Effectiveness of mRNA Covid-19 Vaccine among U.S. Health Care Personnel.

BACKGROUND: The prioritization of U.S. health care personnel for early receipt of messenger RNA (mRNA) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (Covid-19), allowed for the evaluation of the effectiveness of these new vaccines in a real-world setting. METHODS: We conducted a test-negative case-control study involving health care personnel across 25 U.S. states. Cases were defined on the basis of a positive polymerase-chain-reaction (PCR) or antigen-based test for SARS-CoV-2 and at least one Covid-19-like symptom. Controls were defined on the basis of a negative PCR test for SARS-CoV-2, regardless of symptoms, and were matched to cases according to the week of the test date and site. Using conditional logistic regression with adjustment for age, race and ethnic group, underlying conditions, and exposures to persons with Covid-19, we estimated vaccine effectiveness for partial vaccination (assessed 14 days after receipt of the first dose through 6 days after receipt of the second dose) and complete vaccination (assessed ≥7 days after receipt of the second dose). RESULTS: The study included 1482 case participants and 3449 control participants. Vaccine effectiveness for partial vaccination was 77.6% (95% confidence interval [CI], 70.9 to 82.7) with the BNT162b2 vaccine (Pfizer-BioNTech) and 88.9% (95% CI, 78.7 to 94.2) with the mRNA-1273 vaccine (Moderna); for complete vaccination, vaccine effectiveness was 88.8% (95% CI, 84.6 to 91.8) and 96.3% (95% CI, 91.3 to 98.4), respectively. Vaccine effectiveness was similar in subgroups defined according to age (<50 years or ≥50 years), race and ethnic group, presence of underlying conditions, and level of patient contact. Estimates of vaccine effectiveness were lower during weeks 9 through 14 than during weeks 3 through 8 after receipt of the second dose, but confidence intervals overlapped widely. CONCLUSIONS: The BNT162b2 and mRNA-1273 vaccines were highly effective under real-world conditions in preventing symptomatic Covid-19 in health care personnel, including those at risk for severe Covid-19 and those in racial and ethnic groups that have been disproportionately affected by the pandemic. (Funded by the Centers for Disease Control and Prevention.).

Clinical Decision Support Systems to Reduce Unnecessary Clostridioides difficile Testing Across Multiple Hospitals.

BACKGROUND: Inappropriate Clostridioides difficile testing has adverse consequences for patients, hospitals, and public health. Computerized clinical decision support (CCDS) systems in the electronic health record (EHR) may reduce C. difficile test ordering; however, effectiveness of different approaches, ease of use, and best fit into healthcare providers' (HCP) workflow are not well understood. METHODS: Nine academic and 6 community hospitals in the United States participated in this 2-year cohort study. CCDS (hard stop or soft stop) triggered when a duplicate C. difficile test order was attempted or if laxatives were recently received. The primary outcome was the difference in testing rates pre- and post-CCDS interventions, using incidence rate ratios (IRRs) and mixed-effect Poisson regression models. We performed qualitative evaluation (contextual inquiry, interviews, focus groups) based on a human factors model. We identified themes using a codebook with primary nodes and subnodes. RESULTS: In 9 hospitals implementing hard-stop CCDS and 4 hospitals implementing soft-stop CCDS, C. difficile testing incidence rate (IR) reduction was 33% (95% confidence interval [CI]: 30%-36%) and 23% (95% CI: 21%-25%), respectively. Two hospitals implemented a non-EHR-based human intervention with IR reduction of 21% (95% CI: 15%-28%). HCPs reported generally favorable experiences and highlighted time efficiencies such as inclusion of the patient's most recent laxative administration on the CCDS. Organizational factors, including hierarchical cultures and communication between HCPs caring for the same patient, impact CCDS acceptance and integration. CONCLUSIONS: CCDS systems reduced unnecessary C. difficile testing and were perceived positively by HCPs when integrated into their workflow and when displaying relevant patient-specific information needed for decision making.

Environmental Contamination of Contact Precaution and Non-Contact Precaution Patient Rooms in Six Acute Care Facilities.

BACKGROUND: Environmental contamination is an important source of hospital multidrug-resistant organism (MDRO) transmission. Factors such as patient MDRO contact precautions (CP) status, patient proximity to surfaces, and unit type likely influence MDRO contamination and bacterial bioburden levels on patient room surfaces. Identifying factors associated with environmental contamination in patient rooms and on shared unit surfaces could help identify important environmental MDRO transmission routes. METHODS: Surfaces were sampled from MDRO CP and non-CP rooms, nursing stations, and mobile equipment in acute care, intensive care, and transplant units within 6 acute care hospitals using a convenience sampling approach blinded to cleaning events. Precaution rooms had patients with clinical or surveillance tests positive for methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, carbapenem-resistant Enterobacteriaceae or Acinetobacter within the previous 6 months, or Clostridioides difficile toxin within the past 30 days. Rooms not meeting this definition were considered non-CP rooms. Samples were cultured for the above MDROs and total bioburden. RESULTS: Overall, an estimated 13% of rooms were contaminated with at least 1 MDRO. MDROs were detected more frequently in CP rooms (32% of 209 room-sample events) than non-CP rooms (12% of 234 room-sample events). Surface bioburden did not differ significantly between CP and non-CP rooms or MDRO-positive and MDRO-negative rooms. CONCLUSIONS: CP room surfaces are contaminated more frequently than non-CP room surfaces; however, contamination of non-CP room surfaces is not uncommon and may be an important reservoir for ongoing MDRO transmission. MDRO contamination of non-CP rooms may indicate asymptomatic patient MDRO carriage, inadequate terminal cleaning, or cross-contamination of room surfaces via healthcare personnel hands.

Interim Estimates of Vaccine Effectiveness of Pfizer-BioNTech and Moderna COVID-19 Vaccines Among Health Care Personnel - 33 U.S. Sites, January-March 2021.

Throughout the COVID-19 pandemic, health care personnel (HCP) have been at high risk for exposure to SARS-CoV-2, the virus that causes COVID-19, through patient interactions and community exposure (1). The Advisory Committee on Immunization Practices recommended prioritization of HCP for COVID-19 vaccination to maintain provision of critical services and reduce spread of infection in health care settings (2). Early distribution of two mRNA COVID-19 vaccines (Pfizer-BioNTech and Moderna) to HCP allowed assessment of the effectiveness of these vaccines in a real-world setting. A test-negative case-control study is underway to evaluate mRNA COVID-19 vaccine effectiveness (VE) against symptomatic illness among HCP at 33 U.S. sites across 25 U.S. states. Interim analyses indicated that the VE of a single dose (measured 14 days after the first dose through 6 days after the second dose) was 82% (95% confidence interval [CI] = 74%-87%), adjusted for age, race/ethnicity, and underlying medical conditions. The adjusted VE of 2 doses (measured ≥7 days after the second dose) was 94% (95% CI = 87%-97%). VE of partial (1-dose) and complete (2-dose) vaccination in this population is comparable to that reported from clinical trials and recent observational studies, supporting the effectiveness of mRNA COVID-19 vaccines against symptomatic disease in adults, with strong 2-dose protection.

Evaluation of a Redesigned Personal Protective Equipment Gown.

BACKGROUND: In healthcare, the goal of personal protective equipment (PPE) is to protect healthcare personnel (HCP) and patients from body fluids and infectious organisms via contact, droplet, or airborne transmission. The critical importance of using PPE properly is highlighted by 2 potentially fatal viral infections, severe acute respiratory syndrome-associated coronavirus and Ebola virus, where HCP became infected while caring for patients due to errors in the use of PPE. However, PPE in dealing with less dangerous, but highly infectious organisms is important as well. This work proposes a framework to test and evaluate PPE with a focus on gown design. METHODS: An observational study identified issues with potential for contamination related to gown use. After redesigning the existing gown, a high-fidelity patient simulator study with 40 HCP as participants evaluated the gown redesign using 2 commonly performed tasks. Variables of interest were nonadherence to procedural standards, use problems with the gown during task performance, and usability and cognitive task load ratings of the standard and redesigned gowns. RESULTS: While no differences were found in terms of nonadherence and use problems between the current and the redesigned gown, differences in usability and task load ratings suggested that the redesigned gown is perceived more favorably by HCP. CONCLUSIONS: This work proposes a framework to guide the evaluation of PPE. The results suggest that the current design of the PPE gown can be improved in usability and user satisfaction. Although our data did not find an increase in adherence to protocol when using the redesigned gown, it is likely that higher usability and lower task load could result in higher adherence over longer periods of use.

Understanding Workflow and Personal Protective Equipment Challenges Across Different Healthcare Personnel Roles.

BACKGROUND: Hospitals use standard and transmission-based precautions, including personal protective equipment (PPE), to prevent the spread of infectious organisms. However, little attention has been paid to the potentially unique challenges of various healthcare personnel (HCP) in following precaution practices. METHODS: From September through December 2016, 5 physicians, 5 nurses, and 4 physical therapists were shadowed for 1 hour 30 minutes to 3 hours 15 minutes at an academic medical center. Observers documented activities using unstructured field notes. Focus groups were conducted to better understand HCP perspectives about precautions and PPE-related challenges. Data were analyzed by comparing workflow and challenges (observed and stated) in precaution practices across HCP roles. RESULTS: Precaution patients were interspersed throughout physician rounds, which covered a broad geographic range throughout the hospital. Patient encounters were generally brief, and appropriate use of gowns and cleaning of personal stethoscopes varied among observed physicians. Nurses were unit based and frequently entered/exited rooms. Frustration with donning/doffing was especially apparent when needing supplies while in a precaution room, which nurses acknowledged was a time when practice lapses could occur. The observed physical therapists worked in one geographic location, spent extended periods of time with patients, and noted that given their close physical contact with patients, gowns do not fully protect them. CONCLUSIONS: Movement patterns, time with patients, care activities, and equipment use varied across HCP, leading to a diverse set of challenges in following precaution practices and PPE use. Attention to these differences among HCP is important for understanding and developing effective strategies to prevent the potential spread of infectious organisms.

How Clean Is the Linen at My Hospital? The Mucorales on Unclean Linen Discovery Study of Large United States Transplant and Cancer Centers.

Mucormycosis outbreaks have been linked to contaminated linen. We performed fungal cultures on freshly-laundered linens at 15 transplant and cancer hospitals. At 33% of hospitals, the linens were visibly unclean. At 20%, Mucorales were recovered from >10% of linens. Studies are needed to understand the clinical significance of our findings.

Estimating the Incidence of Influenza at the State Level - Utah, 2016-17 and 2017-18 Influenza Seasons.

The 2017-18 U.S. influenza season was notable for its high severity, with approximately 45 million illnesses and 810,000 influenza-associated hospitalizations throughout the United States (1). The purpose of the investigation reported here was to create a state-level estimate of the number of persons in Utah who became ill with influenza disease during this severe national seasonal influenza epidemic and to create a sustainable system for making timely updates in future influenza seasons. Knowing the extent of influenza-associated illness can help public health officials, policymakers, and clinicians tailor influenza messaging, planning, and responses for seasonal influenza epidemics or during pandemics. Using national methods and existing influenza surveillance and testing data, the influenza burden (number of influenza illnesses, medical visits for influenza, and influenza-associated hospitalizations) in Utah during the 2016-17 and 2017-18 influenza seasons was estimated. During the 2016-17 season, an estimated 265,000 symptomatic illnesses affecting 9% of Utah residents occurred, resulting in 125,000 medically attended illnesses and 2,700 hospitalizations. During the 2017-18 season, an estimated 338,000 symptomatic illnesses affecting 11% of Utah residents occurred, resulting in 160,000 medically attended illnesses and 3,900 hospitalizations. Other state or county health departments could adapt similar methods in their jurisdictions to estimate the burden of influenza locally and support prompt public health activities.

Human Factors Engineering Contributions to Infection Prevention and Control.

OBJECTIVE: This article provides a review of areas that present significant challenges in infection prevention and control and describes human factors engineering (HFE) approaches that have been applied successfully to these areas. In addition, implications and recommendations for HFE use in future research are discussed. BACKGROUND: Infection prevention and control aims to prevent patients and health care personnel from acquiring preventable infections in healthcare. Effective infection control practices of healthcare-associated infections have recently become even more critical with the emergence of life-threatening infections. HFE could benefit infection prevention and control in addressing older and more recent challenges, but uptake has been limited. METHOD/RESULTS: This literature review is an integration and synthesis of recently published research that describes HFE-based approaches in infection prevention and control to address the challenges for three specific topics. The results of the review suggests that HFE is in a position to support work in infection prevention and control and improve overall healthcare safety. CONCLUSION: HFE provides conceptual frameworks and methods that have significant potential to improve infection prevention and control. APPLICATION: The work reviewed can provide potential solutions for current infection prevention and control challenges by applying HFE based recommendations.

The Drivers of Acute and Long-term Care Clostridium difficile Infection Rates: A Retrospective Multilevel Cohort Study of 251 Facilities.

Background: Drivers of differences in Clostridium difficile incidence across acute and long-term care facilities are poorly understood. We sought to obtain a comprehensive picture of C. difficile incidence and risk factors in acute and long-term care. Methods: We conducted a case-cohort study of persons spending at least 3 days in one of 131 acute care or 120 long-term care facilities managed by the United States Veterans Health Administration between 2006 and 2012. Patient (n = 8) and facility factors (n = 5) were included in analyses. The outcome was the incidence of facility-onset laboratory-identified C. difficile infection (CDI), defined as a person with a positive C. difficile test without a positive test in the prior 8 weeks. Results: CDI incidence in acute care was 5 times that observed in long-term care (median, 15.6 vs 3.2 per 10000 person-days). History of antibiotic use was greater in acute care compared to long-term care (median, 739 vs 513 per 1000 person-days) and explained 72% of the variation in C. difficile rates. Importation of C. difficile cases (acute care: patients with recent long-term care attributable infection; long-term care: residents with recent acute care attributable infection) was 3 times higher in long-term care as compared to acute care (median, 52.3 vs 16.2 per 10000 person-days). Conclusions: Facility-level antibiotic use was the main factor driving differences in CDI incidence between acute and long-term care. Importation of acute care C. difficile cases was a greater concern for long-term care as compared to importation of long-term care cases for acute care.

Importation, Antibiotics, and Clostridium difficile Infection in Veteran Long-Term Care: A Multilevel Case-Control Study.

BACKGROUND: Although clinical factors affecting a person's susceptibility to Clostridium difficile infection are well-understood, little is known about what drives differences in incidence across long-term care settings. OBJECTIVE: To obtain a comprehensive picture of individual and regional factors that affect C difficile incidence. DESIGN: Multilevel longitudinal nested case-control study. SETTING: Veterans Health Administration health care regions, from 2006 through 2012. PARTICIPANTS: Long-term care residents. MEASUREMENTS: Individual-level risk factors included age, number of comorbid conditions, and antibiotic exposure. Regional risk factors included importation of cases of acute care C difficile infection per 10 000 resident-days and antibiotic use per 1000 resident-days. The outcome was defined as a positive result on a long-term care C difficile test without a positive result in the prior 8 weeks. RESULTS: 6012 cases (incidence, 3.7 cases per 10 000 resident-days) were identified in 86 regions. Long-term care C difficile incidence (minimum, 0.6 case per 10 000 resident-days; maximum, 31.0 cases per 10 000 resident-days), antibiotic use (minimum, 61.0 days with therapy per 1000 resident-days; maximum, 370.2 days with therapy per 1000 resident-days), and importation (minimum, 2.9 cases per 10 000 resident-days; maximum, 341.3 cases per 10 000 resident-days) varied substantially across regions. Together, antibiotic use and importation accounted for 75% of the regional variation in C difficile incidence (R2 = 0.75). Multilevel analyses showed that regional factors affected risk together with individual-level exposures (relative risk of regional antibiotic use, 1.36 per doubling [95% CI, 1.15 to 1.60]; relative risk of importation, 1.23 per doubling [CI, 1.14 to 1.33]). LIMITATIONS: Case identification was based on laboratory criteria. Admission of residents with recent C difficile infection from non-Veterans Health Administration acute care sources was not considered. CONCLUSION: Only 25% of the variation in regional C difficile incidence in long-term care remained unexplained after importation from acute care facilities and antibiotic use were accounted for, which suggests that improved infection control and antimicrobial stewardship may help reduce the incidence of C difficile in long-term care settings. PRIMARY FUNDING SOURCE: U.S. Department of Veterans Affairs and Centers for Disease Control and Prevention.

Human Rabies - Wyoming and Utah, 2015.

In September 2015, a Wyoming woman was admitted to a local hospital with a 5-day history of progressive weakness, ataxia, dysarthria, and dysphagia. Because of respiratory failure, she was transferred to a referral hospital in Utah, where she developed progressive encephalitis. On day 8 of hospitalization, the patient's family told clinicians they recalled that, 1 month before admission, the woman had found a bat on her neck upon waking, but had not sought medical care. The patient's husband subsequently had contacted county invasive species authorities about the incident, but he was not advised to seek health care for evaluation of his wife's risk for rabies. On October 2, CDC confirmed the patient was infected with a rabies virus variant that was enzootic to the silver-haired bat (Lasionycteris noctivagans). The patient died on October 3. Public understanding of rabies risk from bat contact needs to be improved; cooperation among public health and other agencies can aid in referring persons with possible bat exposure for assessment of rabies risk.

Utility of a commercial PCR assay and a clinical prediction rule for detection of toxigenic Clostridium difficile in asymptomatic carriers.

A commercial PCR assay of perirectal swab specimens detected 17 (68%) of 25 asymptomatic carriers of toxigenic Clostridium difficile, including 93% with skin and/or environmental contamination. A clinical prediction rule, followed by PCR screening, could be used to identify carriers at high risk of C. difficile shedding.

Factors associated with testing positive for SARS-CoV-2 and evaluation of a recruitment protocol among healthcare personnel in a COVID-19 vaccine effectiveness study.

Objective: The objective of this study was to determine factors associated with testing positive for SARS-CoV-2 among healthcare personnel. Secondary objectives were to assess representativeness of recruited participants and the effectiveness of a multiple-contact protocol for recruiting healthcare personnel in this COVID-19 study. Design: Survey study, conducted as part of an observational test-negative study of COVID-19 vaccine effectiveness. Setting: University of Utah Health system, including both inpatient and outpatient facilities. Participants: Clinical and non-clinical healthcare personnel at University of Utah Health. 1456 were contacted and 503 (34.5%) completed the survey. Cases were all eligible employees testing positive for COVID-19, with 3:1 randomly selected, matched controls (test negative) selected weekly. Methods: Online survey. Results: Significant differences in the demographics of participants and the source population were observed; e.g., nursing staff comprised 31.6% of participants but only 23.3% of the source population. The multiple-contact recruitment protocol increased participation by ten percentage points and ensured equal representation of controls. Potential exposure to illness outside of work was strongly predictive of testing positive for SARS-CoV-2 (OR = 3.74; 95% CI: 2.29, 6.11) whereas potential exposure at work was protective against testing positive (OR: 0.51, 95% CI: 0.29, 0.88). Conclusions: Carefully designed recruitment protocols increase participation and representation of controls, but bias in participant demographics still exists. The negative association between potential workplace exposure and positive test suggests testing bias in the test-negative design. Healthcare personnel's potential exposures to COVID-19 outside of the workplace are important predictors of SARS-CoV-2 seropositivity.

Evaluation of hospital-onset bacteraemia and fungaemia in the USA as a potential healthcare quality measure: a cross-sectional study.

BACKGROUND: Hospital-onset bacteraemia and fungaemia (HOB) is being explored as a surveillance and quality metric. The objectives of the current study were to determine sources and preventability of HOB in hospitalised patients in the USA and to identify factors associated with perceived preventability. METHODS: We conducted a cross-sectional study of HOB events at 10 academic and three community hospitals using structured chart review. HOB was defined as a blood culture on or after hospital day 4 with growth of one or more bacterial or fungal organisms. HOB events were stratified by commensal and non-commensal organisms. Medical resident physicians, infectious disease fellows or infection preventionists reviewed charts to determine HOB source, and infectious disease physicians with training in infection prevention/hospital epidemiology rated preventability from 1 to 6 (1=definitely preventable to 6=definitely not preventable) using a structured guide. Ratings of 1-3 were collectively considered 'potentially preventable' and 4-6 'potentially not preventable'. RESULTS: Among 1789 HOB events with non-commensal organisms, gastrointestinal (including neutropenic translocation) (35%) and endovascular (32%) were the most common sources. Overall, 636/1789 (36%) non-commensal and 238/320 (74%) commensal HOB events were rated potentially preventable. In logistic regression analysis among non-commensal HOB events, events attributed to intravascular catheter-related infection, indwelling urinary catheter-related infection and surgical site infection had higher odds of being rated preventable while events with neutropenia, immunosuppression, gastrointestinal sources, polymicrobial cultures and previous positive blood culture in the same admission had lower odds of being rated preventable, compared with events without those attributes. Of 636 potentially preventable non-commensal HOB events, 47% were endovascular in origin, followed by gastrointestinal, respiratory and urinary sources; approximately 40% of those events would not be captured through existing healthcare-associated infection surveillance. DISCUSSION: Factors identified as associated with higher or lower preventability should be used to guide inclusion, exclusion and risk adjustment for an HOB-related quality metric.

Agreement in classifying bloodstream infections among multiple reviewers conducting surveillance.

BACKGROUND: Mandatory reporting of healthcare-associated infections (HAIs) is increasing. Evidence for agreement among different reviewers applying HAI surveillance criteria is limited. We aim to characterize agreement among infection preventionists (IPs) conducting surveillance for central line-associated bloodstream infection (CLABSI) with each other and as compared with simplified laboratory-based definitions. METHODS: Abstracted electronic health records were assembled from inpatients with positive blood cultures at a tertiary-care Veterans Affairs (VA) hospital over a 5-year period. Identical patient records were made available to VA IPs from different facilities to report on CLABSI using their usual surveillance methods. Positive blood cultures were also evaluated using laboratory-based definitions. Standard indices of interrater agreement, expressed as a κ statistic, were computed between IPs, and between IPs and simplified laboratory-based methods. RESULTS: Overall, 114 patient records were reviewed by 18 IPs, the majority of whom specified they followed National Healthcare Safety Network criteria. The overall agreement among IPs by κ statistic was 0.42 (standard error [SE], 0.06). IPs had better agreement with a simple laboratory-based definition with an average κ of 0.55 (SE, 0.05). The proportion of patient records that 18 IPs reported with CLABSI ranged from 14% to 39% (overall mean, 28% with a coefficient of variation of 25%). When simple laboratory-based methods were applied to different sets of patient records, classification was more consistent with CLABSI assigned in a proportion ranging from 36% to 42% (overall mean, 39%). CONCLUSIONS: Reliability of IP-conducted surveillance to identify HAI may not be ideal for public reporting goals of interhospital comparisons.

Development and evaluation of a structured guide to assess the preventability of hospital-onset bacteremia and fungemia.

OBJECTIVE: To assess preventability of hospital-onset bacteremia and fungemia (HOB), we developed and evaluated a structured rating guide accounting for intrinsic patient and extrinsic healthcare-related risks. DESIGN: HOB preventability rating guide was compared against a reference standard expert panel. PARTICIPANTS: A 10-member panel of clinical experts was assembled as the standard of preventability assessment, and 2 physician reviewers applied the rating guide for comparison. METHODS: The expert panel independently rated 82 hypothetical HOB scenarios using a 6-point Likert scale collapsed into 3 categories: preventable, uncertain, or not preventable. Consensus was defined as concurrence on the same category among ≥70% experts. Scenarios without consensus were deliberated and followed by a second round of rating.Two reviewers independently applied the rating guide to adjudicate the same 82 scenarios in 2 rounds, with interim revisions. Interrater reliability was evaluated using the κ (kappa) statistic. RESULTS: Expert panel consensus criteria were met for 52 scenarios (63%) after 2 rounds.After 2 rounds, guide-based rating matched expert panel consensus in 40 of 52 (77%) and 39 of 52 (75%) cases for reviewers 1 and 2, respectively. Agreement rates between the 2 reviewers were 84% overall (κ, 0.76; 95% confidence interval [CI], 0.64-0.88]) and 87% (κ, 0.79; 95% CI, 0.65-0.94) for the 52 scenarios with expert consensus. CONCLUSIONS: Preventability ratings of HOB scenarios by 2 reviewers using a rating guide matched expert consensus in most cases with moderately high interreviewer reliability. Although diversity of expert opinions and uncertainty of preventability merit further exploration, this is a step toward standardized assessment of HOB preventability.

The impact of ICD-9-CM code rank order on the estimated prevalence of Clostridium difficile infections.

BACKGROUND: US estimates of the Clostridium difficile infection (CDI) burden have utilized International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis codes. Whether ICD-9-CM code rank order affects CDI prevalence estimates is important because the National Hospital Discharge Survey (NHDS) and the Nationwide Inpatient Sample (NIS) have varying limits on the number of ICD-9-CM codes collected. METHODS: ICD-9-CM codes for CDI (008.45), C. difficile toxin assay results, and dates of admission and discharge were collected from electronic hospital databases for adult patients admitted to 4 hospitals in the United States from July 2000 through June 2006. CDI prevalence per 1000 discharges was calculated and compared for NHDS and NIS limits and toxin assay results from the same hospitals. CDI prevalence estimates were compared using the χ(2) test, and the test of equality was used to compare slopes. RESULTS: CDI prevalence measured by NIS criteria was significantly higher than that measured using NHDS criteria (10.7 cases per 1000 discharges versus 9.4 cases per 1000 discharges; P<.001) in the 4 hospitals. CDI prevalence measured by toxin assay results was 9.4 cases per 1000 discharges (P=.57 versus NHDS). However, the CDI prevalence increased more rapidly over time when measured according to the NHDS criteria than when measured according to toxin assay results (ß=1.09 versus 0.84; P=.008). CONCLUSIONS: Compared with the NHDS definition, the NIS definition captured 12% more CDI cases and reported significantly higher CDI rates. Rates calculated using toxin assay results were not different from rates calculated using NHDS criteria, but CDI prevalence appeared to increase more rapidly when measured by NHDS criteria than when measured by toxin assay results.

Efficient and effective single-step screening of individual samples for SARS-CoV-2 RNA using multi-dimensional pooling and Bayesian inference.

Rapid and widespread implementation of infectious disease surveillance is a critical component in the response to novel health threats. Molecular assays are the preferred method to detect a broad range of viral pathogens with high sensitivity and specificity. The implementation of molecular assay testing in a rapidly evolving public health emergency, such as the ongoing COVID-19 pandemic, can be hindered by resource availability or technical constraints. We present a screening strategy that is easily scaled up to support a sustained large volume of testing over long periods of time. This non-adaptive pooled-sample screening protocol employs Bayesian inference to yield a reportable outcome for each individual sample in a single testing step (no confirmation of positive results required). The proposed method is validated using clinical specimens tested using a real-time reverse transcription polymerase chain reaction test for SARS-CoV-2. This screening protocol has substantial advantages for its implementation, including higher sample throughput, faster time to results, no need to retrieve previously screened samples from storage to undergo retesting, and excellent performance of the algorithm's sensitivity and specificity compared with the individual test's metrics.