Clinical impact of active screening cultures for carbapenem-resistant Acinetobacter baumannii: A systematic review and meta-analysis.

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a significant health care-associated infection carrying substantial mortality. We assessed the clinical impact of active screening cultures for CRAB. METHODS: A systematic review and meta-analysis, aiming to answer 2 questions: (1) Does screening versus no screening improve clinical outcomes? (2) Does positive screening ("CRAB carrier") predict CRAB infections? We searched the literature until January 2024 for comparative studies reporting clinical outcomes (mortality, invasive CRAB infections). RESULTS: Of 5,407 screened publications, 9 studies (10,865 individuals) were included. Invasive CRAB infection rate was significantly higher among CRAB carriers (OR 11.14, 95% CI 4.95-25.05, with substantial heterogeneity stemming from size rather than direction of the effect). Negative predictive value of noncarriage for invasive infection was 97%. CRAB bloodstream infection rate was significantly higher among carriers (odds ratio 16.23, 95% confidence interval 2.9-110.08). No difference was demonstrated between the groups for CRAB ventilator-associated pneumonia, length of stay, and mortality. Only 1 study reported outcomes for study question #1. CONCLUSIONS: Data to support active CRAB screening are scarce regarding its clinical benefit for patients. Positively screened patients are at significantly higher risk for invasive CRAB infections, with high negative predictive value for noncarriage. This did not translate to reduced mortality.

How effective are monthly departmental tracer surveys? A 5-year retrospective study of 138 surveys in 96 departments.

BACKGROUND: Repeat department-wide surveys are commonly employed for infection control. There remains debate concerning their cost-effectivess. The aim of the study was to measure the impact of repeat department-wide surveys in major in-patient departments (IPDs) and ambulatory facilities (AFs) in a tertiary care hospital. This was a retrospective study of 138 surveys condcuted in 96 departments over a 5-year period. METHODS: Two itemized questionnaires were designed to assess the most frequently inadequately adhered to infection control measures: one for IPD (with 21 items) and the other for AF (with 17 items). RESULTS: A total of 72 surveys were conducted in 49 IPDs, of which 39 (54%) were repeat surveys, and 66 surveys in 47 AFs, of which 33 (50%) were repeat surveys. The baseline rate of adherence/department was 71% ± 14 for the IPD, with an increase from the first to the last survey to 82% ± 13 (P = .037). In 15/21 measured infection control items, adherence improved. Adherence to infection control items was lower at baseline in the AFs than in the IPDs (63 ± 27), with an increase to 76 ± 20 (non significant). Although adherence improved for 9 items, it deteriorated in another 8, producing an overall statistically unchanged outcome. CONCLUSION: Repeat whole-department surveys contribute moderately to increased adherence to infection control guidelines. AFs demonstrate lower rates of adherence to infection control guidelines and are less receptive to educational measures.

An Update From the National Healthcare Safety Network on Hospital Antibiotic Stewardship Programs in the United States, 2014-2021.

Background: In 2014, the Centers for Disease Control and Prevention (CDC) released the Core Elements of Hospital Antibiotic Stewardship Programs (ASPs) and began monitoring uptake through the National Healthcare Safety Network (NHSN) Annual Hospital Survey. In 2019, CDC updated the Core Elements and in 2022 released the Priorities for Hospital Core Element Implementation. We describe Core Element uptake from 2014 to 2021, provide a snapshot of specific ASP practices in acute care hospitals in 2021, and describe how we plan to monitor stewardship moving forward. Methods: We used the NHSN Annual Hospital Survey to summarize facility demographics and ASP practices and to monitor uptake of Core Elements. Questions have been updated over time, so not all data could be compared across years. Results: Uptake of all 7 Core Elements increased from 41% in 2014 to 95% in 2021. Uptake of all 6 Priority Elements was 10% in 2021, though 46% of hospitals met 4 or 5 of the possible 6 elements. Antibiotic stewardship was specifically listed in a contract or job description for about 60% of program leaders. The percentage of physician-pharmacist co-led programs rose from 23% to 64%. Seventy-six percent of hospitals reported implementing audit with feedback interventions. Conclusions: With nearly all acute care hospitals reporting uptake of the 7 Core Elements in 2021, and with more evidence for which ASP practices are most effective, the Priorities for Hospital Core Element Implementation were released in 2022 to help enhance the quality and impact of existing ASPs.

Rethinking Clostridioides difficile infection (CDI) surveillance definitions based on changing healthcare utilisation and a more realistic incubation period: reviewing data from a tertiary-referral hospital, Ireland, 2012 to 2021.

BackgroundCommunity-associated Clostridioides difficile infections (CA-CDI) have increased worldwide. Patients with CDI-related symptoms occurring < 48 hours after hospitalisation and no inpatient stay 12 weeks prior are classified as CA-CDI, regardless of hospital day attendances 3 months before CDI onset. Healthcare-associated (HA) CDIs include those with symptom onset ≥ 48 hours post hospitalisation.AimTo consider an incubation period more reflective of CDI, and changing healthcare utilisation, we measured how varying surveillance specifications to categorise patients according to their CDI origin resulted in changes in patients' distribution among CDI origin categories.MethodsNew CDI cases between 2012-2021 from our hospital were reviewed. For patients with CA-CDI, hospital day attendances in the 3 months prior were recorded. CA-CDI patients with hospital day attendances and recently discharged CDI patients (RD-CDI; CDI onset 4-12 weeks after discharge) were combined into a new 'healthcare-exposure' category (HE-CDI). Time from hospitalisation to disease onset was varied and the midpoint between optimal and balanced cut-offs was used instead of 48 hours to categorise HA-CDI.ResultsOf 1,047 patients, 801 (76%) were HA-CDI, 205 (20%) CA-CDI and 41 (4%) were RD-CDI. Of the CA-CDI cohort, 45 (22%) met recent HE-CDI criteria and, when reassigned, reduced CA-CDI to 15%. Sensitivity analysis indicated a day 4 cut-off for assigning HA-CDI. Applying this led to 46 HA-CDI reassigned as CA-CDI. Applying both HE and day 4 criteria led to 72% HA-CDI, 20% CA-CDI, and 8% HE-CDI (previously RD-CDI).ConclusionCDI surveillance specifications reflecting healthcare exposure and an incubation period more characteristic of C. difficile may improve targeted CDI prevention interventions.

Descriptive epidemiology of central line-associated bloodstream infections at an academic medical center in Iowa, 2019-2022.

BACKGROUND: Central line-associated bloodstream infections (CLABSIs) increased nationally during the COVID-19 pandemic. We described CLABSIs at our institution during 2019 to 2022. METHODS: This retrospective observational study examined CLABSIs among adult inpatients at an 866-bed teaching hospital in the Midwest. CLABSI incidence was trended over time and compared to monthly COVID-19 admissions. Manual chart review was performed to obtain patient demographics, catheter-associated variables, pathogens, and clinical outcomes. RESULTS: We identified 178 CLABSIs. The CLABSI incidence (cases per 1,000 line days) tripled in October 2020 as COVID-19 admissions increased. CLABSIs in 2020 were more frequently caused by coagulase-negative staphylococci and more frequently occurred in the intensive care units 7+ days after central line insertion. The CLABSI incidence normalized in early 2021 and did not increase during subsequent COVID-19 surges. Throughout 2019 to 2022, about half of the nontunneled central venous catheters involved in CLABSI were placed emergently. One-quarter of CLABSIs involved multiple central lines. Chlorhexidine skin treatment adherence was limited by patient refusal. CONCLUSIONS: The increase in CLABSIs in late 2020 during a surge in COVID-19 admissions was likely related to central line maintenance but has resolved. Characterizing CLABSI cases can provide insight into adherence to guideline-recommended prevention practices and identify areas for improvement at individual institutions.

Impact of the COVID-19 Pandemic on Inpatient Antibiotic Use in the United States, January 2019 Through July 2022.

Antimicrobial use data reported to the National Healthcare Safety Network's Antimicrobial Use and Resistance Module between January 2019 and July 2022 were analyzed to assess the impact of the COVID-19 pandemic on inpatient antimicrobial use.

Clostridioides difficile infection in neurosurgical patients in a national centre over 10 years: less common but associated with longer hospital stays.

BACKGROUND: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated (HA) diarrhoea, contributing to patient morbidity and prolonged length-of-stay (LOS). We retrospectively assessed CDI over a decade in a national neurosurgical centre, with a multi-disciplinary approach to CDI surveillance and antimicrobial stewardship, by comparing CDI patients with other patient groups. METHODS: Data on CDI in neurosurgical inpatients between January 2012 and December 2021 were collated. Disease-specific variables were compared to other inpatients with CDI. Rates per 10,000 bed days used were calculated. Patient-specific differences were compared with neurosurgical patients without CDI. CDI rates by patient group were explored using odds ratio (OR) and χ2 analyses. Negative binomial regression was used to investigate CDI rates over time. RESULTS: Of 50 neurosurgical patients with CDI, all were HA; the average age was 53 years (standard deviation (SD) 16.3 years), 49 were first-episode CDI, and three had severe CDI. The majority (76.7%) had received recent antimicrobials. Compared with non-neurosurgical CDI patients, neurosurgical CDI rates differed significantly (1.9 versus 3.6 per 10,000 bed days used, p < 0.05), neurosurgical patients were younger (p ≤ 0.01), C. difficile testing was more likely to be requested by neurosurgeons (OR 2.4; p ≤ 0.01), and the proportion of severe CDI was higher (6% versus 2%, OR 3.0, p = 0.07, confidence interval (CI) 0.54 to 11.3). Within the neurosurgical cohort, CDI patients had an average LOS four times that of other patients (CI 15.2 to 35.1; p < 0.01) and were older (53.5 versus 47.8 years, CI 0.1 to 11 years; p < 0.05). Only one CDI outbreak was linked to neurosurgical patients. CONCLUSION: CDI in neurosurgery patients differed from the wider hospital, with greater awareness of CDI testing. Longer LOS impacted bed utilisation with limited capacity. Robust surveillance supports proactive antimicrobial stewardship programmes in this vulnerable population.

In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia.

Multidrug-resistant (MDR) Pseudomonas aeruginosa has been declared a serious threat by the United States Centers for Disease Control and Prevention. Here, we used whole genome sequencing (WGS) to investigate recurrent P. aeruginosa bloodstream infections in a severely immunocompromised patient. The infections demonstrated unusual, progressive increases in resistance to beta lactam antibiotics in the setting of active treatment with appropriate, guideline-directed agents. WGS followed by comparative genomic analysis of isolates collected over 44 days demonstrated in host evolution of a single P. aeruginosa isolate characterized by stepwise acquisition of two de-novo genetic resistance mechanisms over the course of treatment. We found a novel deletion affecting the ampC repressor ampD and neighboring gene ampE, which associated with initial cefepime treatment failure. This was followed by acquisition of a porin nonsense mutation, OprD, associated with resistance to carbapenems. This study highlights the potential for in-host evolution of P. aeruginosa during bloodstream infections in severely immunocompromised patients despite appropriate antimicrobial therapy. In addition, it demonstrates the utility of WGS for understanding unusual resistance patterns in the clinical context.

Clinico-Demographic Profiles of Herpes Zoster Cases in Patients With and Without COVID-19 Infection During the Pandemic: A Retrospective Analysis of 32 Cases.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has multiple impacts on the human body. The immunological effect is one of the prominent ones, which is thought to be fundamental in many physical manifestations and disease severity. Herpes zoster (HZ) reactivation has been well-linked to immunity; immunocompromised states predispose a person to HZ. Studies have raised concerns about HZ incidences in COVID-19 patients; however, the clinical characteristics of the HZ cases among patients with and without COVID-19 are another area to be explored. METHODS: In this retrospective analysis, we compared the clinical and demographic characteristics of HZ cases presented to our outpatient department immediately before and during the early second wave of the COVID-19 pandemic (September 2020 to April 2021) in India. The cases were divided into two groups based on the history of COVID-19 infections. The clinico-demographic characteristics were then compared using an unpaired t-test, Fisher's exact test, and analysis of variance as applicable using InStat software; a two-sided p-value <0.05 was considered significant. RESULTS: During the period, 32 cases (17 HZ cases with a history of COVID-19; 15 HZ cases without) were detected. The age and gender distribution were indifferent statistically. Our analysis showed that multi-dermatomal and disseminated involvements were significantly higher in HZ cases having a history of COVID-19. CONCLUSION: The present retrospective analysis of 32 cases indicates that persons who suffered from COVID-19 and presented with HZ were likely to have a higher chance of multi-dermatomal and disseminated involvement. While our analysis cannot establish a true association between COVID-19 infection and HZ reactivation, which will require a large-scale study, clinicians might get a clue of the possible progression of the extent of HZ manifestations from our findings.

Clostridioides difficile Infection: Clinical Practice and Health Outcomes in 6 Large Tertiary Hospitals in Eastern Australia.

Background: Clostridioides difficile infection (CDI) is associated with significant morbidity and mortality in both healthcare and community settings. We aimed to define the predisposing factors, risks for severe disease, and mortality determinants of CDI in eastern Australia over a 1-year period. Methods: This is an observational retrospective study of CDI in hospitalized patients aged ≥18 years in 6 tertiary institutions from 1 January 2016 to 31 December 2016. Patients were identified through laboratory databases and medical records of participating institutions. Clinical, imaging, and laboratory data were input into an electronic database hosted at a central site. Results: A total of 578 patients (578 CDI episodes) were included. Median age was 65 (range, 18-99) years and 48.2% were male. Hospital-onset CDI occurred in 64.0%. Recent antimicrobial use (41.9%) and proton pump inhibitor use (35.8%) were common. Significant risk factors for severe CDI were age <65 years (P < .001), malignancy within the last 5 years (P < .001), and surgery within the previous 30 days (P < .001). Significant risk factors for first recurrence included severe CDI (P = .03) and inflammatory bowel disease (P = .04). Metronidazole was the most common regimen for first episodes of CDI with 65.2% being concordant with Australian treatment guidelines overall. Determinants for death at 60 days included age ≥65 years (P = .01), severe CDI (P < .001), and antibiotic use within the prior 30 days (P = .02). Of those who received metronidazole as first-line therapy, 10.1% died in the 60-day follow-up period, compared to 9.8% of those who received vancomycin (P = .86). Conclusions: Patients who experience CDI are vulnerable and require early diagnosis, clinical surveillance, and effective therapy to prevent complications and improve outcomes.

Quantifying and Interpreting Inequality in Surgical Site Infections per Quarter Among Anesthetizing Locations and Specialties.

Background Earlier studies have shown that prevention of surgical site infection can achieve net cost savings when targeted to operating rooms with the most surgical site infections. Methodology This retrospective cohort study included all 231,057 anesthetics between May 2017 and June 2022 at a large teaching hospital. The anesthetics were administered in operating rooms, procedure rooms, radiology, and other sites. The 8,941 postoperative infections were identified from International Classification of Diseases diagnosis codes relevant to surgical site infections documented during all follow-up encounters over 90 days postoperatively. To quantify the inequality in the counts of infections among anesthetizing locations, the Gini index was used, with the Gini index being proportional to the sum of the absolute pairwise differences among anesthetizing locations in the counts of infections. Results The Gini index for infections among the 112 anesthetizing locations at the hospital was 0.64 (99% confidence interval = 0.56 to 0.71). The value of 0.64 is so large that, for comparison, it exceeds nearly all countries' Gini index for income inequality. The 50% of locations with the fewest infections accounted for 5% of infections. The 10% of locations with the most infections accounted for 40% of infections and 15% of anesthetics. Among the 57 operating room locations, there was no association between counts of cases and infections (Spearman correlation coefficient r = 0.01). Among the non-operating room locations (e.g., interventional radiology), there was a significant association (Spearman r = 0.79). Conclusions Targeting specific anesthetizing locations is important for the multiple interventions to reduce surgical site infections that represent fixed costs irrespective of the number of patients (e.g., specialized ventilatory systems and nightly ultraviolet-C disinfection).

A decade of Clostridioides difficile infection: a constant challenge to maintain the status quo.

INTRODUCTION: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated (HA) diarrhoea. We retrospectively investigated data from a comprehensive, multidisciplinary C. difficile surveillance programme focusing on hospitalized patients in a tertiary Irish hospital over 10 years. METHODS: Data from 2012 to 2021 were extracted from a centralized database, including patient demographics, admission, case and outbreak details, ribotypes (RTs), and (since 2016) antimicrobial exposures and CDI treatments. Counts of CDI by origin of infection were explored using ꭓ2 analyses, Poisson regression was used to investigate trends in rates of CDI and possible risk factors. Time to recurrent CDI was examined by a Cox proportional hazards regression. RESULTS: Over 10 years, 954 CDI patients had a 9% recurrent CDI rate. CDI testing requests occurred in only 22% of patients. Most CDIs were HA (82.2%) and affected females (odds ratio: 2.3, P<0.01). Fidaxomicin significantly reduced the hazard ratio of time to recurrent CDI. No trends in HA-CDI incidence were observed despite key time-point events and increasing hospital activity. In 2021, community-associated (CA)-CDI increased. RTs did not differ for HA versus CA for the most common RTs (014, 078, 005 and 015). Average length-of-stay differed significantly between HA (67.1 days) and CA (14.6 days) CDI. CONCLUSION: HA-CDI rates remained unchanged despite key events and increased hospital activity, whereas by 2021, CA-CDI was at its highest in a decade. The convergence of CA and HA RTs, and the proportion of CA-CDI, question the relevance of current case definitions when increasingly patients receive hospital care without an overnight hospital stay.

The Epidemiology of Healthcare-Associated Bloodstream Infection in an Adult Intensive Care Unit: A Retrospective Cohort Study in a Single Tertiary Care Hospital in Hanoi, Vietnam.

Background Healthcare-associated infections (HAIs), including bloodstream infections (BSIs) in the intensive care unit (ICU), are growing global public health problems. While high-income countries have reported the burden of HAIs precisely, low- and middle-income countries (LMICs), including Vietnam, often lack surveillance systems for HAIs. In Vietnam, few reports described HAI-associated BSIs. Therefore, in this study, we aim to clarify the characteristics of HAI-associated BSI in an adult ICU. Materials and methods We conducted a retrospective cohort study of HAI-associated BSI in the adult ICU of Bach Mai Hospital (BMH), Vietnam, between December 2013 and August 2015. For every case identified with bacteremia, we collected characteristics and laboratory findings of the case and followed the length of hospital stay and seven-day and 30-day survival. Predictors of 30-day mortality were analyzed using univariate and multivariate analyses. Results Among the 90 cases identified, the median age of the study cohort was 57 (range: 18-90) years, and 59 (65.6%) were male. Chronic heart disease was the most frequent comorbidity (n = 26, 28.9%). The pathogens isolated were mostly Candida spp. (n = 26, 26.3%) and Enterococcus spp. (n = 19, 19.2%). Among the 90 patients with confirmed HAI-associated BSI, 34 (37.8%) patients survived, while 31 (34.4%) patients died in 30 days. In multivariate analysis, chronic heart disease tended to increase with 30-day all-cause mortality (odds ratio (OR) = 3.5, 95% confidence interval (CI) = 1.0-11.9, p = 0.051). Conclusions Our retrospective cohort study is the largest investigation to describe HAI-associated BSI in an adult ICU in a tertiary care hospital in Vietnam. Improved laboratory detection and infection surveillance systems are needed to reduce HAI-associated BSI.

Kocuria rosea Bacteremia in a Sickle Cell Patient: A Case Report.

Central line-associated bloodstream infections (CLABSI) are a significant risk factor for poor patient outcomes. It is important to correctly diagnose and treat these infections to ensure the best chance of recovery. Kocuria rosea is a novel bacteria that is native to the human flora and has been on the rise as a culprit in recent nosocomial infections. However, due to its characteristics, it is often misclassified by commonly used hospital tests. We present a case of a 55-year-old female with sickle cell disease who developed a K. rosea infection during her hospital course and was effectively diagnosed and treated. This case report aims to bring awareness to this unusual bacteria as a possible cause of inpatient infection and CLABSI. Further research should be conducted to determine the incidence of this bacteria and the best testing to be done for its proper recognition.

Burden of multidrug and extensively drug-resistant ESKAPEE pathogens in a secondary hospital care setting in Greece.

Bacterial antibiotic resistance (AMR) is a significant threat to public health, with the sentinel 'ESKAPEE' pathogens, being of particular concern. A cohort study spanning 5.5 years (2016-2021) was conducted at a provincial general hospital in Crete, Greece, to describe the epidemiology of ESKAPEE-associated bacteraemia regarding levels of AMR and their impact on patient outcomes. In total, 239 bloodstream isolates were examined from 226 patients (0.7% of 32 996 admissions) with a median age of 75 years, 28% of whom had severe comorbidity and 46% with prior stay in ICU. Multidrug resistance (MDR) was lowest for Pseudomonas aeruginosa (30%) and Escherichia coli (33%), and highest among Acinetobacter baumannii (97%); the latter included 8 (22%) with extensive drug-resistance (XDR), half of which were resistant to all antibiotics tested. MDR bacteraemia was more likely to be healthcare-associated than community-onset (RR 1.67, 95% CI 1.04-2.65). Inpatient mortality was 22%, 35% and 63% for non-MDR, MDR and XDR episodes, respectively (P = 0.004). Competing risks survival analysis revealed increasing mortality linked to longer hospitalisation with increasing AMR levels, as well as differential pathogen-specific effects. A. baumannii bacteraemia was the most fatal (14-day death hazard ratio 3.39, 95% CI 1.74-6.63). Differences in microbiology, AMR profile and associated mortality compared to national and international data emphasise the importance of similar investigations of local epidemiology.

Impact of antimicrobial stewardship programs on antibiotic consumption and antimicrobial resistance in four Colombian healthcare institutions.

BACKGROUND: Antimicrobial stewardship programs (ASPs) have become a fundamental pillar in optimizing antimicrobial usage, improving patient care, and reducing antimicrobial resistance (AMR). Herein we evaluated the impact of an ASP on antimicrobial consumption and AMR in Colombia. METHODS: We designed a retrospective observational study and measured trends in antibiotic consumption and AMR before and after the implementation of an ASP using interrupted time series analysis over a 4-year period (24 months before and 24 months after ASP implementation). RESULTS: ASPs were implemented according to the available resources in each of the institutions. Before ASP implementation, there was a trend toward an increase in the antibiotic consumption of all measured antimicrobials selected. Afterward, an overall decrease in antibiotic consumption was observed. The use of ertapenem and meropenem decreased in hospital wards, while a decrease in the use of ceftriaxone, cefepime, piperacillin/tazobactam, meropenem, and vancomycin was observed in intensive care units. After ASP implementation, the trend toward an increase of oxacillin-resistant Staphylococcus aureus, ceftriaxone-resistant Escherichia coli, and meropenem-resistant Pseudomonas aeruginosa was reversed. CONCLUSIONS: In our study, we showed that ASPs are a key strategy in tackling the emerging threat of AMR and have a positive impact on antibiotic consumption and resistance.

Trends and patterns of cause-specific hospitalizations in mainland Portugal between 2000 and 2016.

OBJECTIVES: This study aimed to describe trends and patterns of cause-specific hospitalizations in mainland Portugal between 2000 and 2016. STUDY DESIGN: This was a retrospective observational study based on hospital discharge data during the period 2000-2016 in mainland Portugal. METHODS: All inpatient hospital discharges among mainland Portuguese public hospitals were considered to evaluate trends and patterns over the years through hospitalization proportions, number of hospitalizations, age-standardized hospitalization rates (direct standardization using the European standard population), and the number of in-hospital stay days (bed-days). Health Cost and Utilization Project Clinical Classifications Software was used to categorize and cluster inpatients' principal diagnosis. RESULTS: Between 2000 and 2002 and between 2014 and 2016, age-standardized hospitalization rates decreased by 8.6%. Moreover, "liveborn," "diseases of the heart," and "respiratory infections" were the leading hospitalization causes in both periods with a variation of -8.8%, -8.3%, and 13.4% on age-standardized hospitalization rate, respectively. The age-standardized hospitalization rate due to "bacterial infection" increased by 108.7%. "Respiratory diseases" are the leading cause responsible for more in-hospital stay days in the period 2014-2016 (48.6% increase). All Portuguese regions presented decreasing overall trends in their age-standardized hospitalization rates in the study period, yet increasing trends were observed until 2004 except for the Lisbon region; in addition, the number of in-hospital stay days remained relatively stable through time. CONCLUSIONS: Hospitalizations in mainland Portugal decreased between 2000 and 2016 with heterogeneous patterns considering time, age group, and gender. "Aspiration pneumonitis; food/vomitus," "diseases of the white blood cells," "other nutritional, endocrine, and metabolic disorders," "bacterial infection," and "pathological fractures" revealed substantial increases, and further evaluations and monitoring are required.

Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing.

BACKGROUND: Though detection of transmission clusters of methicillin-resistant Staphylococcus aureus (MRSA) infections is a priority for infection control personnel in hospitals, the transmission dynamics of MRSA among hospitalized patients with bloodstream infections (BSIs) has not been thoroughly studied. Whole genome sequencing (WGS) of MRSA isolates for surveillance is valuable for detecting outbreaks in hospitals, but the bioinformatic approaches used are diverse and difficult to compare. METHODS: We combined short-read WGS with genotypic, phenotypic, and epidemiological characteristics of 106 MRSA BSI isolates collected for routine microbiological diagnosis from inpatients in 2 hospitals over 12 months. Clinical data and hospitalization history were abstracted from electronic medical records. We compared 3 genome sequence alignment strategies to assess similarity in cluster ascertainment. We conducted logistic regression to measure the probability of predicting prior hospital overlap between clustered patient isolates by the genetic distance of their isolates. RESULTS: While the 3 alignment approaches detected similar results, they showed some variation. A gene family-based alignment pipeline was most consistent across MRSA clonal complexes. We identified 9 unique clusters of closely related BSI isolates. Most BSIs were healthcare associated and community onset. Our logistic model showed that with 13 single-nucleotide polymorphisms, the likelihood that any 2 patients in a cluster had overlapped in a hospital was 50%. CONCLUSIONS: Multiple clusters of closely related MRSA isolates can be identified using WGS among strains cultured from BSI in 2 hospitals. Genomic clustering of these infections suggests that transmission resulted from a mix of community spread and healthcare exposures long before BSI diagnosis.

Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis.

Background: Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmission, however, whole genome sequencing can identify highly-related patient isolates providing opportunities for precision infection control interventions. We investigated the feasibility and potential impact of a prospective multi-centre genomics workflow for hospital infection control. Methods: We conducted a prospective genomics implementation study across eight Australian hospitals over 15 months (2017,2018), collecting all clinical and screening isolates from inpatients with vanA VRE, MRSA, ESBL Escherichia coli (ESBL-Ec), or ESBL Klebsiella pneumoniae (ESBL-Kp). Genomic and epidemiologic data were integrated to assess MDRO transmission. Findings: In total, 2275 isolates were included from 1970 patients, predominantly ESBL-Ec (40·8%) followed by MRSA (35·6%), vanA VRE (15·2%), and ESBL-Kp (8·3%).Overall, hospital and genomic epidemiology showed 607 patients (30·8%) acquired their MDRO in hospital, including the majority of vanA VRE (266 patients, 86·4%), with lower proportions of ESBL-Ec (186 patients, 23·0%), ESBL-Kp (42 patients, 26·3%), and MRSA (113 patients, 16·3%). Complex patient movements meant the majority of MDRO transmissions would remain undetected without genomic data.The genomics implementation had major impacts, identifying unexpected MDRO transmissions prompting new infection control interventions, and contributing to vanA VRE becoming a notifiable condition. We identified barriers to implementation and recommend strategies for mitigation. Interpretation: Implementation of a multi-centre genomics-informed infection control workflow is feasible and identifies many unrecognised MDRO transmissions. This provides critical opportunities for interventions to improve patient safety in hospitals. Funding: Melbourne Genomics Health Alliance (supported by State Government of Victoria, Australia), and National Health and Medical Research Council (Australia).