted accounting for both vaccine efficacy (VE) and between-dose correlation (BdC). Measles vaccination coverage was sourced from WHO-UNICEF estimates of Malaysia’s routine immunisation coverage and supplementary immunisation activities (SIAs). United Nations World population estimates and projections (UNWPP) provided birth cohort sizes stratified by age and year. A step wise joint Bernoulli distribution was used to proportionate the Malaysian population born between 1982, the first year of Malaysia’s measles vaccination programme, and 2021, into individuals who received zero dose, one dose and multiple doses of MCV. VE estimates by age and doses received are then adopted to derive EVC. A sensitivity analysis was conducted using 1000 random combinations of BdC and VE parameters. Results This study suggests that no birth cohort in the Malaysian population has achieved > 95% population immunity (EVC) conferred through measles vaccination since the measles immunisation programme began in Malaysia. Conclusion The persistence of measles in Malaysia is due to pockets of insufficient vaccination coverage against measles in the population. Monitoring BdC through immunisation surveillance systems may allow for the identification of susceptible subpopulations (primarily zero-dose MCV individuals) and increase the coverage of individuals who are vaccinated with multiple doses of MCV. This study provides a tool for assessment of national-level population immunity of measles conferred through vaccination and does not consider subnational heterogeneity or vaccine waning. This tool can be readily applied to other regions and vaccine-preventable diseases.

The effective reproductive number R t has taken a central role in the scientific, political, and public discussion during the COVID-19 pandemic, with numerous real-time estimates of this quantity routinely published. Disagreement between estimates can be substantial and may lead to confusion among decision-makers and the general public. In this work, we compare different estimates of the national-level effective reproductive number of COVID-19 in Germany in 2020 and 2021. We consider the agreement between estimates from the same method but published at different time points (within-method agreement) as well as retrospective agreement across eight different approaches (between-method agreement). Concerning the former, estimates from some methods are very stable over time and hardly subject to revisions, while others display considerable fluctuations. To evaluate between-method agreement, we reproduce the estimates generated by different groups using a variety of statistical approaches, standardizing analytical choices to assess how they contribute to the observed disagreement. These analytical choices include the data source, data pre-processing, assumed generation time distribution, statistical tuning parameters, and various delay distributions. We find that in practice, these auxiliary choices in the estimation of R t may affect results at least as strongly as the selection of the statistical approach. They should thus be communicated transparently along with the estimates.

Background Pre-exposure prophylaxis (PrEP) with oral emtricitabine/tenofovir disoproxil (FTC/TDF) proved highly efficient in preventing HIV. Since 09/2019, FTC/TDF-PrEP is covered by health insurances in Germany, if prescribed by licensed specialists. However, methods to longitudinally monitor progress in PrEP implementation in Germany are lacking. Methods Utilizing anonymous FTC/TDF prescription data from 2017–2021, we developed a mathematical model to disentangle HIV-treatment from PrEP prescriptions, as well as to translate PrEP prescriptions into number of PrEP users. We used the model to estimate past- and future PrEP uptake dynamics, to predict coverage of PrEP needs and to quantify the impact of COVID-19 on PrEP uptake on a national and regional level. Results We identified significant (p < 0.01) decelerating effects of the first- and second COVID-19-lockdown on PrEP uptake in 04/2020 and 12/2020. We estimated 26,159 (CI: 25,751 − 26,571) PrEP users by 12/2021, corresponding to 33% PrEP coverage of people in need. We projected 64,794 (CI: 62,956 − 66,557) PrEP users by 12/2030, corresponding to 67% PrEP coverage. We identified profound regional differences, with high PrEP coverage and uptake in metropoles and low coverage in more rural regions. Conclusions Our approach presents a comprehensive solution to monitor and forecast PrEP implementation from anonymous data and highlighted that the COVID-19 pandemic significantly decelerated PrEP uptake in Germany. Moreover, slow PrEP uptake in rural areas indicate that structural barriers in PrEP care, education or information exist that may hamper the goal of ending the AIDS epidemic by 2030.

Introduction The I-MOVE-COVID-19 and VEBIS hospital networks have been measuring COVID-19 vaccine effectiveness (VE) in participating European countries since early 2021. Aim We aimed to measure VE against PCR-confirmed SARS-CoV-2 in patients ≥ 20 years hospitalised with severe acute respiratory infection (SARI) from December 2021 to July 2022 (Omicron-dominant period). Methods In both networks, 46 hospitals (13 countries) follow a similar test-negative case–control protocol. We defined complete primary series vaccination (PSV) and first booster dose vaccination as last dose of either vaccine received ≥ 14 days before symptom onset (stratifying first booster into received < 150 and ≥ 150 days after last PSV dose). We measured VE overall, by vaccine category/product, age group and time since first mRNA booster dose, adjusting by site as a fixed effect, and by swab date, age, sex, and presence/absence of at least one commonly collected chronic condition. Results We included 2,779 cases and 2,362 controls. The VE of all vaccine products combined against hospitalisation for laboratory-confirmed SARS-CoV-2 was 43% (95% CI: 29–54) for complete PSV (with last dose received ≥ 150 days before onset), while it was 59% (95% CI: 51–66) after addition of one booster dose. The VE was 85% (95% CI: 78–89), 70% (95% CI: 61–77) and 36% (95% CI: 17–51) for those with onset 14–59 days, 60–119 days and 120–179 days after booster vaccination, respectively. Conclusions Our results suggest that, during the Omicron period, observed VE against SARI hospitalisation improved with first mRNA booster dose, particularly for those having symptom onset < 120 days after first booster dose.

In September 2023, a severe outbreak of type B botulism with fifteen cases was linked to consumption of canned sardines at a restaurant in Bordeaux, France, during the Rugby World Cup. The cases were from seven countries. One death was recorded. Outbreak investigation using credit card data, rapid communication between health authorities of the affected countries and broad media communication allowed identification of cases and exposed persons and prevented further severe outcomes.

Introduction Two large multicentre European hospital networks have estimated vaccine effectiveness (VE) against COVID-19 since 2021. Aim We aimed to measure VE against PCR-confirmed SARS-CoV-2 in hospitalised severe acute respiratory illness (SARI) patients ≥ 20 years, combining data from these networks during Alpha (March–June)- and Delta (June–December)-dominant periods, 2021. Methods Forty-six participating hospitals across 14 countries follow a similar generic protocol using the test-negative case–control design. We defined complete primary series vaccination (PSV) as two doses of a two-dose or one of a single-dose vaccine ≥ 14 days before onset. Results We included 1,087 cases (538 controls) and 1,669 cases (1,442 controls) in the Alpha- and Delta-dominant periods, respectively. During the Alpha period, VE against hospitalisation with SARS-CoV2 for complete Comirnaty PSV was 85% (95% CI: 69–92) overall and 75% (95% CI: 42–90) in those aged ≥ 80 years. During the Delta period, among SARI patients ≥ 20 years with symptom onset ≥ 150 days from last PSV dose, VE for complete Comirnaty PSV was 54% (95% CI: 18–74). Among those receiving Comirnaty PSV and mRNA booster (any product) ≥ 150 days after last PSV dose, VE was 91% (95% CI: 57–98). In time-since-vaccination analysis, complete all-product PSV VE was > 90% in those with their last dose < 90 days before onset; ≥ 70% in those 90–179 days before onset. Conclusions Our results from this EU multi-country hospital setting showed that VE for complete PSV alone was higher in the Alpha- than the Delta-dominant period, and addition of a first booster dose during the latter period increased VE to over 90%.

Zusammenfassung Qualität in der biomedizinischen Forschung ist ein viel diskutiertes Thema unter Expertinnen und Experten, Forschungsinstituten und Förderorganisationen. In der wissenschaftlichen und allgemeinen Presse wird häufig von Qualitätsproblemen berichtet (Bsp.: Ergebnisstabilität nach Testwiederholung – „replication crisis“). Qualitätsmanagementsysteme sind weltweit ein anerkanntes und etabliertes Tool, um Qualität zu lenken und zu leiten sowie Qualitätsprobleme zu beheben. Der Begriff Qualitätsmanagement stößt unter Forschenden jedoch immer wieder auf Widerstand: Geringe Ressourcen, zu starke Regulation, Restriktion der Forschung und unnötige Bürokratie sind hier die Gegenargumente. Der Gedanke eines Qualitätsmanagementsystems für Forschungslabore ist weltweit nichts Neues. Es bestehen verschiedenste Ansätze von Wissenschaftlerinnen und Wissenschaftlern sowie Organisationen, ein Qualitätsmanagementsystem in Forschungslaboren zu etablieren und für sich ein mehrwertbringendes System zu entwickeln. Ihre Erwartungen: eine Optimierung der Forschungsprozesse sowie eine Effektivitäts- und Effizienzsteigerung. Dieser Bericht fasst Publikationen zum Thema Qualität in der biomedizinischen Forschung zusammen und erläutert Hintergrund und Vorteile von Qualitätsmanagementsystemen in Organisationen, Laboren und in der Forschung. Als Ausblick wird ein aktuelles Projekt des Robert Koch-Instituts vorgestellt. Der Artikel basiert auf einer Literaturrecherche in englischer und deutscher Sprache. Darüber hinaus wurden international und national gültige Leitfäden berücksichtigt.

Background Malaria is a leading cause of death and reduced life span in Guinea and Sierra Leone, where plans for rolling out the malaria vaccine for children are being made. There is little evidence about caregiver acceptance rates to guide roll-out policies. To inform future vaccine implementation planning, this analysis aimed to assess potential malaria vaccine acceptance by caregivers and identify factors associated with acceptance in Guinea and Sierra Leone. Methods A cross-sectional household survey using lot quality assurance sampling was conducted in three regions per country between May 2022 and August 2022. The first survey respondent in each household provided sociodemographic information. A household member responsible for childcare shared their likelihood of accepting a malaria vaccine for their children under 5 years and details about children’s health. The prevalence of caregiver vaccine acceptance was calculated and associated factors were explored using multivariable logistic regression modelling calculating adjusted odds ratios (aOR) with 95% confidence intervals (CI). Results Caregivers in 76% of 702 sampled households in Guinea and 81% of 575 households in Sierra Leone were accepting of a potential vaccine for their children. In both countries, acceptance was lower in remote areas than in urban areas (Guinea: aOR 0.22 [95%CI 0.09–0.50], Sierra Leone: 0.17 [0.06–0.47]). In Guinea, acceptance was lower among caregivers living in the richest households compared to the poorest households (0.10 [0.04–0.24]), among those whose children were tested for malaria when febrile (0.54 [0.34–0.85]) and in households adopting more preventative measures against malaria (0.39 [0.25–0.62]). Better knowledge of the cause of malaria infection was associated with increased acceptance (3.46 [1.01–11.87]). In Sierra Leone, vaccine acceptance was higher among caregivers living in households where the first respondent had higher levels of education as compared to lower levels (2.32 [1.05–5.11]). Conclusion In both countries, malaria vaccine acceptance seems promising for future vaccine roll-out programmes. Policy makers might consider regional differences, sociodemographic factors, and levels of knowledge about malaria for optimization of implementation strategies. Raising awareness about the benefits of comprehensive malaria control efforts, including vaccination and other preventive measures, requires attention in upcoming campaigns.

Introduction The study aimed to investigate the association between the start age of non-parental Early Childhood Education and Care (ECEC) and psycho-social problems in adolescence. The similarities and differences between West and East Germany were also investigated in a natural experiment. Methods Our sample consisted of 1022 children (621 from West Germany, 401 from East Germany) aged 3–4 years at wave 2003–2006 that were followed up to wave 2014–2017 as adolescents (mean ± SD age = 14.4 ± 0.03 years) in the KiGGS study. The psycho-social problems were measured by the parent-reported Strengths and Difficulties Questionnaire (SDQ) at wave 2014–2017. Linear regression was used to explore the relationship between ECEC-start-age and psycho-social problems in adolescence in Germany, and stratified by West and East Germany. Results Those who started ECEC between 2 and 3 years old (reference) had the lowest scores of psycho-social problems in the whole Germany and in West Germany in adolescence. In comparison, those who started ECEC older than 3 years old had higher scores of internalizing psycho-social problems in both West Germany (with statistically significant results) and East Germany (with a relatively larger effect size but insignificant results). Those who started ECEC younger than 1 year old had statistically significant higher scores for externalizing psycho-social problems in West Germany, even though less children started ECEC younger than 1 in West Germany compared to East Germany. This significant association was not found in East Germany. Those who started ECEC between 1 and 2 years old tended to have higher scores of externalizing psycho-social problems in both West and East Germany. Conclusion The results suggest that if children start ECEC older than 3 years or younger than 2 years, more attention needs to be given to internalizing or externalizing psycho-social problems respectively. The regional differences for children younger than 1 year old may suggest a selection effect in West Germany where only fewer parents bring babies to ECEC, while the regional similarities for children over 3 years old indicate the importance of providing access to ECEC for children over 3 years old.

The global prevalence of inflammatory bowel disease (IBD) is on the rise, prompting significant attention from researchers worldwide. IBD entails chronic inflammatory disorders of the intestinal tract, characterized by alternating flares and remissions. Through high-throughput sequencing, numerous studies have unveiled a potential microbial signature for IBD patients showing intestinal enrichment of oral-associated bacteria. Simultaneously, the oral microbiome can be perturbed by intestinal inflammation. Our prior investigation, based on 16S rRNA amplicon sequencing, underscored elevated abundance of Veillonella spp. and Prevotella spp. in the salivary microbiomes of IBD patients. Noteworthy, Prevotella salivae emerged as a distinct species significantly associated with IBD. P. salivae is an under-recognized pathogen that was found to play a role in both oral and systemic diseases. In this study, we delve deeper into the salivary microbiomes of both IBD patients and healthy controls. Employing diverse cultivation techniques and real-time quantitative polymerase chain reactions (RT-qPCR), we gauged the prevalence and abundance of Veillonella spp., Prevotella spp., and P. salivae. Our isolation efforts yielded 407 and 168 strains of Veillonella spp., as well as 173 and 90 strains of Prevotella spp., from the saliva samples of IBD patients and healthy controls, respectively. Veillonella-vancomycin agar emerged as the discerning choice for optimal Veillonella spp. cultivation, while Schaedler kanamycin-vancomycin agar proved to be the most suitable medium for cultivating Prevotella spp. strains. Comparing our RT-qPCR findings to the previous 16S rRNA amplicon sequencing data, the results corroborated the higher abundance of Veillonella spp., Prevotella spp., and P. salivae in the saliva of IBD patients compared to healthy controls. However, it's worth noting that in contrast to RT-qPCR, the 16S rRNA amplicon sequencing data revealed greater absolute abundance of all three bacterial groups in both IBD patients and controls. KEYWORDS Veillonella spp., Prevotella spp., Prevotella salivae, inflammatory bowel disease, real-time quantitative PCR, 16S rRNA amplicon sequencing Frontiers in Cellular and Infection Microbiology CITATION Hammad MI, Conrads G and Abdelbary MMH (2023) Isolation, identification, and significance of salivary Veillonella spp., Prevotella spp., and Prevotella salivae in patients with inflammatory bowel disease.