Whole-genome sequencing (WGS) has traditionally been used in infection prevention to confirm or refute the presence of an outbreak after it has occurred. Due to decreasing costs of WGS, an increasing number of institutions have been utilizing WGS-based surveillance. Additionally, machine learning or statistical modeling to supplement infection prevention practice have also been used. We systematically reviewed the use of WGS surveillance and machine learning to detect and investigate outbreaks in healthcare settings.

We performed a PubMed search using separate terms for WGS surveillance and/or machine-learning technologies for infection prevention through March 15, 2021.

Of 767 studies returned using the WGS search terms, 42 articles were included for review. Only 2 studies (4.8%) were performed in real time, and 39 (92.9%) studied only 1 pathogen. Nearly all studies (n = 41, 97.6%) found genetic relatedness between some isolates collected. Across all studies, 525 outbreaks were detected among 2,837 related isolates (average, 5.4 isolates per outbreak). Also, 35 studies (83.3%) only utilized geotemporal clustering to identify outbreak transmission routes. Of 21 studies identified using the machine-learning search terms, 4 were included for review. In each study, machine learning aided outbreak investigations by complementing methods to gather epidemiologic data and automating identification of transmission pathways.

WGS surveillance is an emerging method that can enhance outbreak detection. Machine learning has the potential to identify novel routes of pathogen transmission. Broader incorporation of WGS surveillance into infection prevention practice has the potential to transform the detection and control of healthcare outbreaks.

Anticholinergic medications block cholinergic transmission. The central effects of anticholinergic drugs can be particularly marked in patients with dementia. Furthermore, anticholinergics antagonise the effects of cholinesterase inhibitors, the main dementia treatment.

This study aimed to assess anticholinergic drug prescribing among dementia patients before and after admission to UK acute hospitals.

352 patients with dementia were included from 17 hospitals in the UK. All were admitted to surgical, medical or Care of the Elderly wards in 2019. Information about patients’ prescriptions were recorded on a standardised form. An evidence-based online calculator was used to calculate the anticholinergic drug burden of each patient. The correlation between two subgroups upon admission and discharge was tested with Spearman’s Rank Correlation.

Table 1 shows patient demographics. On admission, 37.8% of patients had an anticholinergic burden score ≥1 and 5.68% ≥3. At discharge, 43.2% of patients had an anticholinergic burden score ≥1 and 9.1% ≥3. The increase was statistically significant (rho 0.688; p=2.2x10-16). The most common group of anticholinergic medications prescribed at discharge were psychotropics (see Figure 1). Among patients prescribed cholinesterase inhibitors, 44.9% were also taking anticholinergic medications.

This multicentre cross-sectional study found that people with dementia are frequently prescribed anticholinergic drugs, even if also taking cholinesterase inhibitors, and are significantly more likely to be discharged with a higher anticholinergic drug burden than on admission to hospital.

This project was planned and executed by the authors on behalf of SPARC (Student Psychiatry Audit and Research Collaborative). We thank the National Student Association of Medical Research for allowing us use of the Enketo platform. Judith Harrison was su

Identifying routes of transmission among hospitalized patients during a healthcare-associated outbreak can be tedious, particularly among patients with complex hospital stays and multiple exposures. Data mining of the electronic health record (EHR) has the potential to rapidly identify common exposures among patients suspected of being part of an outbreak.

We retrospectively analyzed 9 hospital outbreaks that occurred during 2011–2016 and that had previously been characterized both according to transmission route and by molecular characterization of the bacterial isolates. We determined (1) the ability of data mining of the EHR to identify the correct route of transmission, (2) how early the correct route was identified during the timeline of the outbreak, and (3) how many cases in the outbreaks could have been prevented had the system been running in real time.

Correct routes were identified for all outbreaks at the second patient, except for one outbreak involving >1 transmission route that was detected at the eighth patient. Up to 40 or 34 infections (78% or 66% of possible preventable infections, respectively) could have been prevented if data mining had been implemented in real time, assuming the initiation of an effective intervention within 7 or 14 days of identification of the transmission route, respectively.

Data mining of the EHR was accurate for identifying routes of transmission among patients who were part of the outbreak. Prospective validation of this approach using routine whole-genome sequencing and data mining of the EHR for both outbreak detection and route attribution is ongoing.

Recovery of multidrug-resistant (MDR) Pseudomonas aeruginosa and Klebsiella pneumoniae from a cluster of patients in the medical intensive care unit (MICU) prompted an epidemiologic investigation for a common exposure.

Clinical and microbiologic data from MICU patients were retrospectively reviewed, MICU bronchoscopes underwent culturing and borescopy, and bronchoscope reprocessing procedures were reviewed. Bronchoscope and clinical MDR isolates epidemiologically linked to the cluster underwent molecular typing using pulsed-field gel electrophoresis (PFGE) followed by whole-genome sequencing.

Of the 33 case patients, 23 (70%) were exposed to a common bronchoscope (B1). Both MDR P. aeruginosa and K. pneumonia were recovered from the bronchoscope’s lumen, and borescopy revealed a luminal defect. Molecular testing demonstrated genetic relatedness among case patient and B1 isolates, providing strong evidence for horizontal bacterial transmission. MDR organism (MDRO) recovery in 19 patients was ultimately linked to B1 exposure, and 10 of 19 patients were classified as belonging to an MDRO pseudo-outbreak.

Surveillance of bronchoscope-derived clinical culture data was important for early detection of this outbreak, and whole-genome sequencing was important for the confirmation of findings. Visualization of bronchoscope lumens to confirm integrity should be a critical component of device reprocessing.

Determining risk factors for acquisition of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals is important for defining infection-control measures that may lead to fewer hospital-acquired infections.

To determine patient-associated risk factors for acquisition of MRSA in a tertiary care hospital with the goal of identifying modifiable risk factors.

A retrospective matched case-control study was performed. Case patients who acquired MRSA during hospitalization and 2 matched control patients were selected among inpatients admitted to target units during the period from 2001 through 2008. The odds of exposure to potential risk factors were compared between case patients and control patients, using matched univariate conditional logistic regression. A single multivariate conditional logistic regression model identifying independent patient-specific risk factors was generated.

A total of 451 case patients and 866 control patients were analyzed. Factors positively associated with MRSA acquisition were as follows: target unit stay before index culture; primary diagnosis of respiratory disease, digestive tract disease, injury or trauma, or other diagnosis compared with cardiocirculatory disease; peripheral vascular disease; mechanical ventilation with pneumonia; ventricular shunting or ventriculostomy; and ciprofloxacin use. Factors associated with decreased risk were receipt of a solid-organ transplant and use of penicillins, cephalosporins, rifamycins, daptomycin or linezolid, and proton pump inhibitors.

Among the factors associated with increased risk, few are modifiable. Patients with at-risk conditions could be targeted for intensive surveillance to detect acquisition sooner. The association of MRSA acquisition with target unit exposure argues for rigorous application of hand hygiene, appropriate barriers, environmental control, and strict aseptic technique for all procedures performed on such Patients. Our findings support focusing efforts to prevent MRSA transmission and restriction of ciprofloxacin use.

Methicillin-resistant Staphylococcus aureus (MRSA) transmission and infections are a continuing problem in hospitals. Although some have recommended universal surveillance for MRSA at hospital admission to identify and to isolate MRSA-colonized patients, there is a need for formal economic studies to determine the cost-effectiveness of such a strategy.

We developed a stochastic computer simulation model to determine the potential economic impact of performing MRSA surveillance (ie, single culture of an anterior nares specimen) for all hospital admissions at different MRSA prevalences and basic reproductive rate thresholds from the societal and third party-payor perspectives. Patients with positive surveillance culture results were placed under isolation precautions to prevent transmission by way of respiratory droplets. MRSA-colonized patients who were not isolated could transmit MRSA to other hospital patients.

The performance of universal MRSA surveillance was cost-effective (defined as an incremental cost-effectiveness ratio of less than $50,000 per quality-adjusted life-year) when the basic reproductive rate was 0.25 or greater and the prevalence was 1% or greater. In fact, surveillance was the dominant strategy when the basic reproductive rate was 1.5 or greater and the prevalence was 15% or greater, the basic reproductive rate was 2.0 or greater and the prevalence was 10% or greater, and the basic reproductive rate was 2.5 or greater and the prevalence was 5% or greater.

Universal MRSA surveillance of adults at hospital admission appears to be cost-effective at a wide range of prevalence and basic reproductive rate values. Individual hospitals and healthcare systems could compare their prevailing conditions (eg, the prevalence of MRSA colonization and MRSA transmission dynamics) with the benchmarks in our model to help determine their optimal local strategies.

Methicillin-resistant Staphylococcus aureus (MRSA) can cause severe infection in patients who are undergoing vascular surgical operations. Testing all vascular surgery patients preoperatively for MRSA and attempting to decolonize those who have positive results may be a strategy to prevent MRSA infection. The economic value of such a strategy has not yet been determined.

We developed a decision-analytic computer simulation model to determine the economic value of using such a strategy before all vascular surgical procedures from the societal and third-party payer perspectives at different MRSA prevalence and decolonization success rates.

The model showed preoperative MRSA testing to be cost-effective (incremental cost-effectiveness ratio, <$50,000 per quality-adjusted life year) when the MRSA prevalence is ≥0.01 and the decolonization success rate is ≥0.25. In fact, this strategy was dominant (ie, less costly and more effective) at the following thresholds: MRSA prevalence ≥0.01 and decolonization success rate ≥0.5, and MRSA prevalence ≥0.025 and decolonization success rate ≥0.25.

Testing and decolonizing patients for MRSA before vascular surgery may be a cost-effective strategy over a wide range of MRSA prevalence and decolonization success rates.

To determine the mortality, hospital stay, and total hospital charges and cost of hospitalization attributable to candidemia by comparing patients with candidemia with control-patients who have otherwise similar illnesses. Prior studies lack broad patient and hospital representation or cost-related information that accurately reflects current medical practices.

Our case-control study included case-patients with candidemia and their cost-related data, ascertained from laboratory-based candidemia surveillance conducted among all residents of Connecticut and Baltimore and Baltimore County, Maryland, during 1998 to 2000. Control-patients were matched on age, hospital type, admission year, discharge diagnoses, and duration of hospitalization prior to candidemia onset.

We identified 214 and 529 sets of matched case-patients and control-patients from the two locations, respectively. Mortality attributable to candidemia ranged between 19% and 24%. On multivariable analysis, candidemia was associated with mortality (OR, 5.3 for Connecticut and 8.5 for Baltimore and Baltimore County; P < .05), whereas receiving adequate treatment was protective (OR, 0.5 and 0.4 for the two locations, respectively; P < .05). Candidemia itself did not increase the total hospital charges and cost of hospitalization; when treatment status was accounted for, having received adequate treatment for candidemia significantly increased the total hospital charges and cost of hospitalization ($6,000 to $29,000 and $3,000 to $22,000, respectively) and the length of stay (3 to 13 days).

Our findings underscore the burden of candidemia, particularly regarding the risk of death, length of hospitalization, and cost associated with treatment (Infect Control Hosp Epidemiol 2005;26:540-547).

Fluoroquinolones have not been frequently implicated as a cause of Clostridium difficile outbreaks. Nosocomial C. difficile infections increased from 2.7 to 6.8 cases per 1,000 discharges (P < .001). During the first 2 years of the outbreak, there were 253 nosocomial C. difficile infections; of these, 26 resulted in colectomy and 18 resulted in death. We conducted an investigation of a large C. difficile outbreak in our hospital to identify risk factors and characterize the outbreak.

A retrospective case-control study of case-patients with C. difficile infection from January 2000 through April 2001 and control-patients matched by date of hospital admission, type of medical service, and length of stay; an analysis of inpatient antibiotic use; and antibiotic susceptibility testing and molecular subtyping of isolates were performed.

On logistic regression analysis, clindamycin (odds ratio [OR], 4.8; 95% confidence interval [CI95], 1.9-12.0), ceftriaxone (OR, 5.4; CI95, 1.8-15.8), and levofloxacin (OR, 2.0; CI95, 1.2-3.3) were independently associated with infection. The etiologic fractions for these three agents were 10.0%, 6.7%, and 30.8%, respectively. Fluoroquinolone use increased before the onset of the outbreak (P < .001); 59% of case-patients and 41% of control-patients had received this antibiotic class. The outbreak was polyclonal, although 52% of isolates belonged to two highly related molecular subtypes.

Exposure to levofloxacin was an independent risk factor for C. difficile-associated diarrhea and appeared to contribute substantially to the outbreak. Restricted use of levofloxacin and the other implicated antibiotics may be required to control the outbreak.

Poorly defined cohorts and weak study designs have hampered cross-cultural comparisons of course and outcome in schizophrenia.

To describe long-term outcome in 18 diverse treated incidence and prevalence cohorts. To compare mortality, 15- and 25-year illness trajectory and the predictive strength of selected baseline and short-term course variables.

Historic prospective study. Standardised assessments of course and outcome.

About 75% traced. About 50% of surviving cases had favourable outcomes, but there was marked heterogeneity across geographic centres. In regression models, early (2-year) course patterns were the strongest predictor of 15-year outcome, but recovery varied by location; 16% of early unremitting cases achieved late-phase recovery.

A significant proportion of treated incident cases of schizophrenia achieve favourable long-term outcome. Sociocultural conditions appear to modify long-term course. Early intervention programmes focused on social as well as pharmacological treatments may realise longer-term gains.