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Background: Variation in clinicians' diagnostic test utilization is incompletely explained by demographics and likely relates to cognitive characteristics. We explored clinician factors associated with diagnostic test utilization., Methods: We used a self-administered survey of attitudes, cognitive characteristics, and reported likelihood of test ordering in common scenarios; frequency of lipid and liver testing in patients on statin therapy. Participants were 552 primary care physicians, nurse practitioners, and physician assistants from practices in 8 US states across 3 regions, from June 1, 2018 to November 26, 2019. We measured Testing Likelihood Score: the mean of 4 responses to testing frequency and self-reported testing frequency in patients on statins., Results: Respondents were 52.4% residents, 36.6% attendings, and 11.0% nurse practitioners/physician assistants; most were white (53.6%) or Asian (25.5%). Median age was 32 years; 53.1% were female. Participants reported ordering tests for a median of 20% (stress tests) to 90% (mammograms) of patients; Testing Likelihood Scores varied widely (median 54%, interquartile range 43%-69%). Higher scores were associated with geography, training type, low numeracy, high malpractice fear, high medical maximizer score, high stress from uncertainty, high concern about bad outcomes, and low acknowledgment of medical uncertainty. More frequent testing of lipids and liver tests was associated with low numeracy, high medical maximizer score, high malpractice fear, and low acknowledgment of uncertainty., Conclusions: Clinician variation in testing was common, with more aggressive testing consistently associated with low numeracy, being a medical maximizer, and low acknowledgment of uncertainty. Efforts to reduce undue variations in testing should consider clinician cognitive drivers., (Copyright © 2022 Elsevier Inc. All rights reserved.)

The Infectious Diseases Society of America has identified the use of SARS-CoV-2 genomic load for prognostication purposes as a key research question. We designed a retrospective cohort study that included adult patients with COVID-19 pneumonia who had at least 2 positive nasopharyngeal tests at least 24 hours apart to study the correlation between the change in the genomic load of SARS-CoV-2, as reflected by the Cycle threshold (Ct) value of the RT-PCR, with change in clinical status. The Sequential Organ Failure Assessment (SOFA) score was used as a surrogate for patients' clinical status. Among 457 patients with COVID-19 pneumonia between 3/31/2020-4/10/2020, we identified 42 patients who met the inclusion criteria. The median initial SOFA score was 2 (IQR 2-3). 20 out of 42 patients had a lower SOFA score on their subsequent tests. We identified a statistically significant inverse correlation between the change in SOFA score and change in the Ct value with a decrease in SOFA score by 0.05 (SE 0.02; p<0.05) for an increase in Ct values by 1. This correlation was independent of the duration of symptoms. Our findings suggest that an increasing Ct value in sequential tests may be of prognostic value for patients diagnosed with COVID-19 pneumonia., Competing Interests: The authors have declared that no competing interests exist.

A 78-year-old man developed right knee pain and swelling without other systemic symptoms. He had travelled frequently to the Central Valley of California. He was diagnosed with coccidioidomycosis based on joint fluid culture. Coccidioidal complement fixation antibody titres were extremely elevated. Arthroscopic debridement and fluconazole therapy did not lead to satisfactory improvement. Subsequent open debridement and change to itraconazole was followed by resolution of clinical signs of infection., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

A 74-year-old man experienced worsening asthma for several years. Oral steroids were required on multiple occasions for asthma treatment. During his steroid courses, he developed a hive-like rash, which would resolve after completion of each steroid course. He was from Romania, and had lived in the USA for many years. Laboratory testing had shown eosinophilia. He was eventually diagnosed with strongyloidiasis by serology. Treatment with ivermectin led to marked improvement but not resolution of his long-term asthma. His hive-like rash, which was likely larva currens, did not recur with a subsequent steroid course. Improved recognition of strongyloidiasis, particularly in steroid-treated patients, is needed., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

A 63-year-old man developed scrotal swelling that became bilateral over 2 months. His symptoms persisted after treatment for epididymitis, and he developed a scrotal fistula with drainage. Mycobacterium tuberculosis grew from the urine and fistula. His symptoms resolved and fistula closed with medical therapy. His case highlights the importance of early recognition, diagnosis and treatment of this form of extrapulmonary tuberculosis., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

BACKGROUND To design better antimicrobial stewardship programs, detailed data on the primary drivers and patterns of antibiotic use are needed. OBJECTIVE To characterize the indications for antibiotic therapy, agents used, duration, combinations, and microbiological justification in 6 acute-care US facilities with varied location, size, and type of antimicrobial stewardship programs. DESIGN, PARTICIPANTS, AND SETTING Retrospective medical chart review was performed on a random cross-sectional sample of 1,200 adult inpatients, hospitalized (>24 hrs) in 6 hospitals, and receiving at least 1 antibiotic dose on 4 index dates chosen at equal intervals through a 1-year study period (October 1, 2009-September 30, 2010). METHODS Infectious disease specialists recorded patient demographic characteristics, comorbidities, microbiological and radiological testing, and agents used, dose, duration, and indication for antibiotic prescriptions. RESULTS On the index dates 4,119 (60.5%) of 6,812 inpatients were receiving antibiotics. The random sample of 1,200 case patients was receiving 2,527 antibiotics (average: 2.1 per patient); 540 (21.4%) were prophylactic and 1,987 (78.6%) were therapeutic, of which 372 (18.7%) were pathogen-directed at start. Of the 1,615 empirical starts, 382 (23.7%) were subsequently pathogen-directed and 1,231 (76.2%) remained empirical. Use was primarily for respiratory (27.6% of prescriptions) followed by gastrointestinal (13.1%) infections. Fluoroquinolones, vancomycin, and antipseudomonal penicillins together accounted for 47.1% of therapy-days. CONCLUSIONS Use of broad-spectrum empirical therapy was prevalent in 6 US acute care facilities and in most instances was not subsequently pathogen directed. Fluoroquinolones, vancomycin, and antipseudomonal penicillins were the most frequently used antibiotics, particularly for respiratory indications. Infect. Control Hosp. Epidemiol. 2015;37(1):70-79.

Background: Modification of empirical antimicrobials when warranted by culture results or clinical signs is recommended to control antimicrobial overuse and resistance. We aimed to assess the frequency with which patients were started on empirical antimicrobials, characteristics of the empirical regimen and the clinical characteristics of patients at the time of starting antimicrobials, patterns of changes to empirical therapy at different timepoints, and modifiable factors associated with changes to the initial empirical regimen in the first 5 days of therapy., Methods: We did a chart review of adult inpatients receiving one or more antimicrobials in six US hospitals on 4 days during 2009 and 2010. Our primary outcome was the modification of antimicrobial regimen on or before the 5th day of empirical therapy, analysed as a three-category variable. Bivariate analyses were used to establish demographic and clinical variables associated with the outcome. Variables with p values below 0·1 were included in a multivariable generalised linear latent and mixed model with multinomial logit link to adjust for clustering within hospitals and accommodate a non-binary outcome variable., Findings: Across the six study sites, 4119 (60%) of 6812 inpatients received antimicrobials. Of 1200 randomly selected patients with active antimicrobials, 730 (61%) met inclusion criteria. At the start of therapy, 220 (30%) patients were afebrile and had normal white blood cell counts. Appropriate cultures were collected from 432 (59%) patients, and 250 (58%) were negative. By the 5th day of therapy, 12·5% of empirical antimicrobials were escalated, 21·5% were narrowed or discontinued, and 66·4% were unchanged. Narrowing or discontinuation was more likely when cultures were collected at the start of therapy (adjusted OR 1·68, 95% CI 1·05-2·70) and no infection was noted on an initial radiological study (1·76, 1·11-2·79). Escalation was associated with multiple infection sites (2·54, 1·34-4·83) and a positive culture (1·99, 1·20-3·29)., Interpretation: Broad-spectrum empirical therapy is common, even when clinical signs of infection are absent. Fewer than one in three inpatients have their regimens narrowed within 5 days of starting empirical antimicrobials. Improved diagnostic methods and continued education are needed to guide discontinuation of antimicrobials., Funding: US Centers for Disease Control and Prevention, Division of Healthcare Quality Promotion; Robert Wood Johnson Foundation; US Department of Veterans Administration; US Department of Homeland Security., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Background: Extremely drug-resistant gram-negative bacilli (XDR-GNB) increasingly cause health care-associated infections (HAIs) in intensive care units (ICUs)., Methods: A matched case-control (1:2) study was conducted from February 2007 to January 2010 in 16 ICUs. Case and control subjects had HAIs caused by GNB susceptible to ≤1 antibiotic versus ≥2 antibiotics, respectively. Logistic and Cox proportional hazards regression assessed risk factors for HAIs and predictors of mortality, respectively., Results: Overall, 103 case and 195 control subjects were enrolled. An immunocompromised state (odds ratio [OR], 1.55; P = .047) and exposure to amikacin (OR, 13.81; P < .001), levofloxacin (OR, 2.05; P = .005), or trimethoprim-sulfamethoxazole (OR, 3.42; P = .009) were factors associated with XDR-GNB HAIs. Multiple factors in both case and control subjects significantly predicted increased mortality at different time intervals after HAI diagnosis. At 7 days, liver disease (hazard ratio [HR], 5.52), immunocompromised state (HR, 3.41), and bloodstream infection (HR, 2.55) predicted mortality; at 15 days, age (HR, 1.02 per year increase), liver disease (HR, 3.34), and immunocompromised state (HR, 2.03) predicted mortality; and, at 30 days, age (HR, 1.02 per 1-year increase), liver disease (HR, 3.34), immunocompromised state (HR, 2.03), and hospitalization in a medical ICU (HR, 1.85) predicted mortality., Conclusion: HAIs caused by XDR-GNB were associated with potentially modifiable factors. Age, liver disease, and immunocompromised state, but not XDR-GNB HAIs, were associated with mortality., (Copyright © 2014 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.)

Two cases of domestically acquired fascioliasis are reported. Patient One was a 63-year-old male who developed a febrile illness 2 months after eating watercress in Marin County. Patient Two was a 38-year-old male who had eaten watercress with Patient One, and also developed a febrile illness. Both patients had eosinophilia and liver lesions on imaging. Diagnosis was made by serology and treatment was with triclabendazole.

Objective: To assess how healthcare professionals caring for patients in intensive care units (ICUs) understand and use antimicrobial susceptibility testing (AST) for multidrug-resistant gram-negative bacilli (MDR-GNB)., Design: A knowledge, attitude, and practice survey assessed ICU clinicians' knowledge of antimicrobial resistance, confidence interpreting AST results, and beliefs regarding the impact of AST on patient outcomes., Setting: Sixteen ICUs affiliated with NewYork-Presbyterian Hospital., Participants: Attending physicians and subspecialty residents with primary clinical responsibilities in adult or pediatric ICUs as well as infectious diseases subspecialists and clinical pharmacists., Methods: Participants completed an anonymous electronic survey. Responses included 4-level Likert scales dichotomized for analysis. Multivariate analyses were performed using generalized estimating equation logistic regression to account for correlation of respondents from the same ICU., Results: The response rate was 51% (178 of 349 eligible participants); of the respondents, 120 (67%) were ICU physicians. Those caring for adult patients were more knowledgeable about antimicrobial activity and were more familiar with MDR-GNB infections. Only 33% and 12% of ICU physicians were familiar with standardized and specialized AST methods, respectively, but more than 95% believed that AST improved patient outcomes. After adjustment for demographic and healthcare provider characteristics, those familiar with treatment of MDR-GNB bloodstream infections, those aware of resistance mechanisms, and those aware of AST methods were more confident that they could interpret AST results and/or request additional in vitro testing., Conclusions: Our study uncovered knowledge gaps and educational needs that could serve as the foundation for future interventions. Familiarity with MDR-GNB increased overall knowledge, and familiarity with AST increased confidence interpreting the results.

Background: Genetic tracking of Mycobacterium tuberculosis is a cornerstone of tuberculosis (TB) control programs. The RD(Rio) M. tuberculosis sublineage was previously associated with TB in Brazil. We investigated 3847 M. tuberculosis isolates and registry data from New York City (NYC) (2001-2005) to: (1) affirm the position of RD(Rio) strains within the M. tuberculosis phylogenetic structure, (2) determine its prevalence, and (3) define transmission, demographic, and clinical characteristics associated with RD(Rio) TB., Methods: Isolates classified as RD(Rio) or non-RD(Rio) M. tuberculosis by multiplex PCR were further classified as clustered (≥2 isolates) or unique based primarily upon IS6110-RFLP patterns and lineage-specific cluster proportions were calculated. The secondary case rate of RD(Rio) was compared with other prevalent M. tuberculosis lineages. Genotype data were merged with the data from the NYC TB Registry to assess demographic and clinical characteristics., Results: RD(Rio) strains were found to: (1) be restricted to the Latin American-Mediterranean family, (2) cause approximately 8% of TB cases in NYC, and (3) be associated with heightened transmission as shown by: (i) a higher cluster proportion compared to other prevalent lineages, (ii) a higher secondary case rate, and (iii) cases in children. Furthermore, RD(Rio) strains were significantly associated with US-born Black or Hispanic race, birth in Latin American and Caribbean countries, and isoniazid resistance., Conclusions: The RD(Rio) genotype is a single M. tuberculosis strain population that is emerging in NYC. The findings suggest that expanded RD(Rio) case and exposure identification could be of benefit due to its association with heightened transmission., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Background: We performed this study 1) to determine the prevalence of community-associated extended spectrum beta-lactamase producing Enterobacteriaceae (ESBLPE) colonization and infection in New York City (NYC); 2) to determine the prevalence of newly-acquired ESBLPE during travel; 3) to look for similarities in contemporaneous hospital-associated bloodstream ESBLPE and travel-associated ESBLPE., Methods: Subjects were recruited from a travel medicine practice and consented to submit pre- and post-travel stools, which were assessed for the presence of ESBLPE. Pre-travel stools and stools submitted for culture were used to estimate the prevalence of community-associated ESBLPE. The prevalence of ESBLPE-associated urinary tract infections was calculated from available retrospective data. Hospital-associated ESBLPE were acquired from saved bloodstream isolates. All ESBLPE underwent multilocus sequence typing (MLST) and ESBL characterization., Results: One of 60 (1.7%) pre- or non-travel associated stool was colonized with ESBLPE. Among community-associated urine specimens, 1.3% of Escherichia coli and 1.4% of Klebsiella pneumoniae were identified as ESBLPE. Seven of 28 travelers (25.0%) acquired a new ESBLPE during travel. No similarities were found between travel-associated ESBLPE and hospital-associated ESBLPE. A range of imported ESBL genes were found, including CTX-M-14 and CTX-15., Conclusion: ESBL colonization and infection were relatively low during the study period in NYC. A significant minority of travelers acquired new ESBLPE during travel.

We retrospectively calculated the prevalence and epidemiologic characteristics of Chagas infection in the New York blood donor population over three years utilizing the New York Blood Center's database of the New York metropolitan area donor population. Seventy Trypanosoma cruzi positive donors were identified from among 876,614 donors over a 3-year period, giving an adjusted prevalence of 0.0083%, with 0.0080% in 2007, 0.0073% in 2008, and 0.0097% in 2009. When filtered only for self-described "Hispanic/Latino" donors, there were 52 Chagas positive donors in that 3-year period (among 105,122 self-described Hispanic donors) with an adjusted prevalence of 0.052%, with 0.055% in 2007, 0.047% in 2008, and 0.053% in 2009. In conclusion, we found a persistent population of patients with Chagas infection in the New York metropolitan area donor population. There was geographic localization of cases which aligned with Latin American immigration clusters.

We report an unusual case of extraintestinal infection with adult Enterobius vermicularis worms in the nares and ocular orbit of a 14-year-old girl in Illinois. Only one other similar case has been reported in the English-language literature.

The study aimed to determine the natural history of Staphylococcus aureus nasal colonization in hemodialysis outpatients. Surveillance cultures were taken from patients presenting for hemodialysis or routine care to identify S. aureus nasal carriers. A prospective cohort study was performed to identify risks for persistent colonization. Detailed microbiologic and molecular studies of colonizing isolates were performed. Only 23/145 (15.9%) dialysis patients were persistently colonized, and only HIV-positive status was associated with persistence (P = 0.05). Prior hospitalization was the only risk factor for methicillin-resistant S. aureus carriage (OR 2.5, P = 0.03). In isolates from patients with ≤ 42 days of vancomycin exposure, vancomycin minimum bactericidal concentrations (MBCs) increased with duration of exposure. Among dialysis patients, S. aureus colonization was limited and transient; only HIV status was associated with persistence. Nevertheless, duration of vancomycin exposure was associated with increasing vancomycin MBCs. Vancomycin exposure in S. aureus carriers may be involved in increasing resistance., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Background: Acinetobacter baumannii is an increasingly multidrug-resistant (MDR) cause of hospital-acquired infections, often associated with limited therapeutic options. We investigated A. baumannii isolates at a New York hospital to characterize genetic relatedness., Methods: Thirty A. baumannii isolates from geographically-dispersed nursing units within the hospital were studied. Isolate relatedness was assessed by repetitive sequence polymerase chain reaction (rep-PCR). The presence and characteristics of integrons were assessed by PCR. Metabolomic profiles of a subset of a prevalent strain isolates and sporadic isolates were characterized and compared., Results: We detected a hospital-wide group of closely related carbapenem resistant MDR A. baumannii isolates. Compared with sporadic isolates, the prevalent strain isolates were more likely to be MDR (p = 0.001). Isolates from the prevalent strain carried a novel Class I integron sequence. Metabolomic profiles of selected prevalent strain isolates and sporadic isolates were similar., Conclusion: The A. baumannii population at our hospital represents a prevalent strain of related MDR isolates that contain a novel integron cassette. Prevalent strain and sporadic isolates did not segregate by metabolomic profiles. Further study of environmental, host, and bacterial factors associated with the persistence of prevalent endemic A. baumannii strains is needed to develop effective prevention strategies.

We report a case of recurrent Staphylococcus aureus bacteremia in a patient who failed vancomycin due to a vancomycin-heteroresistant strain lacking methicillin resistance. Although initial isolates were susceptible, isolates obtained after vancomycin chemotherapy were vancomycin heteroresistant. This case thus illustrates the clinical emergence of vancomycin heteroresistance.

We report the robustness of silica hydride stationary phase, aqueous normal phase (ANP) chromatography to the chemical complexity of the intracellular metabolomes of Staphylococcus aureus and Enterococcus faecium. We specifically demonstrate that the chromatographic behavior of known metabolites is unaffected by the intracellular chemical matrix of these microbes and that this method enables untargeted profiling of their intracellular metabolites using accurate mass-retention time (AMRT) identifiers. We further demonstrate the ability of AMRT-based metabolite profiling to differentiate bacteria along genetic and phenotypic lines. Overall, these data commend the utility of ANP-based chromatography for untargeted metabolomics-based studies of microbial physiology and antibiotic resistance.

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae may appear susceptible to imipenem or meropenem by routine susceptibility testing. We report a series of patients with infections caused by K. pneumoniae isolates, which yielded imipenem-susceptible results but were subsequently KPC-positive by polymerase chain reaction. When these infections were treated with imipenem or meropenem, frequent clinical and microbiologic failures were observed.