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Background: Traditional hospital outbreak-detection methods are typically limited to select multidrug-resistant pathogens in a single unit, which can miss transmission of many medically important healthcare-transmissible pathogens. Whole-genome sequencing (WGS) enables comprehensive genomic resolution for accurate identification of clonal transmission. Previously, lack of scalability limited the use of WGS for hospital surveillance. Methods: We conducted prospective surveillance of select bacteria from all inpatient clinical cultures plus all bacteria from clinical cultures from ICUs and oncology units at the University of California Irvine (UCI) Clinical Microbiology Laboratory from September 2021 to February 2022. Due to pandemic stressors, this pilot test was a prelude to a real-time demonstration project. Its goal was to demonstrate the efficiency and scalability of the WGS platform when receiving samples monthly and analyzing results quarterly without the intent for real-time response. Bacterial isolates slated for discard were collected weekly and sent monthly to Day Zero Diagnostics for sequencing. In total, 1,036 samples from 926 patients were analyzed for genomic relatedness, a scalable and automated analysis pipeline already in use for rapid (days) characterization of genomic-relatedness in small and large sets of isolates. Mapping and SNP calling was performed against high-quality, best-match reference genomes. Sets of samples with pairwise distance of 2 persons with genomically related isolates and were denoted as “clusters.” Separately, we also investigated within-patient diversity by quantifying the genomic relatedness of isolates collected from individual patients. Results: Isolates represented 28 distinct species. We identified 10 Escherichia coli clusters (range, 2–4 patients; median, 2 patients), 2 Klebsiella pneumoniae clusters (range, 2–4 patients), and 1 Enterococcus faecium cluster (3 patients). All but 1 involved genomically matched isolates from multiple hospital locations. There were 4 Escherichia coli ST131 clusters spanning 4 months, including 1 with 4 patients across 3 different hospital locations. At a species level, there were distinct differences between the observed SNP distances between samples isolated from the same versus different patients (Fig. 1). All identified clusters had not been flagged by routine outbreak detection methods used by the UCI infection prevention program. Conclusions: Comprehensive WGS-based surveillance of hospital clinical isolates identified multiple potential transmission events between patients not in the same unit at the time cultures were taken. Combining WGS detection and real-time epidemiologic investigation may identify new avenues of transmission risk and could provide early warnings of clonal transmission to prevent larger outbreaks. High-volume surveillance of hospital isolates can also provide species- and context-specific clonality.
Financial support: This study was funded by Day Zero Diagnostics.
To describe the genomic analysis and epidemiologic response related to a slow and prolonged methicillin-resistant Staphylococcus aureus (MRSA) outbreak.
Prospective observational study.
Neonatal intensive care unit (NICU).
We conducted an epidemiologic investigation of a NICU MRSA outbreak involving serial baby and staff screening to identify opportunities for decolonization. Whole-genome sequencing was performed on MRSA isolates.
A NICU with excellent hand hygiene compliance and longstanding minimal healthcare-associated infections experienced an MRSA outbreak involving 15 babies and 6 healthcare personnel (HCP). In total, 12 cases occurred slowly over a 1-year period (mean, 30.7 days apart) followed by 3 additional cases 7 months later. Multiple progressive infection prevention interventions were implemented, including contact precautions and cohorting of MRSA-positive babies, hand hygiene observers, enhanced environmental cleaning, screening of babies and staff, and decolonization of carriers. Only decolonization of HCP found to be persistent carriers of MRSA was successful in stopping transmission and ending the outbreak. Genomic analyses identified bidirectional transmission between babies and HCP during the outbreak.
In comparison to fast outbreaks, outbreaks that are “slow and sustained” may be more common to units with strong existing infection prevention practices such that a series of breaches have to align to result in a case. We identified a slow outbreak that persisted among staff and babies and was only stopped by identifying and decolonizing persistent MRSA carriage among staff. A repeated decolonization regimen was successful in allowing previously persistent carriers to safely continue work duties.
To evaluate the National Health Safety Network (NHSN) hospital-onset Clostridioides difficile infection (HO-CDI) standardized infection ratio (SIR) risk adjustment for general acute-care hospitals with large numbers of intensive care unit (ICU), oncology unit, and hematopoietic cell transplant (HCT) patients.
Retrospective cohort study.
Eight tertiary-care referral general hospitals in California.
We used FY 2016 data and the published 2015 rebaseline NHSN HO-CDI SIR. We compared facility-wide inpatient HO-CDI events and SIRs, with and without ICU data, oncology and/or HCT unit data, and ICU bed adjustment.
For these hospitals, the median unmodified HO-CDI SIR was 1.24 (interquartile range [IQR], 1.15–1.34); 7 hospitals qualified for the highest ICU bed adjustment; 1 hospital received the second highest ICU bed adjustment; and all had oncology-HCT units with no additional adjustment per the NHSN. Removal of ICU data and the ICU bed adjustment decreased HO-CDI events (median, −25%; IQR, −20% to −29%) but increased the SIR at all hospitals (median, 104%; IQR, 90%–105%). Removal of oncology-HCT unit data decreased HO-CDI events (median, −15%; IQR, −14% to −21%) and decreased the SIR at all hospitals (median, −8%; IQR, −4% to −11%).
For tertiary-care referral hospitals with specialized ICUs and a large number of ICU beds, the ICU bed adjustor functions as a global adjustment in the SIR calculation, accounting for the increased complexity of patients in ICUs and non-ICUs at these facilities. However, the SIR decrease with removal of oncology and HCT unit data, even with the ICU bed adjustment, suggests that an additional adjustment should be considered for oncology and HCT units within general hospitals, perhaps similar to what is done for ICU beds in the current SIR.
To assess the impact of a newly developed Central-Line Insertion Site Assessment (CLISA) score on the incidence of local inflammation or infection for CLABSI prevention.
A pre- and postintervention, quasi-experimental quality improvement study.
Setting and participants:
Adult inpatients with central venous catheters (CVCs) hospitalized in an intensive care unit or oncology ward at a large academic medical center.
We evaluated CLISA score impact on insertion site inflammation and infection (CLISA score of 2 or 3) incidence in the baseline period (June 2014–January 2015) and the intervention period (April 2015–October 2017) using interrupted times series and generalized linear mixed-effects multivariable analyses. These were run separately for days-to-line removal from identification of a CLISA score of 2 or 3. CLISA score interrater reliability and photo quiz results were evaluated.
Among 6,957 CVCs assessed 40,846 times, percentage of lines with CLISA score of 2 or 3 in the baseline and intervention periods decreased by 78.2% (from 22.0% to 4.7%), with a significant immediate decrease in the time-series analysis (P < .001). According to the multivariable regression, the intervention was associated with lower percentage of lines with a CLISA score of 2 or 3, after adjusting for age, gender, CVC body location, and hospital unit (odds ratio, 0.15; 95% confidence interval, 0.06–0.34; P < .001). According to the multivariate regression, days to removal of lines with CLISA score of 2 or 3 was 3.19 days faster after the intervention (P < .001). Also, line dwell time decreased 37.1% from a mean of 14 days (standard deviation [SD], 10.6) to 8.8 days (SD, 9.0) (P < .001). Device utilization ratios decreased 9% from 0.64 (SD, 0.08) to 0.58 (SD, 0.06) (P = .039).
The CLISA score creates a common language for assessing line infection risk and successfully promotes high compliance with best practices in timely line removal.
The government publishes 3 different public report surgical site infection (SSI) metrics, all called standardized infection ratios (SIRs), that impact perceived hospital quality. We conducted a non-random cross-sectional observational pilot study of 20 California hospitals that voluntarily submitted colon surgery and SSI data. Discordant SIR values, leading to contradictory conclusions, occurred in 35% of these hospitals.
In implementing a hospital mandatory influenza vaccination policy, we developed an automated, real-time tracking and reminder system. Of 6,957 policy-covered individuals automatically identified, automated reminders left only 5 requiring counseling. This decreased Occupational Health workload in contacting noncompliant individuals and hosting vaccination events while simultaneously facilitating a 96% vaccination rate.
Infect Control Hosp Epidemiol 2014;35(11):1421–1424
Central line-associated bloodstream infection (CLABSI) is a national target for mandatory reporting and a Centers for Medicare and Medicaid Services target for value-based purchasing. Differences in chart review versus claims-based metrics used by national agencies and groups raise concerns about the validity of these measures.
Evaluate consistency and reasons for discordance among chart review and claims-based CLABSI events.
We conducted 2 multicenter retrospective cohort studies within 6 academic institutions. A total of 150 consecutive patients were identified with CLABSI on the basis of National Healthcare Safety Network (NHSN) criteria (NHSN cohort), and an additional 150 consecutive patients were identified with CLABSI on the basis of claims codes (claims cohort). Ail events had full-text medical record reviews and were identified as concordant or discordant with the other metric.
In the NHSN cohort, there were 152 CLABSIs among 150 patients, and 73.0% of these cases were discordant with claims data. Common reasons for the lack of associated claims codes included coding omission and lack of physician documentation of bacteremia cause. In the claims cohort, there were 150 CLABSIs among 150 patients, and 65.3% of these cases were discordant with NHSN criteria. Common reasons for the lack of NHSN reporting were identification of non-CLABSI with bacteremia meeting Centers for Disease Control and Prevention (CDC) criteria for an alternative infection source.
Substantial discordance between NHSN and claims-based CLABSI indicators persists. Compared with standardized CDC chart review criteria, claims data often had both coding omissions and misclassification of non-CLABSI infections as CLABSI. Additionally, claims did not identify any additional CLABSIs for CDC reporting. NHSN criteria are a more consistent interhospital standard for CLABSI reporting.
Assessing the relative success of serial strategies for increasing healthcare personnel (HCP) influenza vaccination rates is important to guide hospital policies to increase vaccine uptake.
To evaluate serial campaigns that include a mandatory HCP vaccination policy and to describe HCP attitudes toward vaccination and reasons for declination.
Retrospective cohort study.
We assessed the impact of serial vaccination campaigns on the proportions of HCP who received influenza vaccination during die 2006–2011 influenza seasons. In addition, declination data over these 5 seasons and a 2007 survey of HCP attitudes toward vaccination were collected.
HCP influenza vaccination rates increased from 44.0% (2,863 of 6,510 HCP) to 62.9% (4,037 of 6,414 HCP) after institution of mobile carts, mandatory declination, and peer-to-peer vaccination efforts. Despite maximal attempts to improve accessibility and convenience, 27.2% (66 of 243) of die surveyed HCP were unwilling to wait more than 10 minutes for a free influenza vaccination, and 23.3% (55 of 236) would be indifferent if they were unable to be vaccinated. In this context, institution of a mandatory vaccination campaign requiring unvaccinated HCP to mask during the influenza season increased rates of compliance to over 90% and markedly reduced the proportion of HCP who declined vaccination as a result of preference.
A mandatory influenza vaccination program for HCP was essential to achieving high vaccination rates, despite years of intensive vaccination campaigns focused on increasing accessibility and convenience. Mandatory vaccination policies appear to successfully capture a large portion of HCP who are not opposed to receipt of die vaccine but who have not made vaccination a priority.
Infect Control Hosp Epidemiol 2012;33(1):63-70
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