We aim to highlight the risks of acquiring carbapenemase-producing Enterobacterales (CPE) resistance genes in patients with severe coronavirus disease 2019 (COVID-19) in intensive care.

Outbreak analysis to assess for a transmission risk area (TRA) conducted after identification of potential CPE outbreak within shared room spaces in intensive care.

Analysis conducted within a 24-bed single-room model intensive-care department within a level-3 tertiary center public hospital in regional Victoria, Australia.

3 patients, with severe COVID-19 admitted to intensive care over a 3-month period with shared room spaces requiring prolonged mechanical ventilation and broad-spectrum antimicrobials, identified and were managed for CPE isolated from sputum. Overlap carbapenemase genes were identified among different organisms raising suspicion of transmitted resistance genes. A subsequent case managed for severe community-acquired pneumonia isolated CPE 3 months beyond these cases.

Outbreak analysis via weekly cross-sectional point prevalence screening of fecal samples or rectal swabs for CPE from patients admitted to the intensive-care department over a 4-week period.

34 patients were included in the analysis with 51 tests for CPE screening conducted. No further cases of CPE were identified. Statewide Infection Surveillance team and the Department of Health and Human Services did not find the cases to derive from a TRA. No further action including environmental screening was indicated.

These cases highlight the independent acquisition of CPE genes in patients with severe COVID-19 and antimicrobial selective pressures resulting in significant morbidity and mortality. Increasing awareness, robust antimicrobial stewardship, and infection prevention measures could reduce pressures driving CPE resistance mutations and the risk of CPE transmission.

Clostridioides difficile infection (CDI) is the commonest cause of healthcare-associated diarrhea and undergoes standardized surveillance and mandatory reporting in most Australian states and territories. Historically attributed to nosocomial spread, local and international whole genome sequencing (WGS) data suggest varied sources of acquisition. This study describes C. difficile genotypes isolated at a tertiary center in Melbourne, Australia, their likely source of acquisition, and common risk factors.

Retrospective observational study.

The Royal Melbourne Hospital (RMH), a 570-bed tertiary center in Victoria, Australia.

Short-read whole genome sequencing was performed on 75 out of 137 C. difficile isolates obtained from 1/5/2021 to 28/2/2022 and compared to previous data from 8/11/2015 to 1/11/2016. Existing data from infection control surveillance and electronic medical records were used for epidemiological and risk factor analysis.

Eighty-five (62.1%) of the 137 cases were defined as healthcare-associated from epidemiological data. On genome sequencing, 33 different multi-locus sequence type (MLST) subtypes were identified, with changes in population structure compared to the 2015–16 period. Risk factors for CDI were present in 130 (94.9%) cases, including 108 (78.8%) on antibiotics, 86 (62.8%) on acid suppression therapy, and 25 (18.2) on chemotherapy.

In both study periods, most C. difficile isolates were not closely related, suggesting varied sources of acquisition and that spread of C. difficile within the hospital was unlikely. Current infection control precautions may therefore warrant review. Underlying risk factors for CDI were common and may contribute to the proportion of healthcare-associated infections in the absence of proven hospital transmission.

To conduct a pilot study implementing combined genomic and epidemiologic surveillance for hospital-acquired multidrug-resistant organisms (MDROs) to predict transmission between patients and to estimate the local burden of MDRO transmission.

Pilot prospective multicenter surveillance study.

The study was conducted in 8 university hospitals (2,800 beds total) in Melbourne, Australia (population 4.8 million), including 4 acute-care, 1 specialist cancer care, and 3 subacute-care hospitals.

All clinical and screening isolates from hospital inpatients (April 24 to June 18, 2017) were collected for 6 MDROs: vanA VRE, MRSA, ESBL Escherichia coli (ESBL-Ec) and Klebsiella pneumoniae (ESBL-Kp), and carbapenem-resistant Pseudomonas aeruginosa (CRPa) and Acinetobacter baumannii (CRAb). Isolates were analyzed and reported as routine by hospital laboratories, underwent whole-genome sequencing at the central laboratory, and were analyzed using open-source bioinformatic tools. MDRO burden and transmission were assessed using combined genomic and epidemiologic data.

In total, 408 isolates were collected from 358 patients; 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%), and ESBL-Kp (7.6%). Most MDROs (88.3%) were isolated from patients with recent healthcare exposure.

Combining genomics and epidemiology identified that at least 27.1% of MDROs were likely acquired in a hospital; most of these transmission events would not have been detected without genomics. The highest proportion of transmission occurred with vanA VRE (88.4% of patients).

Genomic and epidemiologic data from multiple institutions can feasibly be combined prospectively, providing substantial insights into the burden and distribution of MDROs, including in-hospital transmission. This analysis enables infection control teams to target interventions more effectively.