To enumerate and describe the effect of whole genome sequencing (WGS) on epidemiological investigations of healthcare-associated transmission of nontuberculous mycobacteria (NTM).

Systematic review.

We performed a literature search using targeted search terms to identify articles meeting inclusion criteria. Data extraction of study characteristics and outcomes was performed by two independent researchers. The primary outcome was the author interpretation of WGS utility in the investigation of suspected healthcare-associated transmission of NTM. The secondary outcome was whether a transmission route was identified through WGS.

Thirty-one studies were included in the final analysis with 28 (90%) concluding that WGS was helpful in transmission investigations and in 19 of these 28 (68%) WGS aided in identifying a transmission route. The most common identified transmission routes were water-borne point sources (10), heater-cooler units (6), patient-to-patient (4), and a healthcare worker (1).

WGS is an informative tool in investigating healthcare transmission of NTM.

Prior studies evaluating the impact of discontinuation of contact precautions (DcCP) on methicillin-resistant Staphylococcus aureus (MRSA) outcomes have characterized all healthcare-associated infections (HAIs) rather than those likely preventable by contact precautions. We aimed to analyze the impact of DcCP on the rate of MRSA HAI including transmission events identified through whole genome sequencing (WGS) surveillance.

Quasi experimental interrupted time series.

Acute care medical center.

Inpatients.

The effect of DcCP (use of gowns and gloves) for encounters among patients with MRSA carriage was evaluated using time series analysis of MRSA HAI rates from January 2019 through December 2022, compared to WGS-defined attributable transmission events before and after DcCP in December 2020.

The MRSA HAI rate was 4.22/10,000 patient days before and 2.98/10,000 patient days after DcCP (incidence rate ratio [IRR] 0.71 [95% confidence interval 0.56–0.89]) with a significant immediate decrease (P = .001). There were 7 WGS-defined attributable transmission events before and 11 events after DcCP (incident rate ratio 0.90 [95% confidence interval 0.30–2.55]).

DcCP did not result in an increase in MRSA HAI or, in WGS-defined attributable transmission events. Comprehensive analyses of the effect of transmission prevention measures should include outcomes specifically measuring transmission-associated HAI.

To evaluate the utility of selective reactive whole-genome sequencing (WGS) in aiding healthcare-associated cluster investigations.

Mixed-methods quality-improvement study.

Thes study was conducted across 8 acute-care facilities in an integrated health system.

We analyzed healthcare-associated coronavirus disease 2019 (COVID-19) clusters between May 2020 and July 2022 for which facility infection prevention and control (IPC) teams selectively requested reactive WGS to aid the epidemiologic investigation. WGS was performed with real-time results provided to IPC teams, including genetic relatedness of sequenced isolates. We conducted structured interviews with IPC teams on the informativeness of WGS for transmission investigation and prevention.

In total, 8 IPC teams requested WGS to aid the investigation of 17 COVID-19 clusters comprising 226 cases and 116 (51%) sequenced isolates. Of these, 16 (94%) clusters had at least 1 WGS-defined transmission event. IPC teams hypothesized transmission pathways in 14 (82%) of 17 clusters and used data visualizations to characterize these pathways in 11 clusters (65%). The teams reported that in 15 clusters (88%), WGS identified a transmission pathway; the WGS-defined pathway was not one that was predicted by epidemiologic investigation in 7 clusters (41%). WGS changed the understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in 8 clusters (47%) and altered infection prevention interventions in 8 clusters (47%).

Selectively utilizing reactive WGS helped identify cryptic SARS-CoV-2 transmission pathways and frequently changed the understanding and response to SARS-CoV-2 outbreaks. Until WGS is widely adopted, a selective reactive WGS approach may be highly impactful in response to healthcare-associated cluster investigations.

To describe a novel attribution metric estimating the causal source location of healthcare-associated Clostridioides difficile and compare it with the current US National Healthcare Safety Network (NHSN) surveillance reporting standard.

Quality improvement study.

Two acute care facilities.

A novel attribution metric assigned days of attribution to locations where patients were located for 14 days before and the day of their C. difficile diagnosis. We correlated the NHSN-assigned unit attribution with the novel attribution measure and compared the proportion of attribution assigned to inpatient units.

During a 30-month period, there were 727 NHSN C. difficile healthcare-associated infections (HAIs) and 409 non-HAIs; the novel metric attributed 17,034 days. The correlation coefficients for NHSN and novel attributions among non-ICU units were 0.79 (95% CI, 0.76–0.82) and 0.74 (95% CI, 0.70–0.78) and among ICU units were 0.70 (95% CI, 0.63–0.76) and 0.69 (95% CI, 0.60–0.77) at facilities A and B, respectively. The distribution of difference in percent attribution showed higher inpatient unit attribution using NHSN measure than the novel attribution metric: 38% of ICU units and 15% of non-ICU units in facility A, and 20% of ICU units and 25% of non-ICU units in facility B had a median difference >0; no inpatient units showed a greater attribution using the novel attribution metric.

The novel attribution metric shifts attribution from inpatient units to other settings and correlates modestly with NHSN methodology of attribution. If validated, the attribution metric may more accurately target C. difficile reduction efforts.

To assess the impact of a 24-hour autocancellation of uncollected Clostridioides difficile samples in reducing reported healthcare-associated infections (HAIs).

Quality-improvement, before-and-after implementation study.

The study was conducted in 17 hospitals in Pennsylvania.

Clostridioides difficile tests that are not collected within 24 hours are automatically canceled (“autocancel”) through the electronic health record. The intervention took place at 2 facilities (intervention period November 2021–July 2022) and subsequently at 15 additional facilities (April 2022–July 2022). Quality measures included percentage of orders canceled, C. difficile HAI rate, percent positivity of completed tests, and potential adverse outcomes of canceled or delayed testing.

Of 6,101 orders, 1,090 (17.9%) were automatically canceled after not being collected for 24 hours during the intervention periods. The reported C. difficile HAI rates per 10,000 patient days did not significantly change. These rates were 8.07 in the 6-month preintervention period and 8.77 in the intervention period for facilities A and B combined (incidence rate ratio [IRR], 1.09; 95% CI, 0.88–1.34; P = .43), and were 5.23 HAIs per 10,000 patient days in the 6-month preintervention period and 5.33 in the intervention period for facilities C–Q combined (IRR, 1.02; 95% CI, 0.79–1.32; P = .87). From the preintervention to the intervention periods, the percent positivity rates of completed C. difficile tests increased by 1.1% for facilities A and B and by 1.4% for facilities C–Q. No adverse outcomes were observed.

The 24-hour autocancellation of uncollected C. difficile orders reduced testing but did not result in reported HAI reduction.

To evaluate the impact of a diagnostic stewardship intervention on Clostridioides difficile healthcare-associated infections (HAI).

Quality improvement study.

Two urban acute care hospitals.

All inpatient stool testing for C. difficile required review and approval prior to specimen processing in the laboratory. An infection preventionist reviewed all orders daily through chart review and conversations with nursing; orders meeting clinical criteria for testing were approved, orders not meeting clinical criteria were discussed with the ordering provider. The proportion of completed tests meeting clinical criteria for testing and the primary outcome of C. difficile HAI were compared before and after the intervention.

The frequency of completed C. difficile orders not meeting criteria was lower [146 (7.5%) of 1,958] in the intervention period (January 10, 2022–October 14, 2022) than in the sampled 3-month preintervention period [26 (21.0%) of 124; P < .001]. C. difficile HAI rates were 8.80 per 10,000 patient days prior to the intervention (March 1, 2021–January 9, 2022) and 7.69 per 10,000 patient days during the intervention period (incidence rate ratio, 0.87; 95% confidence interval, 0.73–1.05; P = .13).

A stringent order-approval process reduced clinically nonindicated testing for C. difficile but did not significantly decrease HAIs.

To develop, implement, and evaluate the effectiveness of a unique centralized surveillance infection prevention (CSIP) program.

Observational quality improvement project.

An integrated academic healthcare system.

The CSIP program comprises senior infection preventionists who are responsible for healthcare-associated infection (HAI) surveillance and reporting, allowing local infection preventionists (LIPs) a greater portion of their time to non-surveillance patient safety activities. Four CSIP team members accrued HAI responsibilities at 8 facilities.

We evaluated the effectiveness of the CSIP program using 4 measures: recovery of LIP time, efficiency of surveillance activities by LIPs and CSIP staff, surveys characterizing LIP perception of their effectiveness in HAI reduction, and nursing leaders’ perception of LIP effectiveness.

The amount of time spent by LIP teams on HAI surveillance was highly variable, while CSIP time commitment and efficiency was steady. Post-CSIP implementation, 76.9% of LIPs agreed that they spend adequate time on inpatient units, compared to 15.4% pre-CSIP; LIPs also reported more time to allot to non-surveillance activities. Nursing leaders reported greater satisfaction with LIP involvement with HAI reduction practices.

CSIP programs are a little-reported strategy to ease burden on LIPs with reallocation of HAI surveillance. The analyses presented here will aid health systems in anticipating the benefit of CSIP programs.

To evaluate variables that affect risk of contamination for endoscopic retrograde cholangiopancreatography and endoscopic ultrasound endoscopes.

Observational, quality improvement study.

University medical center with a gastrointestinal endoscopy service performing ∼1,000 endoscopic retrograde cholangiopancreatography and ∼1,000 endoscopic ultrasound endoscope procedures annually.

Duodenoscope and linear echoendoscope sampling (from the elevator mechanism and instrument channel) was performed from June 2020 through September 2021. Operational changes during this period included standard reprocessing with high-level disinfection with ethylene oxide gas sterilization (HLD–ETO) was switched to double high-level disinfection (dHLD) (June 16, 2020–July 15, 2020), and duodenoscopes changed to disposable tip model (March 2021). The frequency of contamination for the co-primary outcomes were characterized by calculated risk ratios.

The overall pathogenic contamination rate was 4.72% (6 of 127). Compared to duodenoscopes, linear echoendoscopes had a contamination risk ratio of 3.64 (95% confidence interval [CI], 0.69–19.1). Reprocessing using HLD-ETO was associated with a contamination risk ratio of 0.29 (95% CI, 0.06–1.54). Linear echoendoscopes undergoing dHLD had the highest risk of contamination (2 of 18, 11.1%), and duodenoscopes undergoing HLD-ETO and the lowest risk of contamination (0 of 53, 0%). Duodenoscopes with a disposable tip had a 0% contamination rate (0 of 27).

We did not detect a significant reduction in endoscope contamination using HLD-ETO versus dHLD reprocessing. Linear echoendoscopes have a risk of contamination similar to that of duodenoscopes. Disposable tips may reduce the risk of duodenoscope contamination.