Study design and ethics
This is an outbreak report and a systematic review of the literature concerning MDRO outbreaks during the COVID-19 pandemic. The outbreak is reported according to the ORION statement , the review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, where applicable . The review protocol was registered on Prospero (Registration number: 259474) .
We retrospectively studied a CRAB outbreak that involved the medical and surgical ICU in our 700-bed tertiary hospital in Eastern Switzerland. Both COVID-19 and non-COVID-19 patients were treated on the two affected ICUs. Due to the high number of patients during the pandemic, bed capacities were extended from 12 to 16, and from 24 to 32 beds for the medical and surgical ICU, respectively. Cases were defined as patients with CRAB isolation in any kind of sample, including clinical and screening specimens. Patient characteristics including hospital mortality were collected from chart reviews; the impact of CRAB infection (non-related, partially related, and directly attributable) on in-hospital mortality was assessed.
The outbreak investigation was led by a multidisciplinary infection control team (physicians, nurses, hospital epidemiologists) and consisted of contact screenings (defined as sharing the room with a CRAB patient for ≥ 24 h), weekly cross-sectional screening of all ICU patients, routine screenings at day 5 and 10 after ICU discharge for all patients with a stay longer than 48 h on either ICU, and sampling of medical equipment, patient environment, and sinks. Patient screening sites included rectum, skin (axilla and groin), urine (if catheter in situ), and the respiratory tract (if ventilated or in case of tracheostomy). The further containment strategy included cohorting of CRAB positive patients, intensification of environmental cleaning, observations and training regarding correct use of PPE and hand hygiene performance, and restriction of carbapenem use. We used descriptive statistics to summarize patient characteristics.
Microbial culture and gram-negative MDRO detection
Copan eSwabs™ (Copan, Brescia, Italy) were used for swabbing and sent to the laboratory immediately after sampling. Enrichment broth (Trypticase Soy Broth (TSB); Becton Dickinson, Sparks, MD, USA) was inoculated with 10 μl of the liquid medium and incubated overnight. Of the enriched broth 10 ul were inoculated onto a chromID ESBL and chromID OXA-48 (bioMérieux, Marcy l'Etoile, France) with a WASP instrument (Copan, Brescia, Italy). After incubating the plates for 19 h in the smart incubators of a WASPLab™ high-resolution images of media plates were inspected using the WASPLab™ WebApp software. Colonies, indicative for gram-negative MDRO were identified for further processes. Identification was done with a MALDI-ToF instrument using the BDAL 9.0 database (MALDI Biotyper Smart System, Bruker Daltonics, Bremen, Germany) with the colony transfer method (“direct smear”). A BD™ Phoenix instrument (Becton Dickinson, Sparks, MD, USA) with NMIC-417 cartridge was used for susceptibility testing. Antimicrobial susceptibility testing (AST) data were interpreted according to respective EUCAST guidelines (version 10.0 in 2020, AST data not shown). Colonies were further tested with Carba NP (bioMérieux, Marcy l'Etoile, France) and with ESBL CT/CTL, TZ/TZL and PM/PML epsilometer (E-) tests (bioMérieux, Marcy l'Etoile, France) according to accredited procedures.
Whole genome sequencing
DNA was quantified by using the Qubit dsDNA BR HS Assay Kit and Qubit fluorometers (Invitrogen, https://www.thermofisher.com). WGS was performed using Illumina MiSeq with the Nextera XT library preparation kit (Illumina Inc., USA), according to the manufacturer’s procedure. Trimming and assembly of raw reads was performed using the Velvet assembler of the SeqSphere software (Ridom, https://www.ridom.de, version 8.0.1 using A.baumanii cgMLST v1.3). The analysis included MLST and cgMLST (2`390 targets). For detecting beta-lactam resistance genes (e.g. OXA-23) ResFinder on the CGE Website was used (http://www.genomicepidemiology.org/). Coverage was at least 25-fold. We defined cgMLST clusters as groups of isolates with ≤ 10 different SNPs between neighbouring isolates. To generate phylogenetic SNP trees, we used SeqSphere (Ridom; Münster, Germany) in the pairwise ignore missing values mode and an unweighted pair group method. The WGS data has been submitted to NCBI under the following submission number PRJNA778060.
Systematic review: study criteria
Studies reporting MDRO outbreaks in healthcare settings including multidrug resistant (MDR) gram negative bacteria (defined as Enterobacterales, Acinetobacter baumannii and Pseudomonas aeruginosa with resistance to at least 3 of the following antibiotic groups: antipseudomonal penicillins, third-generation cephalosporins, carbapenems, aminoglycosides and fluorochinolones), extended-spectrum beta-lactamase (ESBL) or carbapenemase producers, vancomycin-resistant Enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and Candida auris in patients of any age between December 2019 and March 2021 were included. We considered studies from peer-reviewed journals and pre-prints, regardless of interventional or observational design, such as cohort and case–control studies, outbreak reports, case-series, research letters or editorials, and epidemiologic surveys. Conference abstracts and studies strictly reporting laboratory and no clinical data were excluded.
Literature research was conducted by a scientific librarian in PubMed, EMBASE, CINHAL, MEDLINE, Cochrane and the NIH iSearch COVID-19 Portfolio engines with screening of cross-references and was restricted to documents in English, German, Spanish, Italian and French language. Applied search terms were [“COVID-19”, “SARS-CoV-2”, “pandemic”, “Coronavirus”] AND [“Multidrug-resistant organisms”, “ESBL-E”, “CPE”, “Carbapenem-resistance”, “Acinetobacter baumannii”, “Candida auris”, “Vancomycin-resistant Enterococci”, “Methicillin-resistant Staphylococcus aureus”, “Pseudomonas aeruginosa”], and the respective acronyms (Additional file 1: Table S1).
Screening of records
Initial screening by titles and abstracts and identification of studies that met inclusion- and exclusion criteria were done by eight authors (RT, MSe, GS, SH, DF, DV, PK, MSch). Studies meeting the inclusion criteria were subjected to full text review by two independent reviewers (RT and MSe); any disagreement was solved by a third arbiter (PK). Duplicates were excluded through automated deduplication by the librarian, initial screening and full text review.
Data extraction was again performed by two independent reviewers (RT and MSe), with a third as arbiter (PK). The following data were extracted from studies in the review: name of first author, time span (month/year to month/year) and country of outbreak, setting (acute care, intensive care, long-term care, other), ward type (COVID-19 vs. non-COVID-19 ward), causing organism and mechanism of resistance, proof of clonality (resistance pattern, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS)), number of affected patients (colonized or infected; clinical or screening samples), COVID-19 status of patients and patient outcome (i.e. hospital mortality). Furthermore, we assessed factors which potentially promoted and factors which might have helped in containing the outbreaks, all according to the respective study authors.
Risk of bias
Quality of reporting in included studies was evaluated independently by six authors (RT, MSe, GS, SH, DF, PK) according to an adapted version of the ORION statement . The ORION statement consists of a 22-item checklist and a summary table. We selected 14 items which could be applied to all studies in our review (Additional file 1: Figure S1). Because no established cut-off exists to rate the quality of the studies based on the adapted ORION statement, risk of bias analysis was purely descriptive.
Due to the descriptive nature of the study, no quantitative analysis was conducted.