Setting
The University Hospital Basel (USB) is a tertiary care center in the northwestern part of Switzerland with over 40,000 hospital admissions annually. During the COVID-19 pandemic, patients with SARS-CoV-2 infection were frequently repatriated from institutions abroad and transferred between various Swiss hospitals based on the availability of hospital resources. At the USB, COVID-19 patients needing intensive care, were cohorted in a dedicated area of the ICU.
In September 2021, a bronchial sample from one patient in this dedicated ICU cohort revealed OXA-23-producing CRAB. Subsequent outbreak investigation included environmental and patient screening, collection of epidemiological and clinical data and performance of detailed infection prevention and control audits. All CRAB derived from patients and environmental samples were analyzed using next generation sequencing (NGS) to investigate genetic relationship. As a quality assessment project, the Ethics Commission of Northwestern and Central Switzerland (EKNZ) confirmed that no approval was required (EKNZ-Request-2023-00647) so that the need to provide a consent to participate is waived.
Audits
Control audits were performed by the infection prevention and control team and had two main focuses. First, the handling of personal protective equipment (PPE) by health care workers (HCW), especially during prone positioning of the patients in the ICU was audited. Secondly, the cleaning and disinfection procedures performed by the environmental services staff were looked at to uncover any potential breach.
Screening
Upon detection of the outbreak, all patients hospitalized on the entire ICU were screened for colonization with CRAB. The following body sites were screened to assess colonization: wounds, catheter insertion sites, rectum, urine, tracheal secretion for ventilated patients and nasopharyngeal swabs for non-ventilated patients. Swabing was performed using eSwab® (Copan). Thereafter cross-sectional screenings of all patients in the COVID-19 cohort were performed on a weekly basis.
Due to the regular exchange of patients between the COVID-19 cohorts of the ICU and the general ward, all patients hospitalized in the COVID-19 cohort of the general ward were screened likewise. Patients were screened for colonization with CRAB of the rectum, urine, wounds, and puncture sites, as well as the respiratory tract if mechanically ventilated.
For outbreak investigation purposes, environmental screening swabs of high-touch areas were obtained to identify potential transmission sources.
Microbiological analysis
Search of bacterial growth from clinical specimens was performed using different agar media according to standard bacteriological procedures. Samples for screening for CRAB from patients as well as environmental samples were plated onto selective chromogenic agar plates (chromID® CARBA SMART agar, bioMérieux, Marcy-l’Étoile, France). Colorless bacterial colonies were identified by MALDI-TOF mass spectrometry (Bruker Daltonics, Bremen, Germany). The Vitek 2® system (bioMérieux, Marcy-l’Étoile, France) was used for antimicrobial susceptibility testing of all isolates. Molecular detection of CRAB was performed by eazyplex® SuperBug complete A kit (AmplexDiagnostics, Gars-Bahnhof, Germany) using LAMP technology on a Genie II instrument (AmplexDiagnostics) detecting all relevant carbapenemase genes of A. baumannii.
Next generation sequencing (NGS)
All CRAB strains were whole genome sequenced. Bacterial DNA was extracted with the EZ1 DNA Tissue kit (QIAGEN, Hilden, Germany) in the EZ1 advanced XL workstation (QIAGEN), according to manufacturer’s recommendations. Genomic libraries were prepared using the Illumina DNA Prep kit (Illumina, San Diego) and whole genome sequencing was performed on the NextSeq500 platform (Illumina, San Diego) (read length 2 × 150 bp). Assemblies (unicycler v0.3.0b) were analyzed in Ridom Seqsphere + v7.7.5 using the published core genome MLST scheme [3, 4]. Whole Genome Sequencing read data can be accessed at NCBI sequence read archive https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA977488 [Reviewer Link to be removed post acceptance: https://dataview.ncbi.nlm.nih.gov/object/PRJNA977488?reviewer=mnmrqcmui7n6nv0dqgrm4lbum3].
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