To describe the use of next-generation sequencing (NGS) and to determine whether NGS leads to changes in antimicrobial management.

This retrospective cohort study included patients aged ≥18 years admitted to a single tertiary-care center in Houston, Texas, with an NGS test performed between January 1, 2017, and December 31, 2018.

In total, 167 NGS tests were performed. Most patients were of non-Hispanic ethnicity (n = 129), white (n = 106), and male (n = 116), with a mean age of 52 years (SD, 16). Moreover, 61 patients were immunocompromised: solid-organ transplant (n = 30), patients with human immunodeficiency virus (n = 14), and rheumatology patients on immunosuppressive therapy (n = 12).

Of the 167 NGS tests performed, 118 (71%) were positive. Test results associated with a change in antimicrobial management were found in 120 (72%) of 167 cases, with an average of 0.32 (SD, 1.57) fewer antimicrobials after the test. The largest change in antimicrobial management was in glycopeptide use (36 discontinuations) followed by antimycobacterial drug use (27 additions among 8 patients). Also, 49 patients had negative NGS results, but only 36 patients had their antibiotics discontinued.

Plasma NGS testing is associated with a change in antimicrobial management in most cases. We observed a decrease in glycopeptide use after NGS results, which highlights physicians’ comfort in withdrawing methicillin-resistant Staphylococcus aureus (MRSA) coverage. In addition, antimycobacterial coverage increased, corresponding with early mycobacterial detection by NGS. Further studies are needed to determine effective ways to use NGS testing as an antimicrobial stewardship tool.

Molecular epidemiological description of an OXA-48 CPE outbreak affecting a tertiary-care hospital ward in Ireland over an extended period (2018–2019).

Microbiological testing and whole-genome sequencing (WGS) were performed on all 56 positive OXA-48 outbreak case isolates.

In total, 7 different species were identified: Enterobacter hormaechei (n = 35, 62.5%), Escherichia coli (n = 12, 21.4%), Klebsiella pneumoniae (n = 5, 8.9%), Klebsiella oxytoca (n = 1, 1.8%), Klebsiella michiganensis (n = 1, 1.8%), Citrobacter freundii (n = 1, 1.8%), and Serratia marcesens (n = 1, 1.8%). E. hormaechei ST78 was the most common genotype (n = 14, 25%). Two major pOXA-48 plasmid types were identified throughout the outbreak, ‘types’ 1 and 2, and 5 major E. hormaechei clonal groupings were identified: ST78, ST108, ST1126, ST135, and ST66. Within each of the ST108, ST1126, ST135 and ST66 groups, the pOXA-48 harbored within each isolate were the same. Within ST78, 9 isolates contained the pOXA48 ‘type 2’ plasmid and 5 contained the ‘type 1’ plasmid. Environmental specimens were taken from different outbreak ward locations: handwash basins, sink and shower drains, and taps. Of 394 environmental specimens, OXA-48 CPE was isolated from 26 (6.6%).

This prolonged outbreak of OXA-48 CPE was confined to one ward, but it exemplifies the complexity and difficulty in the control of these organisms. With multiple species and genotypes involved, they may be better described as ‘plasmid outbreaks.’ WGS provided insights into this diversity and potential transmission among cases, though its usefulness would be enhanced by analysis as close as possible to real time so that interventions can be implemented as soon as data are available.

To evaluate the effects early de-escalation of antipseudomonal β-lactam (APBL) on 90-day CDI risk in Enterobacterales bloodstream infections (BSIs).

Retrospective cohort analysis.

An academic medical center in South Carolina.

We included patients aged >18 years with monomicrobial BSIs with Enterobacterales who received APBL between July 1, 2015, and June 30, 2020.

Rates of CDI were compared between patients who received an APBL for >72 hours and <72 hours, followed by comparison between formulary APBLs utilized.

In total, 447 patients were included; 292 and 155 patients received APBL for < 72 hours and > 72 hours, respectively. The incidences of CDI for <72 hours compared to >72 hours were 2.4% and 6.5%, respectively (unadjusted hazard ratio [HR], 2.70; 95% confidence interval [CI], 1.03–7.10; P = .04). This difference was not statistically significant in the adjusted model (HR, 2.66; 95% CI, 0.97–7.31; P = .06). Meropenem was associated with an increased risk of CDI when compared with all other formulary APBLs: 4 (26.7%) of 15 versus 13 (3.0%) of 432 (P < .001).

Utilization of an APBL for >72 hours was associated with a statistically significant increase in the incidence of CDI in an unadjusted model and with a numerically higher CDI incidence in the adjusted model. Meropenem was the formulary APBL that carried the highest risk of CDI. The results of this study provide further evidence supporting active antimicrobial stewardship to reduce unnecessary broad-spectrum antibiotics in the effort to alleviate the burden that CDI imposes on the healthcare system.

Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms.

To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital.

Cost-effectiveness study.

Intensive care unit and burn unit of large metropolitan hospital.

Simulated intensive care unit and burn unit patients.

We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty.

On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively.

The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.

Surgical site infections (SSIs) greatly burden healthcare systems around the world, particularly in low- and middle-income countries. We sought to employ the Systems Engineering Initiative for Patient Safety (SEIPS) model to better characterize SSI prevention practices and factors affecting adherence to prevention guidelines at Jimma University Medical Center (JUMC).

Our cross-sectional study consisted of semistructured interviews designed to elicit perceptions of and barriers and facilitators to SSI prevention among surgical staff and observations of current preoperative, perioperative, and postoperative SSI prevention practices in surgical cases. Interviews were recorded, manually transcribed, and thematically coded within the SEIPS framework. Trained observers recorded compliance with the World Health Organization’s SSI prevention recommendations.

A tertiary-care hospital in Jimma, Ethiopia.

Surgical nurses, surgeons, and anesthetists at JUMC.

Within 16 individual and group interviews, participants cited multiple barriers to SSI prevention including shortages of water and antiseptic materials, lack of clear SSI guidelines and training, minimal Infection Prevention Control (IPC) interaction with surgical staff, and poor SSI tracking. Observations from nineteen surgical cases revealed high compliance with antibiotic prophylaxis (94.7%), hand scrubbing (100%), sterile gloves and instrument use (100%), incision site sterilization (100%), and use of surgical safety checklist (94.7%) but lower compliance with preoperative bathing (26.3%), MRSA screening (0%), and pre- and postoperative glucose (0%, 10.5%) and temperature (57.9%, 47.3%) monitoring.

Utilizing the SEIPS model helped identify institution-specific barriers and facilitators that can inform targeted interventions to increase compliance with currently underperformed SSI prevention practices at JUMC.

To identify preventable factors that contribute to the cross transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) to patients in healthcare facilities.

A case–control study was conducted among inpatients on a coronavirus disease 2019 (COVID-19) outbreak unit.

This study was conducted in a medical-surgical unit of a tertiary-care hospital in Nova Scotia in May 2021.

Patients hospitalized on the unit for at least 12 hours and healthcare workers (HCW) working on the unit within 2 weeks of outbreak declaration were included.

Risk factors for SARS-CoV-2 infection were analyzed using simple and multiple logistic regression. Whole-genome sequencing (WGS) was performed to identify SARS-CoV-2 strain relatedness. Network analysis was used to describe patient accommodation.

SARS-CoV-2 infections were identified in 21 patients (29.6%) and 11 HCWs (6.6%). WGS data revealed 4 distinct clades of related sequences. Several factors likely contributed to the outbreak, including failure to identify SARS-CoV-2, a largely incomplete or unvaccinated population, and patient wandering behaviors. The most significant risk factor for SARS-CoV-2 infection was room sharing with an infectious patient, which was the only factor that remained statistically significant following multivariate analysis (odds ratio [OR], 9.2l; 95% confidence interval [CI], 2.04–41.67; P = .004).

This outbreak likely resulted from admission of 2 patients with COVID-19, with subsequent transmissions to 17 patients and 11 staff. WGS and bioinformatics analyses were critical to identifying previously unrecognized nosocomial transmissions of SARS-CoV-2. This study supports strategies to reduce nosocomial transmissions of SARS-CoV-2, such as single-patient rooms, promotion of COVID-19 vaccination, and infection prevention and control measures including management of wandering behaviors.

With the coronavirus disease 2019 (COVID-19) pandemic, rates of in-hospital antimicrobial use increased due to perceived bacterial and fungal coinfections along with COVID-19. We describe the incidence of these coinfections and antimicrobial use in patients hospitalized with COVID-19 to help guide effective antimicrobial use in this population.

This study was conducted in 3 tertiary-care referral university teaching hospitals in New York City.

This multicenter retrospective observational cohort study involved all patients admitted with COVID-19 from January 1, 2020, to February 1, 2021. Variables of interest were extracted from a de-identified data set of all COVID-19 infections across the health system. Population statistics are presented as median with interquartile range (IQR) or proportions with 95% confidence intervals (CIs) as indicated.

Among 7,209 of patients admitted with COVID-19, 663 (9.2%) had a positive culture from the respiratory tract or blood sometime during their initial hospital admission. Positive respiratory cultures occurred found in 449 (6.2%) patients, and 20% were collected within 48 hours of admission. Blood culture positivity occurred in 334 patients (4.6%), with 33.5% identified within 48 hours of admission. A higher proportion of patients received antimicrobials in the first wave than in the later pandemic period (82.4% vs 52.0%). Antimicrobials were prescribed to 70.1% of inpatients, with a median of 6 antimicrobial days per patient. Infection-free survival decreased over the course of hospitalization.

We detected a very low incidence of coinfection with COVID-19 at admission. A longer duration of hospitalization was associated with an increased risk of coinfection. Antimicrobial use far exceeded the true incidence and detection of coinfections in these patients.

To describe the evolution of respiratory antibiotic prescribing during the coronavirus disease 2019 (COVID-19) pandemic across 3 large hospitals that maintained antimicrobial stewardship services throughout the pandemic.

Retrospective interrupted time-series analysis.

A multicenter study was conducted including medical and intensive care units (ICUs) from 3 hospitals within a Canadian epicenter for COVID-19.

Interrupted time-series analysis was used to analyze rates of respiratory antibiotic utilization measured in days of therapy per 1,000 patient days (DOT/1,000 PD) in medical units and ICUs. Each of the first 3 waves of the pandemic were compared to the baseline.

Within the medical units, use of respiratory antibiotics increased during the first wave of the pandemic (rate ratio [RR], 1.76; 95% CI, 1.38–2.25) but returned to the baseline in waves 2 and 3 despite more COVID-19 admissions. In ICU, the use of respiratory antibiotics increased in wave 1 (RR, 1.30; 95% CI, 1.16–1.46) and wave 2 of the pandemic (RR, 1.21; 95% CI, 1.11–1.33) and returned to the baseline in the third wave, which had the most COVID-19 admissions.

After an initial surge in respiratory antibiotic prescribing, we observed the normalization of prescribing trends at 3 large hospitals throughout the COVID-19 pandemic. This trend may have been due to the timely generation of new research and guidelines developed with frontline clinicians, allowing for the active application of new research to clinical practice.

Most hand hygiene (HH) intervention studies use a quasi-experimental design, are primarily uncontrolled before-and-after studies, or are controlled before-and-after studies with a nonequivalent control group. Well-funded studies with improved designs and HH interventions are needed.

To evaluate healthcare worker (HCW) HH compliance with alcohol-based hand rub (ABHR) through direct observation (human observer), 2 electronic technologies, a radio frequency identification (RFID) badge system, and an invasive device sensor.

In our controlled experimental study, 2,269 observations were made over a 6-month period from July 1 to December 30, 2020, in a 4-bed intensive care unit. We compared HH compliance between a basic feedback loop system with RFID badges and an enhanced feedback loop system that utilized sensors on invasive devices.

Real-time feedback by wireless technology connected to a patient’s invasive device (enhanced feedback loop) resulted in a significant increase in HH compliance (69.5% in the enhanced group vs 59.1% in the basic group; P = .0001).

An enhanced feedback loop system connected to invasive devices, providing real-time alerts to HCWs, is effective in improving HH compliance.

Patients on dialysis are at high risk for severe COVID-19 and associated morbidity and mortality. We examined the humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in a maintenance dialysis population.

Single-center cohort study.

Adult maintenance dialysis patients at 3 outpatient dialysis units of a large academic center.

Participants were vaccinated with 2 doses of BNT162b2, 3 weeks apart. We assessed anti–SARS-CoV-2 spike antibodies (anti-S) ∼4–7 weeks after the second dose and evaluated risk factors associated with insufficient response. Definitions of antibody response are as follows: nonresponse (anti-S level, <50 AU/mL), low response (anti-S level, 50–839 AU/mL), and sufficient response (anti-S level, ≥840 AU/mL).

Among the 173 participants who received 2 vaccine doses, the median age was 60 years (range, 28–88), 53.2% were men, 85% were of Black race, 86% were on in-center hemodialysis and 14% were on peritoneal dialysis. Also, 7 participants (4%) had no response, 27 (15.6%) had a low response, and 139 (80.3%) had a sufficient antibody response. In multivariable analysis, factors significantly associated with insufficient antibody response included end-stage renal disease comorbidity index score ≥5 and absence of prior hepatitis B vaccination response.

Although most of our study participants seroconverted after 2 doses of BNT162b2, 20% of our cohort did not achieve sufficient humoral response. Our findings demonstrate the urgent need for a more effective vaccine strategy in this high-risk patient population and highlight the importance of ongoing preventative measures until protective immunity is achieved.

Ventilator-associated pneumonia (VAP) can be overdiagnosed on the basis of positive respiratory cultures in the absence of clinical findings of pneumonia. We determined the perceived diagnostic importance of 6 clinical attributes in ordering a respiratory culture to identify opportunities for diagnostic stewardship.

A discrete choice experiment presented participants with a vignette consisting of the same “stem” plus variations in 6 clinical attributes associated with VAP: chest imaging, oxygenation, sputum, temperature, white blood cell count, and blood pressure. Each attribute had 3–4 levels, resulting in 32 total scenarios. Participants indicated whether they would order a respiratory culture, and if yes, whether they preferred the bronchoalveolar lavage or endotracheal aspirate sample-collection method. We calculated diagnostic utility of attribute levels and relative importance of each attribute.

The survey was administered electronically to critical-care clinicians via a Qualtrics survey at a tertiary-care academic center in the United States.

In total, 59 respondents completed the survey. New radiograph opacity (utility, 1.15; 95% confidence interval [CI], 0.99–1.3), hypotension (utility, 0.88; 95% CI, 0.74–1.03), fever (utility, 0.76; 95% CI, 0.62–0.91) and copious sputum (utility, 0.75; 95% CI, 0.60–0.90) had the greatest perceived diagnostic value that favored ordering a respiratory culture. Radiograph changes (23%) and temperature (20%) had the highest relative importance. New opacity (utility, 0.35; 95% CI, 0.17–0.52) and persistent opacity on radiograph (utility, 0.32; 95% CI, 0.05–0.59) had the greatest value favoring bronchoalveolar lavage over endotracheal aspirate.

Perceived high diagnostic value of fever and hypotension suggest that sepsis vigilance may drive respiratory culturing and play a role in VAP overdiagnosis.