Search and Contain: Impact of an Integrated Genomic and Epidemiological Surveillance and Response Program for Control of Carbapenemase-producing Enterobacterales.

BACKGROUND: Multiresistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs such as carbapenemase-producing Enterobacterales (CPE) have emerged and evaluation is needed. We assessed the feasibility and impact of a statewide CPE surveillance and response program deployed across Victoria, Australia (population 6.5 million). METHODS: A prospective multimodal intervention including active screening, carrier isolation, centralized case investigation, and comparative pathogen genomics was implemented. We analyzed trends in CPE incidence and clinical presentation, risk factors, and local transmission over the program's first 3 years (2016-2018). RESULTS: CPE case ascertainment increased over the study period to 1.42 cases/100 000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100 000 population, P = .640). KPC-2 infection decreased from 0.29 infections/100 000 population prior to intervention to 0.03 infections/100 000 population in 2018 (P = .003). Comprehensive case investigation identified instances of overseas community acquisition. Median time between isolate referral and genomic and epidemiological assessment for local transmission was 11 days (IQR, 9-14). Prospective surveillance identified numerous small transmission networks (median, 2; range, 1-19 cases), predominantly IMP and KPC, with median pairwise distance of 8 (IQR, 4-13) single nucleotide polymorphisms; low diversity between clusters of the same sequence type suggested genomic cluster definitions alone are insufficient for targeted response. CONCLUSIONS: We demonstrate the value of centralized CPE control programs to increase case ascertainment, resolve risk factors, and identify local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally.

Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016.

Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the state public health laboratory in Victoria, Australia, from 2012 to 2016 and examined using phenotypic, multiplex PCR and whole-genome sequencing (WGS) methods and compared with epidemiological metadata. Carbapenemase genes were detected in 361 isolates from 291 patients (30.8% of suspected CPE isolates), mostly from urine (42.1%) or screening samples (34.8%). IMP-4 (28.0% of patients), KPC-2 (25.3%), NDM (24.1%), and OXA carbapenemases (22.0%) were most common. Klebsiella pneumoniae (48.8% of patients) and Escherichia coli (26.1%) were the dominant species. Carbapenemase-inactivation method (CIM) testing reliably detected carbapenemase-positive isolates (100% sensitivity, 96.9% specificity), identifying an additional five CPE among 159 PCR-negative isolates (IMI and SME carbapenemases). When epidemiologic investigations were performed, all pairs of patients designated "highly likely" or "possible" local transmission had ≤23 pairwise single-nucleotide polymorphisms (SNPs) by genomic transmission analysis; conversely, all patient pairs designated "highly unlikely" local transmission had ≥26 pairwise SNPs. Using this proposed threshold, possible local transmission was identified involving a further 16 patients for whom epidemiologic data were unavailable. Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions. Using our workflow, pairwise SNP distances between CPE isolates of ≤23 SNPs suggest local transmission.

An evaluation of enhanced surveillance of hospitalised COVID-19 patients to inform the public health response in Victoria.

BACKGROUND: Public health surveillance is crucial for supporting a rapid and effective response to public health emergencies. In response to the coronavirus disease (COVID-19) pandemic, an enhanced surveillance system of hospitalised COVID-19 patients was established by the Victorian Department of Health and Human Services (DHHS) and the Victorian Healthcare Associated Infection Surveillance System Coordinating Centre. The system aimed to reduce workforce capacity constraints and increase situational awareness on the status of hospitalised patients. METHODS: The system was evaluated, using guidelines from the United States Centers for Disease Control and Prevention, against eight attributes: acceptability; data quality; flexibility; representativeness; simplicity; stability; timeliness; and usefulness. Evidence was generated from stakeholder consultation, participant observation, document review, systems review, issues log review and audits. Data were collected and analysed over a period of up to three months, covering pre- and post-implementation from March to June 2020. RESULTS: This system was rapidly established by leveraging established relationships and infrastructure. Stakeholders agreed that the system was important but was limited by a reliance on daily manual labour (including weekends), which impeded scalability. The ability of the system to perform well in each attribute was expected to shift with the severity of the pandemic; however, at the time of this evaluation, when there were an average 23 new cases per day (0.3 cases per 100,000 population per day), the system performed well. CONCLUSION: This enhanced surveillance system was useful and achieved its key DHHS objectives during the COVID-19 public health emergency in Victoria. Recommendations for improvement were made to the current and future systems, including the need to plan alternatives to improve the system's scalability and to maintain stakeholder acceptability.

Central line-associated bloodstream infections in Australian intensive care units: Time-trends in infection rates, etiology, and antimicrobial resistance using a comprehensive Victorian surveillance program, 2009-2013.

BACKGROUND: The epidemiology of central line-associated bloodstream infections (CLABSI) in Australian intensive care units (ICUs) has not previously been reported. We sought to describe time-trends in CLABSI rates, infections by ICU peer-groups, etiology, and antimicrobial susceptibility of pathogens in a large cohort of Australian ICUs for the period January 1, 2009-December 31, 2013. METHODS: Using National Healthcare Safety Network methods, CLABSI surveillance in adult patients was performed by hospitals participating in the Victorian Healthcare Associated Infection Surveillance System (n = 29). Hospitals were grouped by location, sector, and teaching status. RESULTS: Overall, 384 CLABSI events were reported over 303,968 central venous catheter (CVC)-days, corresponding to a rate of 1.26/1,000 CVC-days (95% confidence interval, 1.14-1.40). Every 1-year increase was associated with a 26% reduction in CLABSI risk (risk ratio, 0.74, 95% confidence interval, 0.69-0.80; P < .001). The most frequently identified pathogens were Enterococcus spp (26.3%), followed by Candida spp (15.4%) and Staphylococcus aureus (13.3%). CLABSI due to Enterococcus spp, S aureus, and coagulase-negative Staphylococcus spp displayed significant reductions over time. CONCLUSIONS: Internationally accepted surveillance methods have been employed in Australia, demonstrating CLABSI rates comparable to medical/surgical ICUs in the United States and a reduction in pathogen-specific infections over a 5-year period.

Diminishing surgical site infections in Australia: time trends in infection rates, pathogens and antimicrobial resistance using a comprehensive Victorian surveillance program, 2002-2013.

OBJECTIVE: To evaluate time trends in surgical site infection (SSI) rates and SSI pathogens in Australia. DESIGN: Prospective multicenter observational cohort study. SETTING: A group of 81 Australian healthcare facilities participating in the Victorian Healthcare Associated Infection Surveillance System (VICNISS). PATIENTS: All patients underwent surgeries performed between October 1, 2002, and June 30, 2013. National Healthcare Safety Network SSI surveillance methods were employed by the infection prevention staff at the participating hospitals. INTERVENTION: Procedure-specific risk-adjusted SSI rates were calculated. Pathogen-specific and antimicrobial-resistant (AMR) infections were modeled using multilevel mixed-effects Poisson regression. RESULTS: A total of 183,625 procedures were monitored, and 5,123 SSIs were reported. Each year of observation was associated with 11% risk reduction for superficial SSI (risk ratio [RR], 0.89; 95% confidence interval [CI], 0.88-0.90), 9% risk reduction for deep SSI (RR, 0.91; 95% CI, 0.90-0.93), and 5% risk reduction for organ/space SSI (RR, 0.95; 95% CI, 0.93-0.97). Overall, 3,318 microbiologically confirmed SSIs were reported. Of these SSIs, 1,174 (35.4%) were associated with orthopedic surgery, 827 (24.9%) with coronary artery bypass surgery, 490 (14.8%) with Caesarean sections, and 414 (12.5%) with colorectal procedures. Staphylococcus aureus was the most frequently identified pathogen, and a statistically significant increase in infections due to ceftriaxone-resistant Escherichia coli was observed (RR, 1.37; 95% CI, 1.10-1.70). CONCLUSIONS: Standardized SSI surveillance methods have been implemented in Victoria, Australia. Over an 11-year period, diminishing rates of SSIs have been observed, although AMR infections increased significantly. Our findings facilitate the refinement of recommended surgical antibiotic prophylaxis regimens and highlight the need for a more expansive national surveillance strategy to identify changes in epidemiology.

Investigation of an outbreak of Serratia marcescens in a neonatal unit via a case-control study and molecular typing.

BACKGROUND: In March 2004, infection or colonization with Serratia marcescens affected one third of all neonates in a newborn services unit (NBS). METHODS: We performed a case-control study and automated ribotyping. RESULTS: Forty-nine cases were compared with 64 controls. The overall mean length of stay (LOS) in the NBS was 67 days for cases and 36 days for controls, P = .005. Cases were of lower mean birth weight than controls (1566 g vs 1968 g, respectively, P = .02). Risk factors that trended toward significance for S marcescens acquisition included the following: premature rupture of membranes (odds ratio [OR], 2.7; 95% confidence interval [95% CI]: 1.0-7.1; P = .05), vaginal delivery at our hospital (OR, 2.1; 95% CI: 0.9-4.6; P = .06), intubation at delivery (OR, 2.3; 95% CI: 0.9-5.2; P = .05), mechanical ventilation (OR, 2.1; 95% CI: 0.9-4.4; P = .06), and theophylline treatment (OR, 2.5; 95% CI: 1.1-5.4; P = .02). Multiple logistic regression analysis revealed vaginal delivery at our hospital (OR, 3.4; 95% CI: 1.4-8.2; P = .007) and LOS >30 days (OR, 4.4; 95% CI: 1.8-10.6; P = .001) as independent risk factors for S marcescens acquisition. Ribotyping of specimens revealed 5 restriction patterns. CONCLUSION: Cases were of lower birth weight than controls, were born by vaginal delivery at our hospital, had longer LOS in NBS, and had greater requirements for respiratory support. Ribotyping of specimens revealed that this outbreak was not clonal.

Disinfection of Burkholderia cepacia complex from non-touch taps in a neonatal nursery.

Burkholderia cepacia complex (Bcc) comprises nine closely related species or genomovars. It is an important causative agent of opportunistic infections and waterborne nosocomial infections. B. cepacia (formerly genomovar I) was identified from the blood culture of a baby in our neonatal unit (NU) in March 2005. B. cepacia was isolated four times from clinical specimens since the introduction of non-touch taps in the NU from 2000 to 2005 and only once from 1994 to 2000. Environmental samples were collected from the NU, including tap water from non-touch taps. Clinical and environmental isolates of Bcc were characterized using molecular identification and strain typing. A literature review was undertaken to delineate a method for eradication of Bcc. Several variations for hot water eradication of the organism from the taps were attempted. Genotyping and molecular analysis revealed that tap water isolates were B. cenocepacia which was a different species from the B. cepacia isolated from blood cultures of the neonate. However, B. cenocepacia has been known to cause nosocomial outbreaks and it was eventually eradicated from the NU by using repeated thermal shock (hot water at 65 degrees C for 10 min), changing taps and decolonizing sinks with hypochlorite. Molecular typing is useful in assisting the investigation of Bcc nosocomial infections.

Serratia marcescens bacteremia - an indicator for outbreak management and heightened surveillance.

Colonization of neonatal intensive care units by Serratia marcescens is associated with clinical outbreaks. We report the management of an outbreak in a newborn services unit (NBS), in 2004, of a strain of S. marcescens that was present in the unit from 1994. Over the 10-year period, increases in clinical isolates demonstrated three epidemic curves, each spanning 3-4 years and each involving positive blood cultures. In 2004, clinical isolates of S. marcescens bacteremia prompted an investigation. Control measures including screening, creation of a separate unit, use of contact precautions, education, environmental sampling, strategies to reduce overcrowding, surveillance and molecular epidemiological techniques were implemented. In total, 99 babies were either colonized or infected with S. marcescens between December 2003 and December 2005. Isolates were tested with ribotyping identifying one main endemic strain. No environmental source was found, however, the outbreak terminated following adherence to infection control principles. Epidemiological information, structural and practice changes were used to prevent transmission and control the outbreak.