Results of the Cologne Corona Surveillance (CoCoS) project- a cross-sectional study: survey data on risk factors of SARS-CoV-2 infection, and moderate-to-severe course in primarily immunized adults.

BACKGROUND: Amidst the COVID-19 pandemic, vaccination has been a crucial strategy for mitigating transmission and disease severity. However, vaccine-effectiveness may be influenced by various factors, including booster vaccination, as well as personal factors such as age, sex, BMI, smoking, and comorbidities. To investigate the potential effects of these factors on SARS-CoV-2 infection and disease severity, we analyzed data from the third round of the Cologne Corona Surveillance (CoCoS) project, a large cross-sectional survey. METHODS: The study was conducted mid-February to mid-March 2022 in Cologne, Germany. A random sample of 10,000 residents aged 18 years and older were invited to participate in an online survey. Information on participants' demographics (age, sex), SARS-CoV-2 infections, vaccination status, smoking, and preexisting medical conditions were collected. The outcomes of the study were: (1) the occurrence of SARS-CoV-2 infection despite vaccination (breakthrough infection) and (2) the occurrence of moderate-to-severe disease as a result of a breakthrough infection. Cox proportional-hazards regression was used to investigate possible associations between the presence/absence of booster vaccination, personal factors and the occurrence of SARS-CoV-2 infection. Associations with moderate-to-severe infection were analyzed using the Fine and Gray subdistribution hazard model. RESULTS: A sample of 2,991 residents responded to the questionnaire. A total of 2,623 primary immunized participants were included in the analysis of breakthrough infection and 2,618 in the analysis of SARS-CoV-2 infection severity after exclusions due to incomplete data. The multivariable results show that booster vaccination (HR = 0.613, 95%CI 0.415-0.823) and older age (HR = 0.974, 95%CI 0.966-0.981) were associated with a reduced hazard of breakthrough infection. Regarding the severity of breakthrough infection, older age was associated with a lower risk of moderate-to-severe breakthrough infection (HR = 0.962, 95%CI0.949-0.977). Female sex (HR = 2.570, 95%CI1.435-4.603), smoking (HR = 1.965, 95%CI1.147-3.367) and the presence of chronic lung disease (HR = 2.826, 95%CI1.465-5.450) were associated with an increased hazard of moderate-to-severe breakthrough infection. CONCLUSION: The results provide a first indication of which factors may be associated with SARS-CoV-2 breakthrough infection and moderate-to-severe course of infection despite vaccination. However, the retrospective nature of the study and risk of bias in the reporting of breakthrough infection severity limit the strength of the results. TRIAL REGISTRATION: DRKS.de, German Clinical Trials Register (DRKS), Identifier: DRKS00024046, Registered on 25 February 2021.

[Test Concept of the City of Cologne for Critical Infrastructure (KRITIS) during the First Wave of the COVID-19 Pandemic]. / Testkonzept der Stadt Köln für die Kritische Infrastruktur (KRITIS) in der ersten Welle der Corona-Pandemie.

BACKGROUND: At the beginning of the COVID-19 pandemic, the Public Health Department of the City of Cologne established preferential testing for critical infrastructure (KRITIS) personnel. The aim of this study was to retrospectively analyze this concept. METHODS: Test results as well as demographic and job-related data from March to April 2020 were collected and descriptively analyzed using a specially developed software. KRITIS personnel who tested positive were systematically interviewed over the phone. RESULTS: 1521 individuals were tested, of whom 896 (59%) were from the healthcare sector, particularly from the nursing professions (35%). Testing and consultation services were also utilized by employees of non-profit organizations (8%), administration (7%), fire department (11%), and police (4%). KRITIS personnel who tested positive suspected increased risk from contacts at the workplace (58%), mostly without adequate protection (85%). Of those surveyed, 83% rated the KRITIS concept as 'good' or 'very good'. Processes at the testing center were rated as 'good' or 'very good' by 89%, while 47% rated phone support as 'good' or 'very good', and 30% as 'sufficient' or poor. Free comments showed that frequent phone contact from the Public Health Department was perceived as positive and even more often as negative interindividually. Communication and advice were positively highlighted, while lack of competence and coordination were criticized. The respondents criticized the comparatively lower provision of testing services for family members, for example, due to limited resources. CONCLUSION: With the KRITIS concept, the Public Health Department of Cologne developed and implemented an offer for system-relevant professional groups that was intensively used and mostly assessed as positive. This concept can be used as a blueprint for other pandemics.

Mpox outbreak 2022: an overview of all cases reported to the Cologne Health Department.

PURPOSE: The worldwide mpox outbreak starting in May 2022 marks the occurrence of another previously atypical infectious disease in Europe. This study's objective was to present a comprehensive overview based on the gathered data and to illustrate the approach of the Cologne Health Department to contain the mpox outbreak. METHODS: In this retrospective observational study, 368 individuals reported to the Cologne Health Department as PCR-positive for mpox were included. Data were collected in structured telephone interviews and digitally processed. RESULTS: The first mpox case in Cologne was recorded on May 24, 2022. The local outbreak lasted approximately 4 months and reached its peak in July. The last reported case in Cologne occurred on September 17. Transmissions mostly occurred through sexual contacts (67.4%) or other close physical contacts (4.6%) between men, but also through fomites, in the context of events or occasionally in the work environment. In 21.5% of cases, no route of infection could be determined. The mean incubation period was 8.2 days. Clinically, mpox infections usually presented with skin and/or mucosal lesions accompanied by general symptoms. In 74.8% of cases, a prodromal stage was absent. Initially, the rash often had an unspecific appearance, but in the further clinical course, it usually passed through the typical stages. Most infections resolved spontaneously under home care. In 3.5% of cases, however, inpatient hospitalisation was required. Infected persons with a previous smallpox vaccination had 0.43 times the odds of unvaccinated persons to be affected by lesions in 3 or more body regions and 0.30 times the odds to develop lesions in all 5 body regions. Previous vaccination statistically reduced the total duration of symptoms by 2.0 days. CONCLUSIONS: The mpox outbreak 2022 in Cologne primarily affected men who have sex with men and have reported recent sexual encounters. The observed average incubation period was shorter than initially assumed. Mucosal involvement and associated symptoms occur in a relevant number of cases and can lead to more severe clinical courses. Previous smallpox vaccination was statistically significantly associated with milder courses of mpox. In the case of an unclear rash or symptoms suggesting mucosal involvement, mpox should be considered as a differential diagnosis. An equally rapid and well-orchestrated public health response are crucial for infection control.

Implementing the Lolli-Method and pooled RT-qPCR testing for SARS-CoV-2 surveillance in schools: a pilot project.

PURPOSE: School closures have been used as part of lockdown strategies to contain the spread of SARS-CoV-2, adversely affecting children's health and education. To ensure the accessibility of educational institutions without exposing society to the risk of increased transmissions, it is essential to establish SARS-CoV-2 testing strategies that are child-friendly, scalable and implementable in a daily school routine. Self-sampling using non-invasive saliva swabs combined with pooled RT-qPCR testing (Lolli-Method) has been proven to be a sensitive method for the detection of SARS-CoV-2. METHODS: We conducted a pilot project in Cologne, Germany, designed to determine the feasibility of a large-scale rollout of the Lolli-Method for testing without any additional on-site medical staff in schools. Over a period of three weeks, students from 22 schools were sampled using the Lolli-Method. At the end of the project, teachers were asked to evaluate the overall acceptance of the project. RESULTS: We analyzed a total of 757 pooled RT-qPCRs obtained from 8,287 individual swabs and detected 7 SARS-CoV-2 infected individuals. The Lolli-Method was shown to be a feasible and accepted testing strategy whose application is only slightly disruptive to the daily school routine. CONCLUSION: Our observations suggest that the Lolli-Method in combination with pooled RT-qPCR can be implemented for SARS-CoV-2 surveillance in daily school routine, applicable on a large scale.

Results of the Cologne Corona Surveillance (CoCoS) study - a cross-sectional study: survey data on risk factors of SARS-CoV-2 infection in adults.

BACKGROUND: The personal, environmental, and behavioral risk factors that play an important role in the spread of SARS-CoV-2 are still largely unclear. At the same time, there is limited evidence on the effectiveness of specific countermeasures for SARS-CoV-2. As a first approach to these questions, we use data from the Cologne Corona Surveillance (CoCoS) study, a large cross-sectional study conducted in Cologne, Germany, in June 2021. METHODS: This study was conducted in Cologne, Germany. Six thousand randomly selected Cologne residents who were 18 years of age or older were invited to participate in this study. Participant information was obtained via an online survey. Previous SARS-CoV-2 infections were recorded using self-reports. Sociodemographic and environmental information such as age, sex, living situation were collected. Potential SARS-CoV-2 risk behaviors were captured (workplace situation, adherence to hygiene regulations, and regular use of public transportation). Adherence to hygiene regulations was surveyed by determining the compliance with the 'AHA'-rules (German acronym that stands for keeping a distance of 1.5 m from fellow citizens, hand disinfection, and wearing a face mask). Binary logistic regression analysis was used to identify risk factors for SARS-CoV-2 infection. RESULTS: A sample of 2,433 study participants provided information. Comparison of the sample with the general population showed representativeness for most sociodemographic characteristics with a preference for higher level of education in the study sample. Younger age, as well as living with minor children (under 18 years) in the same household were associated with a higher number of self-reported SARS-CoV-2 infections. Adherence to hygiene regulations was associated with fewer self-reported SARS-CoV-2 infections in adults. Gender, size of living space per person, workplace situation (work from home versus working with contact to colleagues/customers), and regular use of public transportation showed no significant association with self-reported SARS-CoV-2 infections in multivariable analysis. CONCLUSION: The presented results provide initial indications of which sociodemographic and behavioral factors may be associated with SARS-CoV-2 infection. However, the fact that these factors were recorded without exact dates and could have changed accordingly during the pandemic or after infection limits the strength of the results. TRIAL REGISTRATION: DRKS.de, German Clinical Trials Register (DRKS), Identifier: DRKS00024046, Registered on 25 February 2021.

[Spreading Dynamics of the Alpha and Beta Virus Variants of SARS-CoV-2 at the Beginning of Their Appearance in the City of Cologne in January and February 2021]. / Ausbreitungsdynamik der Alpha- und Beta-Virusvarianten von SARS-CoV-2 zum Beginn ihres Auftretens in der Stadt Köln im Januar und Februar 2021.

BACKGROUND AND AIM OF THE STUDY: Constantly changing virus variants of the novel coronavirus SARS-CoV-2 pose major challenges to the healthcare system. The aim of the present study was to analyse major outbreaks of the alpha and beta variants in Cologne in order to enable effective and rapid response to new virus variants in future pandemics as well as to derive targeted measures to combat the pandemic. METHODS: In the observation period from January 22 to February 23, 2021, all individuals testing positive for SARS-CoV-2 and their contact persons who were reported to the Cologne Public Health Department were interviewed by employees of the Public Health Department over the telephone. On the one hand, these data formed the basis for the epidemiological and descriptive comparison of the alpha and beta variants to the previously dominant wild type. On the other hand, they were also the basis for the graphical processing of clusters formed by the two virus variants in the form of so-called timelines. For the present work, all clusters with ≥10 individuals were taken into account for the period under consideration. RESULTS: Of the 3780 individuals that tested positive for SARS-CoV-2 in Cologne during the observation period, 818 cases were due to the virus variants alpha and beta. The alpha versus the beta variant spread quickly in Cologne despite strict non-pharmaceutical interventions. As part of the cluster analysis, five major outbreak were identified in Cologne during the observation period. The alpha variant clusters included two daycare centers and one monastery, while the beta variant clusters included a communal accommodation for refugees and an old people's and nursing home. With the help of cluster analysis, the core role of the spread of the virus variants examined was shown, especially in the context of the home setting. In addition, a high proportion of cases of unknown infection site/contact was found for the wild type and alpha variant. CONCLUSION: Cluster analyses are an extremely useful tool in the determination of infection sites/contacts and transmission paths as well as in determining existing protective measures and hygiene concepts. Since clusters are to be regarded as the most unfavorable spread scenario, cluster analyses provide important suggestions for modifying further action for both this, as well as for future pandemics.

Infection and transmission risks of COVID-19 in schools and their contribution to population infections in Germany: A retrospective observational study using nationwide and regional health and education agency notification data.

BACKGROUND: School-level infection control measures in Germany during the early Coronavirus Disease 2019 (COVID-19) pandemic differed across the 16 federal states and lacked a dependable evidence base, with available evidence limited to regional data restricted to short phases of the pandemic. This study aimed to assess the (a) infection risks in students and staff; (b) transmission risks and routes in schools; (c) effects of school-level infection control measures on school and population infection dynamics; and (d) contribution of contacts in schools to population cases. METHODS AND FINDINGS: For this retrospective observational study, we used German federal state (NUTS-2) and county (NUTS-3) data from public health and education agencies from March 2020 to April 2022. We assessed (a) infection risk as cumulative risk and crude risk ratios and (b) secondary attack rates (SARs) with 95% confidence interval (CI). We used (c) multiple regression analysis for the effects of infection control measures such as reduced attendance, mask mandates, and vaccination coverage as absolute reduction in case incidence per 100,000 inhabitants per 14 days and in percentage relative to the population, and (d) infection dynamic modelling to determine the percentage contribution of school contacts to population cases. We included (a) nationwide NUTS-2 data from calendar weeks (W) 46-50/2020 and W08/2021-W15/2022 with 3,521,964 cases in students and 329,283 in teachers; (b) NUTS-3 data from W09-25/2021 with 85,788 student and 9,427 teacher cases; and (c) detailed data from 5 NUTS-3 regions from W09/2020 to W27/2021 with 12,814 cases (39% male, 37% female; median age 14, range 5 to 63), 43,238 contacts and 4,165 secondary cases for students (for teachers, 14,801 [22% male, 50% female; median age 39, range 16 to 75], 5,893 and 472). Infection risk (a) for students and teachers was higher than the population risk in all phases of normal presence class and highest in the early 2022 omicron wave with 30.6% (95% CI 30.5% to 32.6%) of students and 32.7% (95% CI 32.6% to 32.8%) of teachers infected in Germany. SARs (b) for students and staff were below 5% in schools throughout the study period, while SARs in households more than doubled from 13.8% (95% CI 10.6% to 17.6%) W21-39/2020 to 28.7% (95% CI 27% to 30.4%) in W08-23/2021 for students and 10.9% (95% CI 7% to 16.5%) to 32.7% (95% CI 28.2% to 37.6%) for staff. Most contacts were reported for schools, yet most secondary cases originated in households. In schools, staff predominantly infected staff. Mandatory surgical mask wearing during class in all schools was associated with a reduction in the case incidence of students and teachers (c), by 56/100,000 persons per 14 days (students: 95% CI 47.7 to 63.4; teachers: 95% CI 39.6 to 71.6; p < 0.001) and by 29.8% (95% CI 25% to 35%, p < 0.001) and 24.3% (95% CI 13% to 36%, p < 0.001) relative to the population, respectively, as were reduced attendance and higher vaccination coverage. The contribution of contacts in schools to population cases (d) was 2% to 20%, lowest during school closures/vacation and peaked during normal presence class intervals, with the overall peak early during the omicron wave. Limitations include underdetection, misclassification of contacts, interviewer/interviewee dependence of contact-tracing, and lack of individual-level confounding factors in aggregate data regression analysis. CONCLUSION: In this study, we observed that open schools under hygiene measures and testing strategies contributed up to 20% of population infections during the omicron wave early 2022, and as little as 2% during vacations/school closures; about a third of students and teachers were infected during the omicron wave in early 2022 in Germany. Mandatory mask wearing during class in all school types and reduced attendance models were associated with a reduced infection risk in schools.

[Spatio-temporal distribution of COVID-19 in Cologne and associated socio-economic factors in the period from February 2020 to October 2021]. / Die zeitlich-räumliche Verteilung von COVID-19 in Köln und beeinflussende soziale Faktoren im Zeitraum Februar 2020 bis Oktober 2021.

BACKGROUND AND GOALS: Even in the early phase of the COVID-19 pandemic, which took a very different course globally, there were indications that socio-economic factors influenced the dynamics of disease spread, which from the second phase (September 2020) onwards particularly affected people with a lower socio-economic status. Such effects can also be seen within a large city. The present study visualizes and examines the spatio-temporal spread of all COVID-19 cases reported in Cologne, Germany (February 2020-October 2021) at district level and their possible association with socio-economic factors. METHODS: Pseudonymized data of all COVID-19 cases reported in Cologne were geo-coded and their distribution was mapped in an age-standardized way at district level over four periods and compared with the distribution of social factors. The possible influence of the selected factors was also examined in a regression analysis in a model with case growth rates. RESULTS: The small-scale local infection process changed during the pandemic. Neighborhoods with weaker socio-economic indices showed higher incidence over a large part of the pandemic course, with a positive correlation between poverty risk factors and age-standardized incidence. The strength of this correlation changed over time. CONCLUSION: The timely observation and analysis of the local spread dynamics reveals the positive correlation of disadvantaging socio-economic factors on the incidence rate of COVID-19 at the level of a large city and can help steer local containment measures in a targeted manner.

Disinfection of Transvaginal Ultrasound Probes by Ultraviolet C - A clinical Evaluation of Automated and Manual Reprocessing Methods.

PURPOSE: Since pathogens can be transmitted to patients via transvaginal ultrasound probes, it is of particular importance that cleaning and disinfection are performed adequately. This study was designed to do a qualitative comparison of a low-level disinfection technique with disinfectant-impregnated wipes and an automated disinfection technique using ultraviolet C radiation in a clinical setting. MATERIALS AND METHODS: The transvaginal ultrasound probes used in two groups of 160 patients were compared in a prospective controlled study regarding the effectiveness of manual low-level disinfection (Mikrozid sensitive wipes) and automated disinfection using ultraviolet C radiation (Antigermix AS1). Microbiological samples were taken from the whole surface of the probe before and after the disinfection process. RESULTS: Before disinfection, 98.75 % (316/320) of the samples showed bacterial contamination. After automated and manual disinfection, the contamination rates were 34.2 % (54/158, automated) and 40.5 % (64/158, disinfectant wipes) (p > 0.05). Pathogens with the potential to cause healthcare-associated infections, such as Enterococcus faecalis and Klebsiella pneumoniae, were removed completely by both techniques. Manual disinfection showed a lower contamination rate after disinfection of bacteria that usually belong to the vaginal, pharyngeal and skin flora (disinfectant wipes 10.6 %, 11/104, automated 32.5 %, 38/117) (p < 0.001). CONCLUSION: For the clinical routine, automated disinfection with ultraviolet C is a promising technique for transvaginal ultrasound probes because of the simple handling and time efficiency. In our study, this method was completely effective against nosocomial pathogens. However, the study didn't show any significant difference in terms of effectiveness compared to low-level wipe disinfection.

Control of Multidrug-Resistant Pseudomonas aeruginosa in Allogeneic Hematopoietic Stem Cell Transplant Recipients by a Novel Bundle Including Remodeling of Sanitary and Water Supply Systems.

Background: Infections by multidrug-resistant Pseudomonas aeruginosa (MDRPa) are an important cause of morbidity and mortality in patients after allogeneic hematopoietic stem cell transplantation (HSCT). Humid environments can serve as a reservoir and source of infection by this pathogen. To minimize the risk of infection from these reservoirs, we performed extensive remodeling of sanitation and water installations as the focus of our hygiene bundle. Methods: During the reconstruction of our transplantation unit (April 2011-April 2014) we implemented several technical modifications to reduce environmental contamination by and subsequent spreading of MDRPa, including a newly designed shower drain, disinfecting siphons underneath the sinks, and rimless toilets. During a 3-year study period (2012-2014), we tracked the number of patients affected by MDRPa (colonized and/or infected) and the outcome of infected patients, and monitored the environmental occurrence of this pathogen. We further performed whole-genome sequencing of nosocomial MDRPa strains to evaluate genotypic relationships between isolates. Results: Whereas 31 (9.2%; 18 colonized, 13 infected) patients were affected in 2012 and 2013, the number decreased to 3 in 2014 (17%; 3 colonized, 0 infected). Lethality by MDRPa similarly decreased from 3.6% to 0%. Environmental detection of MDRPa decreased in toilets from 18.9% in 2012-2013 to 6.1% in the following year and from 8.1% to 3.0%, respectively, in shower outlets. Whole-genome sequencing showed close relationships between environmental and patient-derived isolates. Conclusions: Hospital construction measures aimed at controlling environmental contamination by and spread of MDRPa are effective at minimizing the risk of highly lethal MDRPa infections.

Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H- Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates.

Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:H- strains, first identified in Germany, have emerged as important pathogens throughout Europe. Besides chromosomally encoded Shiga toxin 2a (the major virulence factor), several putative virulence loci, including the hly, etp, and sfp operons, encoding EHEC hemolysin, type II secretion system proteins, and Sfp fimbriae, respectively, are located on the 121-kb plasmid pSFO157 in German strains. Here we report novel SF EHEC O157:H- strains isolated from patients in the Czech Republic. These strains share the core genomes and chromosomal virulence loci encoding toxins (stx2a and the cdtV-ABC operon) and adhesins (eae-γ, efa1, lpfAO157OI-141, and lpfAO157OI-154) with German strains but differ essentially in their plasmids. In contrast to all previously detected SF EHEC O157:H- strains, the Czech strains carry two plasmids, of 79 kb and 86 kb. The 79-kb plasmid harbors the sfp operon, but neither of the plasmids contains the hly and etp operons. Sequence analyses demonstrated that the 79-kb plasmid (pSFO157 258/98-1) evolved from pSFO157 of German strains by deletion of a 41,534-bp region via homologous recombination, resulting in loss of the hly and etp operons. The 86-kb plasmid (pSFO157 258/98-2) displays 98% sequence similarity to a 92.7-kb plasmid of an extraintestinal pathogenic E. coli bloodstream isolate. Our finding of this novel plasmid composition in SF EHEC O157:H- strains extends the evolutionary history of EHEC O157 plasmids. Moreover, the unique molecular plasmid characteristics permit the identification of such strains, thereby facilitating further investigations of their geographic distribution, clinical significance, and epidemiology.IMPORTANCE Since their first identification in Germany in 1989, sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H- (nonmotile) strains have emerged as important causes of the life-threatening disease hemolytic-uremic syndrome in Europe. They account for 10 to 20% of sporadic cases of this disease and have caused several large outbreaks. The strains isolated throughout Europe share conserved chromosomal and plasmid characteristics. Here we identified novel sorbitol-fermenting enterohemorrhagic E. coli O157:H- patient isolates in the Czech Republic which differ from all such strains reported previously by their unique plasmid characteristics, including plasmid number, composition of plasmid-carried virulence genes, and plasmid origins. Our findings contribute substantially to understanding the evolution of E. coli O157 strains and their plasmids. In practical terms, they enable the identification of strains with these novel plasmid characteristics in patient stool samples and thus the investigation of their roles as human pathogens in other geographic areas.

Ongoing haemolytic uraemic syndrome (HUS) outbreak caused by sorbitol-fermenting (SF) Shiga toxin-producing Escherichia coli (STEC) O157, Germany, December 2016 to May 2017.

We report an ongoing, protracted and geographically dispersed outbreak of haemolytic uraemic syndrome (HUS) and gastroenteritis in Germany, involving 30 cases since December 2016. The outbreak was caused by the sorbitol-fermenting immotile variant of Shiga toxin-producing (STEC) Escherichia coli O157. Molecular typing revealed close relatedness between isolates from 14 cases. One HUS patient died. Results of a case-control study suggest packaged minced meat as the most likely food vehicle. Food safety investigations are ongoing.

Prevalence of Multidrug Resistant Bacteria in Refugees: A Prospective Case Control Study in an Obstetric Cohort.

Purpose To determine the prevalence of multidrug resistant (MDR) bacteria in a cohort of pregnant refugee women. Methods In a prospective case control study, surveillance cultures for MDR bacteria (methicillin-resistant Staphylococcus aureus [MRSA], vancomycin-resistant enterococci [VRE], MDR Gram-negative bacteria [MRGN]) were analysed between October 2015 and June 2016 from a cohort of 50 pregnant refugee women and 50 resident controls in the obstetric unit of a German tertiary referral hospital. Results Prevalence of MRSA was noticeably higher among refugee women compared to residents (6 vs. 0%). In addition, a trend towards a higher prevalence of VRE and MDR Gram-negative bacteria in refugees was shown (1.8 vs. 0%). Conclusions Due to the higher prevalence of MDR bacteria, surveillance cultures are justified in order to prevent nosocomial spread of MDR bacteria.

Whole-Genome Sequencing Elucidates Epidemiology of Nosocomial Clusters of Acinetobacter baumannii.

We characterized two epidemiologically similar Acinetobacter baumannii clusters from two separate intensive care units (ICU) using core genome multilocus sequence typing. Clonal spread was confirmed in ICU-1 (12 of 14 isolates shared genotypes); in ICU-2, all genotypes (13 isolates) were diverse, thus excluding transmissions and enabling adequate infection control measures.

Molecular Characterization of Human Atypical Sorbitol-Fermenting Enteropathogenic Escherichia coli O157 Reveals High Diversity.

Alongside the well-characterized enterohemorrhagic Escherichia coli (EHEC) O157:H7, serogroup O157 comprises sorbitol-fermenting typical and atypical enteropathogenic E. coli (EPEC/aEPEC) strains that carry the intimin-encoding gene eae but not Shiga toxin-encoding genes (stx). Since little is known about these pathogens, we characterized 30 clinical isolates from patients with hemolytic uremic syndrome (HUS) or uncomplicated diarrhea with respect to their flagellin gene (fliC) type and multilocus sequence type (MLST). Moreover, we applied whole-genome sequencing (WGS) to determine the phylogenetic relationship with other eae-positive EHEC serotypes and the composition of the rfbO157 region. fliC typing resulted in five fliC types (H7, H16, H34, H39, and H45). Isolates of each fliC type shared a unique ST. In comparison to the 42 HUS-associated E. coli (HUSEC) strains, only the stx-negative isolates with fliCH7 shared their ST with EHEC O157:H7/H(-) strains. With the exception of one O157:H(-) fliCH16 isolate, HUS was exclusively associated with fliCH7. WGS corroborated the separation of the fliCH7 isolates, which were closely related to the EHEC O157:H7/H(-) isolates, and the diverse group of isolates exhibiting different fliC types, indicating independent evolution of the different serotypes. This was also supported by the heterogeneity within the rfbO157 region that exhibited extensive recombinations. The genotypic subtypes and distribution of clinical symptoms suggested that the stx-negative O157 strains with fliCH7 were originally EHEC strains that lost stx The remaining isolates form a distinct and diverse group of atypical EPEC isolates that do not possess the full spectrum of virulence genes, underlining the importance of identifying the H antigen for clinical risk assessment.

Phylogeny and phenotypes of clinical and environmental Shiga toxin-producing Escherichia coli O174.

Shiga toxin (Stx)-producing Escherichia coli (STEC) of serogroup O174 are human pathogenic intimin gene (eae)-negative STEC. To facilitate diagnosis and subtyping, we genotypically and phenotypically characterized 25 STEC O174 isolates from humans with different clinical outcomes and from animals and the environment. fliC genotyping resulted in four different genotypes (fliCH2 : n = 5; fliCH8 : n = 8; fliCH21 : n = 11; fliCH46 : n = 1). Twenty-three strains were motile expressing the corresponding H antigen; two non-motile isolates possessed fliCH8 . The stx genotypes and non-stx virulence loci, including toxins, serine-proteases and adhesins correlated well with serotypes but showed no differences with respect to the isolates' origins. Multilocus sequence typing identified seven sequence types that correlated with serotypes. Core gene typing further specified the four serotypes, including a previously unknown O174:H46 combination, and revealed distant relationships of the different serotypes within serogroup O174 and in relation to other haemolytic uremic syndrome (HUS)-associated STEC. Only serotype O174:H21 was associated with HUS. Differences in virulence factors and in the adherence capacity of STEC O174 corroborated this separation into four distinct groups. Our study provides a basis for O174 subtyping, unravels considerable genotypic and phenotypic heterogeneity and sheds light to potential environmental and animal reservoirs.

Correction: Where is the greatest risk of COVID-19 infection? Findings from Germany's largest public health department, Cologne.

[This corrects the article DOI: 10.1371/journal.pone.0273496.].

SARS-CoV-2 Test-to-Stay in Daycare.

BACKGROUND AND OBJECTIVES: Test-to-stay concepts apply serial testing of children in daycare after exposure to SARS-CoV-2 without use of quarantine. This study aims to assess the safety of a test-to-stay screening in daycare facilities. METHODS: 714 daycare facilities and approximately 50 000 children ≤6 years in Cologne, Germany participated in a SARS-CoV-2 Pool-polymerase chain reaction (PCR) screening from March 2021 to April 2022. The screening initially comprised post-exposure quarantine and was adapted to a test-to-stay approach during its course. To assess safety of the test-to-stay approach, we explored potential changes in frequencies of infections among children after the adaptation to the test-to-stay approach by applying regression discontinuity in time (RDiT) analyses. To this end, PCR-test data were linked with routinely collected data on reported infections in children and analyzed using ordinary least squares regressions. RESULTS: 219 885 Pool-PCRs and 352 305 Single-PCRs were performed. 6440 (2.93%) Pool-PCRs tested positive, and 17 208 infections in children were reported. We estimated that during a period of 30 weeks, the test-to-stay concept avoided between 7 and 20 days of quarantine per eligible daycare child. RDiT revealed a 26% reduction (Exp. Coef: 0.74, confidence interval 0.52-1.06) in infection frequency among children and indicated no significant increase attributable to the test-to-stay approach. This result was not sensitive to adjustments for 7-day incidence, season, SARS-CoV-2 variant, and socioeconomic status. CONCLUSIONS: Our analyses provide evidence that suggest safety of the test-to-stay approach compared with quarantine measures. This approach offers a promising option to avoid use of quarantine after exposure to respiratory pathogens in daycare settings.

Enterohemorrhagic Escherichia coli O26:H11/H-: a new virulent clone emerges in Europe.

BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC) O26 causes diarrhea and hemolytic uremic syndrome (HUS). Strains harboring the stx1a gene prevail, but strains with stx2a as the sole Shiga toxin-encoding gene are now emerging. The traits and virulence of the latter set of strains are unknown. We correlated stx genotypes of 272 EHEC O26 strains isolated in 7 European countries between 1996 and 2012 with disease phenotypes. We determined phylogeny, clonal structure, and plasmid gene profiles of the isolates and portray geographic and temporal distribution of the different subgroups. METHODS: The stx genotypes and plasmid genes were identified using polymerase chain reaction, phylogeny was assigned using multilocus sequence typing, and clonal relatedness was established using pulsed-field gel electrophoresis. RESULTS: Of the 272 EHEC O26 isolates, 107 (39.3%), 139 (51.1%), and 26 (9.6%) possessed stx1a, stx2a, or both genes, respectively. Strains harboring stx2a only were significantly associated with HUS (odds ratio, 14.2; 95% confidence interval, 7.9-25.6; P < .001) compared to other stx genotypes. The stx2a-harboring strains consist of 2 phylogenetically distinct groups defined by sequence type (ST) 21 and ST29. The ST29 strains are highly conserved and correspond by plasmid genes to the new virulent clone of EHEC O26 that emerged in Germany in the 1990s. This new clone occurred in 6 of the 7 countries and represented approximately 50% of all stx2a-harboring EHEC O26 strains isolated between 1996 and 2012. CONCLUSIONS: A new highly virulent clone of EHEC O26 has emerged in Europe. Its reservoirs and sources warrant identification.