Differentiating patients admitted primarily due to coronavirus disease 2019 (COVID-19) from those admitted with incidentally detected severe acute respiratory syndrome corona-virus type 2 (SARS-CoV-2) at hospital admission: A cohort analysis of German hospital records.

Objective: The number of hospitalized patients with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) does not differentiate between patients admitted due to coronavirus disease 2019 (COVID-19) (ie, primary cases) and incidental SARS-CoV-2 infection (ie, incidental cases). We developed an adaptable method to distinguish primary cases from incidental cases upon hospital admission.

Design: Retrospective cohort study.

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.

[Establishment of genomic pathogen surveillance to strengthen pandemic preparedness and infection prevention in Germany].

The SARS-CoV‑2 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.

Molecular Epidemiology of with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers-A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016.

Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, we assessed the molecular epidemiology of third-generation cephalosporine-resistant isolated between 2007 and 2016 from German soldiers after deployments, with a particular focus on the African Sahel region.

Carbapenem resistance in Acinetobacter pittii isolates mediated by metallo-β-lactamases.

Objectives: To characterize the genetic environment of metallo-β-lactamases (MBL) in carbapenem-resistant clinical Acinetobacter pittii isolates.

Methods: Seventeen carbapenem-resistant A. pittii isolates harbouring an MBL were collected between 2010 and 2015 in Germany.

Epidemiology of Plasmids in and with Acquired Extended Spectrum Beta-Lactamase Genes Isolated from Chronic Wounds in Ghana.

Little information is available on the local epidemiology of mobile genetic elements such as plasmids harboring acquired beta-lactamase genes in Western African Ghana. In the present study, we screened for plasmids in three and four isolates expressing extended spectrum beta-lactamases (ESBL) mediated by the gene from chronically infected wounds of Ghanaian patients. Bacterial isolates were subjected to combined short-read and long-read sequencing to obtain the sequences of their respective plasmids.

Reduced Clostridioides difficile infections in hospitalised older people through multiple quality improvement strategies.

Objectives: To reduce infections with Clostridioides difficile (CDI) in geriatric patients by interventions easily implementable in standard clinical care.

Methods: Prevalence and incidence of CDI between January 2015 and February 2020 were analysed (n = 25,311 patients). Pre-intervention status was assessed from April 2016 to March 2017 (n = 4,922).

Transformation of microbiology data into a standardised data representation using OpenEHR.

The spread of multidrug resistant organisms (MDRO) is a global healthcare challenge. Nosocomial outbreaks caused by MDRO are an important contributor to this threat. Computer-based applications facilitating outbreak detection can be essential to address this issue.

Clonal Clusters, Molecular Resistance Mechanisms and Virulence Factors of Gram-Negative Bacteria Isolated from Chronic Wounds in Ghana.

Wound infections are common medical problems in sub-Saharan Africa but data on the molecular epidemiology are rare. Within this study we assessed the clonal lineages, resistance genes and virulence factors of Gram-negative bacteria isolated from Ghanaian patients with chronic wounds. From a previous study, 49 , 21 complex members and 12 were subjected to whole genome sequencing.

Novel multiplex PCRs for detection of the most prevalent carbapenemase genes in Gram-negative bacteria within Germany.

Gram-negative bacteria are a common source of infection both in hospitals and in the community, and antimicrobial resistance is frequent among them, making antibiotic therapy difficult, especially when these isolates carry carbapenem resistance determinants.. A simple method to detect all the commonly found carbapenemases in Germany was not available.

IS-Mediated Transfer of as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital.

One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing species due to clonal spread and cross-species exchange of plasmids and possibly transposons.

The Washing Machine as a Reservoir for Transmission of Extended-Spectrum-Beta-Lactamase (CTX-M-15)-Producing Klebsiella oxytoca ST201 to Newborns.

During the period from April 2012 to May 2013, 13 newborns (1 to 4 weeks of age) and 1 child in a pediatric hospital ward in Germany were colonized with producing an extended-spectrum beta-lactamase (ESBL) (CTX-M-15). A microbiological source-tracking analysis with human and environmental samples was carried out to identify the source and transmission pathways of the clone. In addition, different hygienic intervention methods were evaluated.

Overestimation of an Outbreak of Enterobacter cloacae in a Neonatal Intensive Care Unit in Germany, 2015.

Background: In August 2015, 17 neonates with Enterobacter cloacae (E. cloacae) colonization were identified in a neonatal intensive care unit (NICU) in Germany. Two developed severe brain abscesses.

Characterization of mutations in Escherichia coli PBP2 leading to increased carbapenem MICs.

Objectives: To examine the impact on carbapenem resistance of mutations in Escherichia coli PBP2 detected in clinical isolates showing increased MICs of imipenem, but not of meropenem.

Methods: The mutations in the PBP2-encoding gene mrdA were introduced into E. coli DH5α using the helper plasmid pTKRED.

LMB-1, a novel family of class B3 MBLs from an isolate of Enterobacter cloacae.

Objectives: To identify and characterize a novel MBL gene conferring carbapenem resistance to an isolate of Enterobacter cloacae from Austria.

Methods: The novel MBL gene was heterologously expressed in Escherichia coli TOP10 to conduct comparative MIC studies and biochemical assays. Furthermore, WGS was performed using Illumina MiSeq and Oxford Nanopore MinION instruments to analyse the genetic environment of the novel MBL gene.

Transmission Risk on a Neonatal Intensive Care Unit: versus .

Isolation precautions required for neonatal intensive care units are part of a bundle with the aim to prevent transmission, colonization, and infection with multidrug-resistant gram-negative pathogens as neonates face an increased risk of mortality and morbidity in case of infection. The following short report describes a transmission of 3MDRGN on a neonatal intensive care unit in a university hospital in Germany. This transmission occurred even though intensified infection control measures were in place, which impressively shows the importance of surveillance, outbreak management, and awareness of contributing factors regarding outbreak situations.

Genome-based analysis of Carbapenemase-producing isolates from German hospital patients, 2008-2014.

Background: By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing isolated from hospitalized patients in Germany between 2008 and 2014.

Methods: We selected a representative subset of 107 carbapenemase-producing clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS.

[Prevention and Detection of Multidrug-resistant Bacteria].

Patients colonized or infected by multidrug-resistant bacteria (MDR) are entitled to the same medical treatment as other patients and infection control measures based on the current evidence are not in conflict with this aim. Recent studies indicate that the correct sampling technique is of utmost importance when screening for MRSA and usage of certain swabs might reduce the sensitivity considerably. Despite improvements in diagnostic strategies for direct MRSA detection by PCR, false positive results cannot be totally excluded.

[Effective management of an outbreak with multiresistent Klebsiella pneumoniae in a neurorehabilitation unit].

Background: In addition to acute care hospitals, rehabilitation centres are increasingly confronted with multi-resistant pathogens. Long durations of stay and intensive treatments impose special hygienic challenges.

Material And Methods: We investigated an extended spectrum beta-lactamase-Klebsiella pneumoniae (ESBL-K.

Whole Genome Sequence Analysis of CTX-M-15 Producing Isolates Allowed Dissecting a Polyclonal Outbreak Scenario.

Extended-spectrum β-lactamase (ESBL) producing pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS.

Stalking a lethal superbug by whole-genome sequencing and phylogenetics: Influence on unraveling a major hospital outbreak of carbapenem-resistant Klebsiella pneumoniae.

Background: From July 2010-April 2013, Leipzig University Hospital experienced the largest outbreak of a Klebsiella pneumoniae carbapenemase 2 (KPC-2)-producing Klebsiella pneumoniae (KPC-2-Kp) strain observed in Germany to date. After termination of the outbreak, we aimed to reconstruct transmission pathways by phylogenetics based on whole-genome sequencing (WGS).

Methods: One hundred seventeen KPC-2-Kp isolates from 89 outbreak patients, 5 environmental KPC-2-Kp isolates, and 24 K pneumoniae strains not linked to the outbreak underwent WGS.

Dissemination of blaOXA-58 in Proteus mirabilis isolates from Germany.

Objectives: Characterization of Proteus mirabilis isolates harbouring bla OXA-58 with emphasis on the genetic environment of this resistance determinant.

Methods: Strains of P. mirabilis ( n  =   37) isolated from different patients were tested for the presence of bla OXA-58 .

Genetic and biochemical characterization of HMB-1, a novel subclass B1 metallo-β-lactamase found in a Pseudomonas aeruginosa clinical isolate.

Objectives: To characterize a novel subclass B1 metallo-β-lactamase (MBL) found in an MDR Pseudomonas aeruginosa clinical isolate.

Methods: The isolate P. aeruginosa NRZ-03096 was recovered in 2012 from an anal swab from a patient hospitalized in Northern Germany and showed high MICs of carbapenems.

Comparison of Phenotypic Tests and an Immunochromatographic Assay and Development of a New Algorithm for Detection of OXA-48-like Carbapenemases.

OXA-48 is the most prevalent carbapenemase in in Europe and the Middle East, but it is frequently missed because many isolates display low MICs for carbapenems. Furthermore, in contrast to metallo-β-lactamases or carbapenemases (KPC), no specific inhibitor is available for the phenotypic detection of OXA-48. Molecular detection of is the "gold standard" but is not available in many laboratories.