Identifying Candida auris transmission in a hospital outbreak investigation using whole-genome sequencing and SNP phylogenetic analysis.

Candida auris poses a global public health challenge, causing multiple outbreaks within healthcare facilities. Despite advancements in strain typing for various infectious diseases, a consensus on the genetic relatedness threshold for identifying C. auris transmission in local hospital outbreaks remains elusive. We investigated genetic variations within our local isolate collection using whole-genome-based single nucleotide polymorphism (SNP) phylogenetic analysis. A total of 74 C. auris isolates were subjected to whole-genome sequencing (WGS) and SNP phylogenetic analysis via the QIAGEN CLC Genomics Workbench. Isolates included known related strains from the same patient, strains from different hospitals, strains from our hospital patients with no epidemiological link, and 19 patient isolates from a recent C. auris outbreak. All but three isolates were identified to be Clade IV. By examining the genetic diversities of C. auris within patients and between patients, we identified a SNP variation range of 0-13 for identifying related isolates. During an outbreak investigation, utilizing this range, maximum likelihood phylogenetic analysis revealed two distinct clusters that aligned with the epidemiological links. Determining a SNP variation range to delineate genetic relatedness among isolates is crucial for the application of WGS and SNP phylogenetic analysis in identifying C. auris transmission during hospital outbreak investigations. The use of WGS SNP phylogenetic analysis via the CLC Genomics Workbench has emerged as a valuable method for typing C. auris in clinical microbiology laboratories.

Machine Learning To Stratify Methicillin-Resistant Staphylococcus aureus Risk among Hospitalized Patients with Community-Acquired Pneumonia.

Methicillin-resistant Staphylococcus aureus (MRSA) is an uncommon but serious cause of community-acquired pneumonia (CAP). A lack of validated MRSA CAP risk factors can result in overuse of empirical broad-spectrum antibiotics. We sought to develop robust models predicting the risk of MRSA CAP using machine learning using a population-based sample of hospitalized patients with CAP admitted to either a tertiary academic center or a community teaching hospital. Data were evaluated using a machine learning approach. Cases were CAP patients with MRSA isolated from blood or respiratory cultures within 72 h of admission; controls did not have MRSA CAP. The Classification Tree Analysis algorithm was used for model development. Model predictions were evaluated in sensitivity analyses. A total of 21 of 1,823 patients (1.2%) developed MRSA within 72 h of admission. MRSA risk was higher among patients admitted to the intensive care unit (ICU) in the first 24 h who required mechanical ventilation than among ICU patients who did not require ventilatory support (odds ratio [OR], 8.3; 95% confidence interval [CI], 2.4 to 32). MRSA risk was lower among patients admitted to ward units than among those admitted to the ICU (OR, 0.21; 95% CI, 0.07 to 0.56) and lower among ICU patients without a history of antibiotic use in the last 90 days than among ICU patients with antibiotic use in the last 90 days (OR, 0.03; 95% CI, 0.002 to 0.59). The final machine learning model was highly accurate (receiver operating characteristic [ROC] area = 0.775) in training and jackknife validity analyses. We identified a relatively simple machine learning model that predicted MRSA risk in hospitalized patients with CAP within 72 h postadmission.

Vancomycin-resistant Enterococcus outbreak in a pre- and post-cardiothoracic transplant population: Impact of discontinuing multidrug-resistant organism surveillance during the coronavirus disease 2019 pandemic.

INTRODUCTION: Many institutions suspended surveillance and contact precautions for multidrug-resistant organisms (MDROs) at the outset of the coronavirus disease 2019 (COVID-19) pandemic due to a lack of resources. Once our institution reinstated surveillance in September 2020, a vancomycin-resistant Enterococcus (VRE) faecium outbreak was detected in the cardiothoracic transplant units, a population in which we had not previously detected outbreaks. METHODS: An outbreak investigation was conducted using pulsed-field gel electrophoresis for strain typing and electronic medical record review to determine the clinical characteristics of involved patients. The infection prevention (IP) team convened a multidisciplinary process improvement team comprised of IP, cardiothoracic transplant nursing and medical leadership, environmental services, and the microbiology laboratory. RESULTS: Between December 2020 and March 2021, the outbreak involved thirteen patients in the cardiothoracic transplant units, four index cases, and nine transmissions. Of the 13, seven (54%) were on the transplant service, including heart and lung transplant recipients, patients with ventricular assist devices, and a patient on extracorporeal membrane oxygenation as a bridge to lung transplantation. Four of 13 (31%) developed a clinical infection. DISCUSSION: Cardiothoracic surgery/transplant patients may have a similar risk for VRE-associated morbidity as abdominal solid organ transplant and stem cell transplant patients, highlighting the need for aggressive outbreak management when VRE transmission is detected. Our experience demonstrates an unintended consequence of discontinuing MDRO surveillance in this population and highlights a need for education, monitoring, and reinforcement of foundational infection prevention measures to ensure optimal outcomes.

Characterizing Risk Factors for Clostridioides difficile Infection among Hospitalized Patients with Community-Acquired Pneumonia.

Hospitalized patients with community-acquired pneumonia (CAP) are at risk of developing Clostridioides difficile infection (CDI). We developed and tested clinical decision rules for identifying CDI risk in this patient population. The study was a single-center retrospective, case-control analysis of hospitalized adult patients empirically treated for CAP between 1 January 2014 and 3 March 2018. Differences between cases (CDI diagnosed within 180 days following admission) and controls (no test result indicating CDI during the study period) with respect to prehospitalization variables were modeled to generate propensity scores. Postadmission variables were used to predict case status on each postadmission day where (i) ≥1 additional case was identified and (ii) each model stratum contained ≥15 subjects. Models were developed and tested using optimal discriminant analysis and classification tree analysis. Forty-four cases and 181 controls were included. The median time to diagnosis was 50 days postadmission. After weighting, three models were identified (20, 117, and 165 days postadmission). The day 20 model yielded the greatest (weighted [w]) accuracy (weighted area under the receiver operating characteristic curve [wROC area] = 0.826) and the highest chance-corrected accuracy (weighted effect strength for sensitivity [wESS] = 65.3). Having a positive culture (odds, 1:4; P = 0.001), receipt of ceftriaxone plus azithromycin for a defined infection (odds, 3:5; P = 0.006), and continuation of empirical broad-spectrum antibiotics with activity against P. aeruginosa when no pathogen was identified (odds, 1:8; P = 0.013) were associated with CDI on day 20. Three models were identified that accurately predicted CDI in hospitalized patients treated for CAP. Antibiotic use increased the risk of CDI in all models, underscoring the importance of antibiotic stewardship.

Genetic Evaluation of Nosocomial Candida auris Transmission.

Whole-genome sequences of Candida auris isolates from nosocomial and nonnosocomial infections were compared. The average numbers of single nucleotide variations were different between the two groups. The small amount of genetic variability between intra- or interhost isolates suggests recovery of all colonizing or infecting genomes for comparison is required for outbreaks.

Understanding the Components, Calculation, and Impact of Monthly and Seasonal Variation of the Standardized Antimicrobial Utilization Ratio (SAAR).

This study sought to characterize the impact of 3 types of variation on the Standardized Antimicrobial Administration Ratio (SAAR) utilizing local National Healthcare Safety Network (NHSN) data. SAAR and antimicrobial days per 1,000 days present (AD/1000DP) were compiled monthly for Northwestern Memorial Hospital from 2014 to 2016. Antimicrobial consumption was aggregated into agent categories (via NHSN criteria). Month-to-month changes in SAAR and AD/1000DP were evaluated. Azithromycin and oseltamivir AD/1000DP from 2012 through 2017 were explored for seasonal variation. A sensitivity analysis was performed to explore the effect of seasonality and altered consumption at other hypothetical hospitals on the SAAR. Across agent categories for both the intensive care unit (n = 4) and general wards (n = 4), the average matched-month percent change in AD/1000DP was correlated with the corresponding change in SAAR (coefficient of determination of 0.99). The monthly mean ± standard deviation (SD) AD/1000DP was 235 (range, 47.2 to 661.5), and the mean ± SD SAAR was 1.09 ± 0.26 (range, 0.79 to 1.09) across the NHSN agent categories. Five seasons exhibited seasonal variation in AD/1000DP for azithromycin with a mean percent change of 26.76% (range, 22.27 to 30.69). Eight seasons exhibited seasonal variation in AD/1000DP for oseltamivir with a mean percent change of 129.1% (range, 32.01 to 352.74). The sensitivity analyses confirm that antimicrobial usage at comparator hospitals does not impact the local SAAR, and seasonal variation of antibiotics has the potential to impact SAAR. Month-to-month changes in the SAAR mirror monthly changes in an institution's AD/1000DP. Seasonal variation is an important variable for future SAAR consideration, and the variable antibiotic use at peer hospitals is not currently captured by the SAAR methodology.

Evaluation of the impact of the Accelerate Pheno™ system on time to result for differing antimicrobial stewardship intervention models in patients with gram-negative bloodstream infections.

BACKGROUND: Initiating early effective antimicrobial therapy is the most important intervention demonstrated to decrease mortality in patients with gram-negative bacteremia with sepsis. Rapid MIC-based susceptibility results make it possible to optimize antimicrobial use through both escalation and de-escalation. METHOD: We prospectively evaluated the performance of the Accelerate Pheno™ system (AXDX) for identification and susceptibility testing of gram-negative species and compared the time to result between AXDX and routine standard of care (SOC) using 82 patient samples and 18 challenge organisms with various confirmed resistance mechanisms. The potential impact of AXDX on time to antimicrobial optimization was investigated with various simulated antimicrobial stewardship (ASTEW) intervention models. RESULTS: The overall positive and negative percent agreement of AXDX for identification were 100 and 99.9%, respectively. Compared to VITEK® 2, the overall essential agreement was 96.1% and categorical agreement was 95.4%. No very major or major errors were detected. AXDX reduced the time to identification by an average of 11.8 h and time to susceptibility by an average of 36.7 h. In 27 patients evaluated for potential clinical impact of AXDX on antimicrobial optimization, 18 (67%) patients could potentially have had therapy optimized sooner with an average of 18.1 h reduction in time to optimal therapy. CONCLUSION: Utilization of AXDX coupled with simulated ASTEW intervention notification substantially shortened the time to potential antimicrobial optimization in this cohort of patients with gram-negative bacteremia. This improvement in time occurred when ASTEW support was limited to an 8-h coverage model.

Measuring the impact of varying denominator definitions on standardized antibiotic consumption rates: implications for antimicrobial stewardship programmes.

Objectives: To quantify the impact of varying the at-risk days definition on the overall report of at-risk days and on the calculated standardized consumption rates (SCRs) for piperacillin/tazobactam, amikacin, daptomycin and vancomycin. Methods: Data were evaluated for two system hospitals, an 894 bed academic centre and a 114 bed community hospital. Aggregate inpatient antibiotic administration and occupancy data were extracted from electronic databases at the facility-wide level. Occupancy data were reported from admission-discharge-transfer systems. At-risk days were defined as hospital days present (DP), patient days (PD), persons present (PP) and billing days (BD). Inpatient antimicrobial days of therapy (DOT) across four major antimicrobial agents were used to calculate facility-wide SCRs using each denominator and were evaluated by least-squares regression and R2 values. Results: Within the 894 bed academic hospital, the average monthly facility-wide days were 28 424, 22 198, 15 957 and 14 789 by the DP, PP, PD and BD definitions, respectively. Within the 114 bed community hospital, the average monthly facility-wide days were 5175, 3523 and 2816 by the DP, PP and PD definitions, respectively. Strong concordance was observed between facility-wide SCRs using the DP and PP definitions in both the academic (R2 = 0.99, y = 0.78x - 0.001) and community (R2 = 0.99, y = 0.68x - 0.03) centres across all four inpatient antibiotics evaluated. In an analysis of piperacillin/tazobactam SCRs, rates were over-predicted by 28%-93% at the facility-wide level across centres using alternative denominators. Conclusions: We found that data source and definitions of at-risk denominator days meaningfully impact antibiotic SCRs. Centres should carefully consider these potential sources of variation when setting consumption benchmarks and internally evaluating use.

Investigation of Respiratory Syncytial Virus Outbreak on an Adult Stem Cell Transplant Unit by Use of Whole-Genome Sequencing.

A viral whole-genome sequencing (WGS) strategy, based on PCR amplification followed by next-generation sequencing, was used to investigate a nosocomial respiratory syncytial virus-B (RSV-B) outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and health care workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes that were acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs who had an identical RSV-B strain which was clearly distinct from strains recovered from individuals unrelated to the outbreak. Sequence variation of the glycoprotein (G) gene alone was insufficient to distinguish the outbreak strains from the outbreak-unrelated strains, thereby demonstrating that WGS is valuable for local outbreak investigation.

Evaluation of targeted antimicrobial prophylaxis for transrectal ultrasound guided prostate biopsy: a prospective cohort trial.

BACKGROUND: We evaluated the effectiveness of targeted antimicrobial prophylaxis in transrectal ultrasound guided prostate biopsy (TRUSP). METHODS: A prospective, non-randomized cohort study was conducted. Rectal swab cultures plated on non-selective blood agar and on selective MacConkey agar supplemented with ciprofloxacin identified ciprofloxacin-susceptible and -resistant gram-negative bacteria (CS-GNB and CR-GNB). Patients with CS-GNB received ciprofloxacin while those with CR-GNB received directed prophylaxis. Infectious complications were defined clinically and microbiologically within 30 days after TRUSP. Data were derived at 7 and 30 days post procedure by questionnaires and electronic medical records. We hypothesized that there would be no difference in the infectious outcomes among the CS and CR groups. RESULTS: From November 1, 2012 to March 31, 2015, 510 men completed the study; 430 (84.3%) had CS-GNB and 80 (15.7%) had CR-GNB. 484 (94.9%) completed the study per protocol, while 26 (5.1%) had an intention-to-treat (ITT) analysis. Of the 484, 475 (98.1%) had no infections, nine (1.9%) had infections, six of which (1.2%) were culture-proven (CP). The nine infections were as follows: five (1.0%) uncomplicated UTIs, one (0.2%) complicated UTI, and three (0.6%) urosepsis. One case of uncomplicated UTI and two cases of urosepsis were not CP, but were diagnosed clinically. ITT outcomes were similar. The infection rates were not statistically different between the CS-and CR-GNB patients (p-value = 0.314; 95% CI 0.8-3.3). The four patients with complicated UTIs or sepsis were hospitalized for a mean of 2.6 days and discharged without sequelae. Of the nine infections, three were antimicrobial prophylaxis failures (two ciprofloxacin and one amikacin); three were likely due to failure of the collection or processing of the rectal swab or increasing bacterial resistance between the time of swab collection and biopsy, and three developed clinical infections with no isolate recovered. CONCLUSIONS: Targeted antimicrobial prophylaxis follows the principles of antimicrobial stewardship and achieved a low rate of infectious complications with limited morbidity and no sequelae. This individualized method of prophylaxis may be widely applied. Further studies are needed to explore reasons for targeted prophylaxis failure and to determine comparative efficacy of non-ciprofloxacin-containing targeted prophylaxis regimens. TRIAL REGISTRATION: ClinicalTrials.gov. NCT01659866 . Registered 9 July 2012. First patient enrolled 1 November 2012.

Comparison of Clinical Features, Virulence, and Relapse among Mycobacterium avium Complex Species.

RATIONALE: Traditionally, Mycobacterium avium complex (MAC) has been composed of M. avium and M. intracellulare; however, advances in genetic sequencing have allowed discovery of several novel species. With these discoveries, investigation of differences in risk factors, virulence, and clinical outcomes have emerged. OBJECTIVES: We conducted a retrospective cohort study evaluating all MAC isolates obtained from pulmonary specimens at our institution from 2000 to 2012 and investigated the clinical courses associated with distinct MAC species. METHODS: To classify isolates into distinct species, a multilocus sequence analysis using rpoB and internal transcribed spacer (ITS) as targets was performed. We reviewed patient medical records to analyze clinical characteristics and outcomes for the cohort. MEASUREMENTS AND MAIN RESULTS: Of the isolates from the 448 included patients, 54% were M. avium, 18% were M. intracellulare, and 28% were M. chimaera. Using American Thoracic Society/Infectious Diseases Society of America criteria, patients whose isolates were identified as M. avium (adjusted odds ratio [AOR], 2.14; 95% confidence interval [CI], 1.33-3.44) or M. intracellulare (AOR, 3.12; 95% CI, 1.62-5.99) were more likely to meet criteria for infection than patients with M. chimaera. Patients infected with M. chimaera were more likely to be prescribed an immunosuppressant compared with all other patients (AOR, 2.75; 95% CI, 1.17-6.40). Patients treated for infections with M. avium (AOR, 5.64; 95% CI, 1.51-21.10) and M. chimaera (AOR, 4.47; 95% CI, 1.08-18.53) were more likely to have a clinical relapse/reinfection than those with M. intracellulare. CONCLUSIONS: Our findings suggest that specific MAC species have varying degrees of virulence and classifying MAC isolates into distinct species aids in identifying which patients are at higher risk of clinical relapse/reinfection.

Optimal timing of oral fosfomycin administration for pre-prostate biopsy prophylaxis.

OBJECTIVES: As the optimal administration time for fosfomycin peri-procedural prophylaxis is unclear, we sought to determine optimal administration times for fosfomycin peri-procedural prophylaxis. METHODS: Plasma, peripheral zone and transition zone fosfomycin concentrations were obtained from 26 subjects undergoing transurethral resection of the prostate (TURP), following a single oral dose of 3 g of fosfomycin. Population pharmacokinetic modelling was completed with the Nonparametric Adaptive Grid (NPAG) algorithm (Pmetrics package for R), with a four-compartment model. Plasma and tissue concentrations were simulated during the first 24 h post-dose, comparing these with EUCAST susceptibility breakpoints for Escherichia coli, a common uropathogen. RESULTS: Non-compartmental-determined pharmacokinetic values in our population were similar to those reported in the package insert. Predicted plasma concentrations rapidly increased after the first hour, giving more than 90% population coverage for organisms with an MIC ≤4 mg/L over the first 12 h post-dose. Organisms with higher MICs fared much worse, with organisms at the EUCAST breakpoint being covered for <10% of the population at any time. Transitional zone prostate concentrations exceeded 4 mg/L for 90% of the population between hours 1 and 9. Peripheral zone prostate concentrations were much lower and only exceeded 4 mg/L for 70% of the population between hours 1 and 4. CONCLUSIONS: Until more precise plasma and tissue data are available, we recommend that fosfomycin prophylaxis be given 1-4 h prior to prostate biopsy. We do not recommend fosfomycin prophylaxis for subjects with known organisms with MICs >4 mg/L.

Pathogenicity of clinical Acinetobacter baumannii isolates in a Galleria mellonella host model according to bla(OXA-40) gene and epidemiological outbreak status.

Clinical studies have suggested that blaOXA-40-positive Acinetobacter baumannii isolates are associated with poor patient outcomes; however, reasons for unfavorable outcomes are difficult to discern in clinical studies. The objective of this study was to assess the virulence of carbapenem-resistant A. baumannii according to blaOXA-40 and epidemiological outbreak status in a Galleria mellonella model. Eight isolates of A. baumannii were studied. Nonoutbreak isolates and blaOXA-40-negative isolates more rapidly killed infected G. mellonella (P < 0.01).

Epidemiology of infections in cancer patients.

Although major advances in the care of cancer patients over the past several decades have resulted in improved survival, infectious complications remain a significant cause of morbidity and mortality. To successfully identify, treat, and prevent infections, a comprehensive understanding of risk factors that predispose to infection and of commonly encountered pathogens is necessary. In addition, clinicians must keep abreast of the changing epidemiology of infections in this population. As therapeutic modalities continue to evolve, as established pathogens become increasingly drug resistant, and as new pathogens are discovered, successful management of infections will continue to present challenges in the years to come.

Characterization of ciprofloxacin resistant Escherichia coli isolates among men undergoing evaluation for transrectal ultrasound guided prostate biopsy.

PURPOSE: We determine the prevalence of ciprofloxacin resistant gram-negative bacilli in patients scheduled for transrectal ultrasound guided prostate biopsy, characterize the Escherichia coli strains recovered from this patient population, and characterize the mechanisms responsible for ß-lactam and ciprofloxacin resistance. MATERIALS AND METHODS: Rectal swabs from 991 patients were cultured for ciprofloxacin resistant gram-negative bacilli with a selective medium. Recovered E. coli isolates were further analyzed with susceptibility testing, pulsed field gel electrophoresis, plasmid isolation and sequencing. RESULTS: A total of 193 ciprofloxacin resistant gram-negative bacilli were recovered and of these isolates 167 (87%) were E. coli. The prevalence of ciprofloxacin resistant E. coli in the study population was 17%. Only 38 (26%) of the 149 E. coli isolates that received susceptibility testing were susceptible to ampicillin and ampicillin-sulbactam. In select isolates transferrable plasmids carrying ß-lactamase were responsible for the resistance to the ß-lactam agents and other nonß-lactam antimicrobials. Diverse combinations of gyrA and parC mutations associated with fluoroquinolone resistance were identified. Strain typing and plasmid typing indicated that the E. coli isolates did not share a common origin. CONCLUSIONS: Of the patients in our study 17% carried ciprofloxacin resistant E. coli. Analysis of resistance mechanisms and plasmid analysis along with strain typing demonstrated that this patient population harbored organisms with heterogeneous phenotypic susceptibility, indicating that universal prophylaxis would not provide optimal coverage for patients undergoing transrectal ultrasound guided prostate biopsy.

The impact of anti-infective drug shortages on hospitals in the United States: trends and causes.

Anti-infective shortages pose significant logistical and clinical challenges to hospitals and may be considered a public health emergency. Anti-infectives often represent irreplaceable life-saving treatments. Furthermore, few new agents are available to treat increasingly prevalent multidrug-resistant pathogens. Frequent anti-infective shortages have substantially altered patient care and may lead to inferior patient outcomes. Because many of the shortages stem from problems with manufacturing and distribution, federal legislation has been introduced but not yet enacted to provide oversight for the adequate supply of critical medications. At the local level, hospitals should develop strategies to anticipate the impact and extent of shortages, to identify therapeutic alternatives, and to mitigate potential adverse outcomes. Here we describe the scope of recent anti-infective shortages in the United States and explore the reasons for inadequate drug supply.

Targeted antimicrobial prophylaxis using rectal swab cultures in men undergoing transrectal ultrasound guided prostate biopsy is associated with reduced incidence of postoperative infectious complications and cost of care.

PURPOSE: We evaluated targeted antimicrobial prophylaxis in men undergoing transrectal ultrasound guided prostate biopsy based on rectal swab culture results. MATERIALS AND METHODS: From July 2010 to March 2011 we studied differences in infectious complications in men who received targeted vs standard empirical ciprofloxacin prophylaxis before transrectal ultrasound guided prostate biopsy. Targeted prophylaxis used rectal swab cultures plated on selective media containing ciprofloxacin to identify fluoroquinolone resistant bacteria. Patients with fluoroquinolone susceptible organisms received ciprofloxacin while those with fluoroquinolone resistant organisms received directed antimicrobial prophylaxis. We identified men with infectious complications within 30 days after transrectal ultrasound guided prostate biopsy using the electronic medical record. RESULTS: A total of 457 men underwent transrectal ultrasound guided prostate biopsy, and of these men 112 (24.5%) had rectal swab obtained while 345 (75.5%) did not. Among those who received targeted prophylaxis 22 (19.6%) men had fluoroquinolone resistant organisms. There were no infectious complications in the 112 men who received targeted antimicrobial prophylaxis, while there were 9 cases (including 1 of sepsis) among the 345 on empirical therapy (p=0.12). Fluoroquinolone resistant organisms caused 7 of these infections. The total cost of managing infectious complications in patients in the empirical group was $13,219. The calculated cost of targeted vs empirical prophylaxis per 100 men undergoing transrectal ultrasound guided prostate biopsy was $1,346 vs $5,598, respectively. Cost-effectiveness analysis revealed that targeted prophylaxis yielded a cost savings of $4,499 per post-transrectal ultrasound guided prostate biopsy infectious complication averted. Per estimation, 38 men would need to undergo rectal swab before transrectal ultrasound guided prostate biopsy to prevent 1 infectious complication. CONCLUSIONS: Targeted antimicrobial prophylaxis was associated with a notable decrease in the incidence of infectious complications after transrectal ultrasound guided prostate biopsy caused by fluoroquinolone resistant organisms as well as a decrease in the overall cost of care.

Decreasing incidence of Acinetobacter baumannii pneumonia and trends in antibiotic consumption: A single-center retrospective observational study.

OBJECTIVE: To describe the epidemiology of Acinetobacter baumannnii (AB) pneumonia at our center, including the antibiotic exposure patterns of individual AB pneumonia cases and to investigate whether hospital-wide antibiotic consumption trends were associated with trends in AB pneumonia incidence. DESIGN: Single-center retrospective study with case-control and ecological components. SETTING: US private tertiary-care hospital. PARTICIPANTS AND METHODS: All hospitalized patients with AB infection from 2008 to 2019 were identified through laboratory records; for those with AB pneumonia, medical records were queried for detailed characteristics and antibiotic exposures in the 30 days preceding pneumonia diagnosis. Hospital-wide antibiotic consumption data from 2015 through 2019 were obtained through pharmacy records. RESULTS: Incidence of both pneumonia and nonrespiratory AB infections decreased from 2008 to 2019. Among the 175 patients with AB pneumonia, the most frequent antibiotic exposure was vancomycin (101 patients). During the 2015-2019 period when hospital-wide antibiotic consumption data were available, carbapenem consumption increased, and trends negatively correlated with those of AB pneumonia (r = -0.48; P = .031) and AB infection at any site (r = -0.63; P = .003). Conversely, the decline in AB infection at any site correlated positively with concurrent declines in vancomycin (r = 0.55; P = .012) and quinolone consumption (r = 0.51; P = .022). CONCLUSIONS: We observed decreasing incidence of AB infection despite concurrently increasing carbapenem consumption, possibly associated with declining vancomycin and quinolone consumption. Future research should evaluate a potential role for glycopeptide and quinolone exposure in the pathogenesis of AB infection.

Serologic Status and SARS-CoV-2 Infection over 6 Months of Follow Up in Healthcare Workers in Chicago: A Cohort Study.

OBJECTIVE: To determine the changes in severe acute respiratory coronavirus virus 2 (SARS-CoV-2) serologic status and SARS-CoV-2 infection rates in healthcare workers (HCWs) over 6-months of follow-up. DESIGN: Prospective cohort study. SETTING AND PARTICIPANTS: HCWs in the Chicago area. METHODS: Cohort participants were recruited in May and June 2020 for baseline serology testing (Abbott anti-nucleocapsid IgG) and were then invited for follow-up serology testing 6 months later. Participants completed monthly online surveys that assessed demographics, medical history, coronavirus disease 2019 (COVID-19), and exposures to SARS-CoV-2. The electronic medical record was used to identify SARS-CoV-2 polymerase chain reaction (PCR) positivity during follow-up. Serologic conversion and SARS-CoV-2 infection or possible reinfection rates (cases per 10,000 person days) by antibody status at baseline and follow-up were assessed. RESULTS: In total, 6,510 HCWs were followed for a total of 1,285,395 person days (median follow-up, 216 days). For participants who had baseline and follow-up serology checked, 285 (6.1%) of the 4,681 seronegative participants at baseline seroconverted to positive at follow-up; 138 (48%) of the 263 who were seropositive at baseline were seronegative at follow-up. When analyzed by baseline serostatus alone, 519 (8.4%) of 6,194 baseline seronegative participants had a positive PCR after baseline serology testing (4.25 per 10,000 person days). Of 316 participants who were seropositive at baseline, 8 (2.5%) met criteria for possible SARS-CoV-2 reinfection (ie, PCR positive >90 days after baseline serology) during follow-up, a rate of 1.27 per 10,000 days at risk. The adjusted rate ratio for possible reinfection in baseline seropositive compared to infection in baseline seronegative participants was 0.26 (95% confidence interval, 0.13-0.53). CONCLUSIONS: Seropositivity in HCWs is associated with moderate protection from future SARS-CoV-2 infection.

Coronavirus disease 2019 (COVID-19) vaccine intentions and uptake in a tertiary-care healthcare system: A longitudinal study.

OBJECTIVES: Healthcare workers (HCWs) are a high-priority group for coronavirus disease 2019 (COVID-19) vaccination and serve as sources for public information. In this analysis, we assessed vaccine intentions, factors associated with intentions, and change in uptake over time in HCWs. METHODS: A prospective cohort study of COVID-19 seroprevalence was conducted with HCWs in a large healthcare system in the Chicago area. Participants completed surveys from November 25, 2020, to January 9, 2021, and from April 24 to July 12, 2021, on COVID-19 exposures, diagnosis and symptoms, demographics, and vaccination status. RESULTS: Of 4,180 HCWs who responded to a survey, 77.1% indicated that they intended to get the vaccine. In this group, 23.2% had already received at least 1 dose of the vaccine, 17.4% were unsure, and 5.5% reported that they would not get the vaccine. Factors associated with intention or vaccination were being exposed to clinical procedures (vs no procedures: adjusted odds ratio [AOR], 1.39; 95% confidence interval [CI], 1.16-1.65) and having a negative serology test for COVID-19 (vs no test: AOR, 1.46; 95% CI, 1.24-1.73). Nurses (vs physicians: AOR, 0.24; 95% CI, 0.17-0.33), non-Hispanic Black (vs Asians: AOR, 0.35; 95% CI, 0.21-0.59), and women (vs men: AOR, 0.38; 95% CI, 0.30-0.50) had lower odds of intention to get vaccinated. By 6-months follow-up, >90% of those who had previously been unsure were vaccinated, whereas 59.7% of those who previously reported no intention of getting vaccinated, were vaccinated. CONCLUSIONS: COVID-19 vaccination in HCWs was high, but variability in vaccination intention exists. Targeted messaging coupled with vaccine mandates can support uptake.