At-home testing for respiratory viruses: a minireview of the current landscape

The landscape of at-home testing using over-the-counter (OTC) tests has been evolving over the last decade. The United States Food and Drug Administration Emergency Use Authorization rule has been in effect since the early 2000s, and it was widely employed during the severe acute respiratory syndrome coronavirus 2 pandemic to authorize antigen and nucleic acid detection tests for use in central laboratories as well as OTC. During the pandemic, the first at-home tests for respiratory viruses became available for consumer use, which opened the door for additional respiratory virus OTC tests. Concerns may exist regarding the public's ability to properly collect samples, perform testing, interpret results, and report results to public health authorities. However, favorable comparison studies between OTC testing and centralized laboratory test results suggest that OTC testing may have a place in healthcare, and it is likely here to stay. This mini-review of OTC tests for viral respiratory diseases will briefly cover the regulatory and reimbursement environment, current OTC test availability, as well as the advantages and limitations of OTC tests.

Validation of a Novel, Rapid Sepsis Diagnostic for Emergency Department Use

OBJECTIVES

To assess the in vitro IntelliSep test, a microfluidic assay that quantifies the state of immune activation by evaluating the biophysical properties of leukocytes, as a rapid diagnostic for sepsis.

DESIGN

Prospective cohort study.

SETTING

Five emergency departments (EDs) in Louisiana, Missouri, North Carolina, and Washington.

PATIENTS

Adult patients presenting to the ED with signs (two of four Systemic Inflammatory Response Syndrome criteria, where one must be temperature or WBC count) or suspicion (provider-ordered culture) of infection.

INTERVENTIONS

All patients underwent testing with the IntelliSep using ethylene diamine tetraacetic acid-anticoagulated whole blood followed by retrospective adjudication for sepsis by sepsis-3 criteria by a blinded panel of physicians.

MEASUREMENTS AND MAIN RESULTS

Of 599 patients enrolled, 572 patients were included in the final analysis. The result of the IntelliSep test is reported as the IntelliSep Index (ISI), ranging from 0.1 to 10.0, divided into three interpretation bands for the risk of sepsis: band 1 (low) to band 3 (high). The median turnaround time for ISI results was 7.2 minutes. The ISI resulted band 1 in 252 (44.1%), band 2 in 160 (28.0%), and band 3 in 160 (28.0%). Sepsis occurred in 26.6% (152 of 572 patients). Sepsis prevalence was 11.1% (95% CI, 7.5-15.7%) in band 1, 28.1% (95% CI, 21.3-35.8%) in band 2, and 49.4% (95% CI, 41.4-57.4%) in band 3. The Positive Percent Agreement of band 1 was 81.6% and the Negative Percent Agreement of band 3 was 80.7%, with an area under the receiver operating characteristic curve of 0.74. Compared with band 1, band 3 correlated with adverse clinical outcomes, including mortality, and resource utilization.

CONCLUSIONS

Increasing ISI interpretation band is associated with increasing probability of sepsis in patients presenting to the ED with suspected infection.

Variability in Provider Assessment of Sepsis and Potential of Host Response Technology to Address this Dilemma-Results of an Online Delphi Study

Potentially septic patients have a huge clinical and economic impact on hospitals and often present to the emergency department (ED) with undifferentiated symptoms. The triage of these patients is complex and has historically relied heavily upon provider judgment. This study aims to evaluate the consistency of provider judgment and the potential of a new host response sepsis test to aid in the triage process. A modified Delphi study involving 26 participants from multiple specialties was conducted to evaluate provider agreement about sepsis risk and to test proposed actions based on the results of a sepsis test. The participants considered case vignettes of potentially septic patients designed to represent diagnostic dilemmas. Provider assessment of sepsis risk in these cases ranged from 10% to 90% and agreement was poor. Agreement about clinical actions to take in response to testing improved when participants considered their own hypothetical borderline cases. New host response testing for sepsis may have the potential to improve sepsis diagnosis and care and should be applied in a protocolized fashion to ensure consistency of results.

Costs and Consequences of a Novel Emergency Department Sepsis Diagnostic Test: The IntelliSep Index

Sepsis causes 270,000 deaths and costs $38 billion annually in the United States. Most cases of sepsis present in the emergency department (ED), where rapid diagnosis remains challenging. The IntelliSep Index (ISI) is a novel diagnostic test that analyzes characteristics of WBC structure and provides a reliable early signal for sepsis. This study performs a cost-consequence analysis of the ISI relative to procalcitonin for early sepsis diagnosis in the ED.

PERSPECTIVE

U.S. healthcare system.

SETTING

Community hospital ED.

METHODS

A decision tree analysis was performed comparing ISI with procalcitonin. Model parameters included prevalence of sepsis, sensitivity and specificity of diagnostic tests (both ISI and procalcitonin), costs of hospitalization, and mortality rate stratified by diagnostic test result. Mortality and prevalence of sepsis were estimated from best available literature. Costs were estimated based on an analysis of a large, national discharge dataset, and adjusted to 2018 U.S. dollars. Outcomes included expected costs and survival.

RESULTS

Assuming a confirmed sepsis prevalence of 16.9% (adjudicated to Sepsis-3), the ISI strategy had an expected cost per patient of $3,849 and expected survival rate of 95.08%, whereas the procalcitonin strategy had an expected cost of $4,656 per patient and an expected survival of 94.98%. ISI was both less costly and more effective than procalcitonin, primarily because of fewer false-negative results. These results were robust in sensitivity analyses.

CONCLUSIONS

ISI was both less costly and more effective in preventing mortality than procalcitonin, primarily because of fewer false-negative results. The ISI may provide health systems with a higher-value diagnostic test in ED sepsis evaluation. Additional work is needed to validate these results in clinical practice.

Rapid identification of sepsis in the emergency department

Objectives

Recent research has helped define the complex pathways in sepsis, affording new opportunities for advancing diagnostics tests. Given significant advances in the field, a group of academic investigators from emergency medicine, intensive care, pathology, and pharmacology assembled to develop consensus around key gaps and potential future use for emerging rapid host response diagnostics assays in the emergency department (ED) setting.

Methods

A modified Delphi study was conducted that included 26 panelists (expert consensus panel) from multiple specialties. A smaller steering committee first defined a list of Delphi statements related to the need for and future potential use of a hypothetical sepsis diagnostic test in the ED. Likert scoring was used to assess panelists agreement or disagreement with statements. Two successive rounds of surveys were conducted and consensus for statements was operationally defined as achieving agreement or disagreement of 75% or greater.

Results

Significant gaps were identified related to current tools for assessing risk of sepsis in the ED. Strong consensus indicated the need for a test providing an indication of the severity of dysregulated host immune response, which would be helpful even if it did not identify the specific pathogen. Although there was a relatively high degree of uncertainty regarding which patients would most benefit from the test, the panel agreed that an ideal host response sepsis test should aim to be integrated into ED triage and thus should produce results in less than 30 minutes. The panel also agreed that such a test would be most valuable for improving sepsis outcomes and reducing rates of unnecessary antibiotic use.

Conclusion

The expert consensus panel expressed strong consensus regarding gaps in sepsis diagnostics in the ED and the potential for new rapid host response tests to help fill these gaps. These finding provide a baseline framework for assessing key attributes of evolving host response diagnostic tests for sepsis in the ED.

Comparison of Methods for Determining the Antibiotic Susceptibility of Aerococcus Species in a Clinical Setting

OBJECTIVES

Aerococcus spp are Gram-positive cocci increasingly recognized as uropathogens. The Clinical and Laboratory Standards Institute recently published specific breakpoints for Aerococcus spp (M45, third edition); however, the standardized method used for antimicrobial susceptibility testing (AST) requires media not often maintained in clinical laboratories. The purpose of this study was to evaluate and compare alternative methods of AST for Aerococcus isolates.

METHODS

AST was performed on 134 clinical isolates using the Etest on three different types of agar, Vitek 2, and BD Phoenix. These results were compared with broth microdilution using the Sensititre STP6F.

RESULTS

Aerococcus exhibited low minimum inhibitory concentrations to benzylpenicillin, meropenem, linezolid, and vancomycin. Variable resistance was seen to levofloxacin, ceftriaxone, and tetracycline. Meropenem and vancomycin met all acceptance criteria with every alternative method tested. Benzylpenicillin and linezolid did not meet essential agreement on any AST method. Tetracycline met the majority of acceptance criteria with the exception of more than 3% very major error when using the Etest on chocolate agar, the Vitek 2, and BD Phoenix.

CONCLUSIONS

Overall, the alternate AST method with the highest agreement with broth microdilution was the Etest on Mueller-Hinton agar with 5% sheep blood and may be an optimal alternative to broth microdilution.

SARS-CoV-2 Cycle Thresholds, Poverty, Race, and Clinical Outcomes

BACKGROUND

Poverty and high viral load are associated with worse outcomes among COVID-19 patients.

METHODS

We included patients admitted to Froedtert Health between March 16 and June 1, 2020. SARS-CoV-2 viral load was proxied by cycle-threshold values. To measure poverty, we used Medicaid or uninsured status and residence in socially disadvantaged areas. We assessed the association between viral load and length of stay and discharge disposition, while controlling for demographics and confounders.

RESULTS

Higher viral load was associated with longer length of stay (coefficient -0.02; 95% CI, -0.04 to 0.01; P = 0.006) and higher likelihood of death (coefficient -0.11; 95% CI, -0.17 to -0.06; P < 0.001). Poverty, residence in disadvantaged areas, and race were not.

DISCUSSION

This study confirms a relationship of viral load with in-hospital death, even after controlling for race and poverty.

Point-of-care COVID-19 testing in the emergency department: current status and future prospects

INTRODUCTION

This expert review outlines current and future point-of-care technologies for the diagnosis of the SARS-CoV-2 virus, which is responsible for causing coronavirus disease COVID-19 in the emergency department. COVID-19 first emerged in late 2019 and is responsible for a range of presentations from minor upper respiratory tract symptoms to severe pneumonia and multisystem organ failure. Among the technologies available include the gold standard of molecular point-of-care tests as well as antigen detection tests.

AREAS COVERED

We discuss point-of-care molecular tests including multiplex, targeted, and single plex panels as well as various antigen testing methodologies in terms of availability and performance characteristics. In addition, we focus on current testing best practices and considerations for point-of-care testing in the emergency department based on a search of the literature available in PubMed to date and a review of FDA and CDC guidance.

EXPERT OPINION

While there have been many advances in SARS-CoV-2 point-of-care testing, there remain challenges to implementation in the emergency department setting. A paradigm shift is needed to improve diagnosis and clinical outcomes.

Cytotoxic CD8-positive T-lymphocyte infiltration in the lungs as a histological pattern of SARS-CoV-2 pneumonitis

Despite millions of PCR confirmed cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, the long-term pathophysiological changes induced by this infection in the lungs and their relationship with possible immune triggers remain incompletely understood. Acute respiratory distress syndrome and subsequent respiratory failure are the most common causes of mortality in hospitalised patients. Severe lung tissue destruction can be due to an overactive immune system that far exceeds the harm that would have been caused by direct virus replication. This study extends our previous investigation and presents detailed histopathological findings on cryotransbronchial biopsy in patients with persistent (range 31–182 days) pneumonitis and severe interstitial inflammatory infiltration in the lungs due to SARS-CoV-2 infection. We describe a novel lung injury pattern associated with SARS-CoV-2 pneumonitis, which manifests as a marked interstitial CD8-positive T-cell lymphocytic infiltration. These findings provide a better understanding of the changes in the lungs that ensue due to SARS-CoV-2 infection.

Rapid identification from rectal swabs of the clinically most relevant carbapenemase genes from gram-negative bacteria using the BD MAX Check-Points CPO Assay

We conducted an international multicentre evaluation to assess the clinical performance characteristics of the new multiplex PCR-based BD MAX Check-Points CPO assay to detect the 5 major carbapenemase families: KPC, VIM/IMP (tested simultaneously), NDM and OXA-48 compared to a reference method consisting of 2 culture methods (to improve recovery of CPO isolates from the rectal swabs), followed by carbapenem susceptibility testing and sequencing of target carbapenemase genes. Tests were performed from rectal swab specimens in ESwab collection and transport devices. Positive percent agreement (PPA) for BD MAX Check-Points CPO for KPC and OXA-48 were 88.2% (95% CI:72.6-96.7) and 96.2% (95% CI:80.4-99.9), respectively. Negative percent agreement was ≥99% for each gene. Insufficient samples (≤10) were positive for VIM/IMP or NDM tests to calculate meaningful PPA values. The BD MAX Check-Points CPO assay represents an accurate tool for rapid recognition of patients with rectal colonization by the most commonly encountered CPOs.

Evaluation of a High-Definition PCR Assay for the Detection of SARS-CoV-2 in Extracted and Nonextracted Respiratory Specimens Collected in Various Transport Media

Objectives

We conducted an analytic and clinical comparison of a novel high-definition polymerase chain reaction PCR (HDPCR) assay to traditional real-time PCR (RT-PCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper respiratory specimens.

Methods

Analytic performance of RT-PCR, HDPCR, and extraction-free HDPCR was established through replicate testing of a serially diluted clinical specimen containing SARS-CoV-2. A clinical comparison of all 3 assays was conducted using 351 prospectively collected upper respiratory swab specimens obtained from symptomatic and asymptomatic individuals collected in various transport media.

Results

RT-PCR and HDPCR assays using extracted nucleic acid demonstrated similar analytic limits of detection (LoD) and clinical performance, with 100% positive and negative agreement. Extraction-free HDPCR demonstrated a 1.5 to 2.0 log₁₀ increase in LoD based on cycle threshold values. However, clinical performance of extraction-free HDPCR remained high, demonstrating 97.8% positive and 99.6% negative agreement with RT-PCR. An overall increase in “invalid” and “presumptive” results was observed when using the extraction-free method, but this was highly variable based on transport medium used.

Conclusions

HDPCR performs similar to RT-PCR for the detection of SARS-CoV-2. The use of an extraction-free HDPCR protocol maintained high clinical performance despite reduced analytic LoD, with the benefit of reduced hands-on time and cost of reagents associated with nucleic acid extraction.

Impact of an Antimicrobial Stewardship Program Pharmacist During Microbiology Rounds

OBJECTIVES

The purpose of this study is to describe and evaluate the impact of the participation of an antimicrobial stewardship program (ASP) pharmacist in microbiology rounds at our institution.

METHODS

This single-center retrospective descriptive study included inpatient and ambulatory adults (≥18 years) with a susceptibility request reviewed during microbiology rounds between October 2018 and March 2019. In October 2018, multidisciplinary telephone microbiology rounds were initiated with the medical directors of the clinical microbiology laboratory and ASP pharmacist to review susceptibility requests. Numbers and types of interventions made by an ASP pharmacist and potential benefits were recorded and analyzed.

RESULTS

Sixty-seven susceptibility requests were reviewed by an ASP pharmacist, of which 83.6% were inpatient. An ASP pharmacist completed chart reviews for 92.5% of requests and contacted the requester or primary team 74.6% of the time. About half (47.8%) of susceptibility requests were approved, and only 65.2% of requests from an infectious diseases provider were approved (P = .039). The most frequent potential benefits of the intervention included preventing unnecessary susceptibility testing (47.8%), improving clinician understanding (40.3%), and preventing treatment of a culture result deemed as a contaminant (19.4%).

CONCLUSIONS

ASP pharmacists are uniquely accessible and able to assist with preventing unnecessary susceptibility testing, optimizing antimicrobial therapy, and providing education to other health care professionals.

A Multi-mRNA Host-Response Molecular Blood Test for the Diagnosis and Prognosis of Acute Infections and Sepsis: Proceedings from a Clinical Advisory Panel

Current diagnostics are insufficient for diagnosis and prognosis of acute infections and sepsis. Clinical decisions including prescription and timing of antibiotics, ordering of additional diagnostics and level-of-care decisions rely on understanding etiology and implications of a clinical presentation. Host mRNA signatures can differentiate infectious from noninfectious etiologies, bacterial from viral infections, and predict 30-day mortality. The 29-host-mRNA blood-based InSep^TM test (Inflammatix, Burlingame, CA, formerly known as HostDx^TM Sepsis) combines machine learning algorithms with a rapid point-of-care platform with less than 30 min turnaround time to enable rapid diagnosis of acute infections and sepsis, as well as prediction of disease severity. A scientific advisory panel including emergency medicine, infectious disease, intensive care and clinical pathology physicians discussed technical and clinical requirements in preparation of successful introduction of InSep into the market. Topics included intended use; patient populations of greatest need; patient journey and sample flow in the emergency department (ED) and beyond; clinical and biomarker-based decision algorithms; performance characteristics for clinical utility; assay and instrument requirements; and result readouts. The panel identified clear demand for a solution like InSep, requirements regarding test performance and interpretability, and a need for focused medical education due to the innovative but complex nature of the result readout. Innovative diagnostic solutions such as the InSep test could improve management of patients with suspected acute infections and sepsis in the ED, thereby lessening the overall burden of these conditions on patients and the healthcare system.

Decrease in Positivity Rate of Influenza Tests Coinciding With Outbreak of SARS-CoV-2: Data From a Southeastern Wisconsin Laboratory

BACKGROUND

The SARS-CoV-2 outbreak prompted public health interventions and changes in public behavior that may have affected the 2019-2020 influenza season.

METHODS

Using data from a laboratory in southeastern Wisconsin, we compared the number of weekly influenza tests and their positivity rates during the 2019-2020 influenza season with the previous 4 seasons.

RESULTS

The number of influenza tests per week at the outset of the SARS-CoV-2 outbreak was higher than the average the previous 4 years, and positivity rates declined to 0% earlier than any of the previous 4 seasons.

CONCLUSION

The testing trajectory and positivity rate for influenza differed during the part of the 2019-2020 season coinciding with the SARS-CoV-2 outbreak as compared to similar periods during the previous 4 seasons.

Distribution of SARS-CoV-2 PCR Cycle Threshold Values Provide Practical Insight Into Overall and Target-Specific Sensitivity Among Symptomatic Patients

OBJECTIVES

We examined the distribution of reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values obtained from symptomatic patients being evaluated for coronavirus disease 2019 (COVID-19) to determine the proportion of specimens containing a viral load near the assay limit of detection (LoD) to gain practical insight to the risk of false-negative results. We also examined the relationship between CT value and patient age to determine any age-dependent difference in viral load or test sensitivity.

METHODS

We collected CT values obtained from the cobas severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay corresponding to 1,213 combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals that were reported as positive or presumptive positive for SARS-CoV-2. CT values were stratified by SARS-CoV target and patient age group.

RESULTS

In total, 93.3% to 98.4% of specimens demonstrated CT values greater than 3× the assay LoD, at which point false-negative results would not be expected. The mean of CT values between age groups was statistically equivalent with the exception of patients in age group 80 to 89 years, which demonstrated slightly lower CTs.

CONCLUSIONS

Based on the distribution of observed CT values, including the small proportion of specimens with values near the assay LoD, there is a low risk of false-negative RT-PCR results in combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals.

Racial Disparities in Incidence and Outcomes Among Patients With COVID-19

IMPORTANCE

Initial public health data show that Black race may be a risk factor for worse outcomes of coronavirus disease 2019 (COVID-19).

OBJECTIVE

To characterize the association of race with incidence and outcomes of COVID-19, while controlling for age, sex, socioeconomic status, and comorbidities.

DESIGN, SETTING, AND PARTICIPANTS

This cross-sectional study included 2595 consecutive adults tested for COVID-19 from March 12 to March 31, 2020, at Froedtert Health and Medical College of Wisconsin (Milwaukee), the largest academic system in Wisconsin, with 879 inpatient beds (of which 128 are intensive care unit beds).

EXPOSURES

Race (Black vs White, Native Hawaiian or Pacific Islander, Native American or Alaska Native, Asian, or unknown).

MAIN OUTCOMES AND MEASURES

Main outcomes included COVID-19 positivity, hospitalization, intensive care unit admission, mechanical ventilation, and death. Additional independent variables measured and tested included socioeconomic status, sex, and comorbidities. Reverse transcription polymerase chain reaction assay was used to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

RESULTS

A total of 2595 patients were included. The mean (SD) age was 53.8 (17.5) years, 978 (37.7%) were men, and 785 (30.2%) were African American patients. Of the 369 patients (14.2%) who tested positive for COVID-19, 170 (46.1%) were men, 148 (40.1%) were aged 60 years or older, and 218 (59.1%) were African American individuals. Positive tests were associated with Black race (odds ratio [OR], 5.37; 95% CI, 3.94-7.29; P = .001), male sex (OR, 1.55; 95% CI, 1.21-2.00; P = .001), and age 60 years or older (OR, 2.04; 95% CI, 1.53-2.73; P = .001). Zip code of residence explained 79% of the overall variance in COVID-19 positivity in the cohort (ρ = 0.79; 95% CI, 0.58-0.91). Adjusting for zip code of residence, Black race (OR, 1.85; 95% CI, 1.00-3.65; P = .04) and poverty (OR, 3.84; 95% CI, 1.20-12.30; P = .02) were associated with hospitalization. Poverty (OR, 3.58; 95% CI, 1.08-11.80; P = .04) but not Black race (OR, 1.52; 95% CI, 0.75-3.07; P = .24) was associated with intensive care unit admission. Overall, 20 (17.2%) deaths associated with COVID-19 were reported. Shortness of breath at presentation (OR, 10.67; 95% CI, 1.52-25.54; P = .02), higher body mass index (OR per unit of body mass index, 1.19; 95% CI, 1.05-1.35; P = .006), and age 60 years or older (OR, 22.79; 95% CI, 3.38-53.81; P = .001) were associated with an increased likelihood of death.

CONCLUSIONS AND RELEVANCE

In this cross-sectional study of adults tested for COVID-19 in a large midwestern academic health system, COVID-19 positivity was associated with Black race. Among patients with COVID-19, both race and poverty were associated with higher risk of hospitalization, but only poverty was associated with higher risk of intensive care unit admission. These findings can be helpful in targeting mitigation strategies for racial disparities in the incidence and outcomes of COVID-19.

Evaluation of NG-Test Carba 5 for Rapid Phenotypic Detection and Differentiation of Five Common Carbapenemase Families: Results of a Multicenter Clinical Evaluation

NG-Test Carba 5 is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of five common carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM) directly from bacterial colonies. The assay is simple to perform and has recently received U.S. Food and Drug Administration clearance. A method comparison study was performed at geographically diverse medical centers (n = 3) in the United States, where 309 Enterobacterales and Pseudomonas aeruginosa isolates were evaluated by NG-Test Carba 5 (NG Biotech, Guipry, France), the Xpert Carba-R assay (Cepheid, Inc., Sunnyvale, CA), the modified carbapenem inactivation method (mCIM), the EDTA-modified carbapenem inactivation method, and disk diffusion with carbapenems. Colonies from tryptic soy agar with 5% sheep blood (blood agar) and MacConkey agar were tested, and the results were compared to those obtained by a composite reference method. Additionally, a fourth medical center performed a medium comparison study by evaluating the performance characteristics of NG-Test Carba 5 from blood, MacConkey, and Mueller-Hinton agars with 110 isolates of Enterobacterales and P. aeruginosa These results were compared to the expected genotypic and mCIM results. For the multicenter method comparison study, the overall positive percent agreement (PPA) and the overall negative percent agreement (NPA) of NG-Test Carba 5 with the composite reference method were 100% for both blood and MacConkey agars. The medium comparison study at the fourth site showed that the PPA ranged from 98.9% to 100% and that the NPA ranged from 95.2% to 100% for blood, MacConkey, and Mueller-Hinton agars. NG-Test Carba 5 accurately detected and differentiated five common carbapenemase families from Enterobacterales and P. aeruginosa colonies on commonly used agar media. The results of this test will support a streamlined laboratory work flow and will expedite therapeutic and infection control decisions.

Association Between Environmental Factors and Toxigenic Clostridioides difficile Carriage at Hospital Admission

IMPORTANCE

Clostridioides difficile infection is the most frequent health care-associated infection in the United States. However, exposure to this organism might occur outside the health care setting.

OBJECTIVE

To examine whether exposure to environmental factors, such as livestock farms, is associated with a higher probability of being colonized with C difficile at hospital admission.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort study was conducted from May 1, 2017, to June 30, 2018, at a teaching-affiliated hospital in Milwaukee, Wisconsin. All consecutive patients underwent C difficile screening using a nucleic acid amplification test at hospital admission. Data analyses were performed from July 2018 to October 2019.

EXPOSURES

The distances from patient residence to the nearest livestock farms, meat processing plants, raw materials services, and sewage facilities were measured in addition to risk factors previously evaluated in other studies.

MAIN OUTCOMES AND MEASURES

The main outcome was a positive result on C difficile screening tests performed within 72 hours of hospital admission.

RESULTS

A total of 3043 patients admitted to the hospital were included in the final analysis. Of those, 1564 (51.4%) were women and 2074 (68.9%) were white, with a mean (SD) age of 62.0 (15.9) years; 978 patients (32.1%) were admitted to hematology-oncology units. At first admission, 318 patients (10.4%) were detected through testing as C difficile carriers. Multivariable logistic regression analyses were performed on a stratified sample of patients based on hematology-oncology admission status. These analyses indicated that although patients admitted to hematology-oncology units were 35% more likely to be colonized with C difficile, no significant association existed between their sociodemographic and economic characteristics or health care and environmental exposures and the likelihood of a positive C difficile test result. In contrast, among patients admitted to non-hematology-oncology units, comorbidities increased the likelihood for colonization by more than 4 times; women had 60% greater colonization than men, and a history of recent hospitalization (ie, within the preceding 6 months) increased the likelihood of colonization by 70%. Residential proximity to livestock farms were all significantly associated with a higher likelihood of a positive C difficile test result. Residential proximity to livestock farms more than doubled the probability of C difficile colonization in patients admitted to non-hematology-oncology units.

CONCLUSIONS AND RELEVANCE

A shorter distance between residence and livestock farms was associated with C difficile colonization. Knowledge of the epidemiology of C difficile in the community surrounding the hospital is important, as it has potential implications for the incidence of hospital-onset C difficile infection.

1045. Impact of an Antimicrobial Stewardship Pharmacist on Microbiology Rounds

Background

Microbiology rounds is an area for antimicrobial stewardship programs (ASP) to potentially intervene on antimicrobial prescribing in both the inpatient and outpatient settings. The purpose of this study was to describe and evaluate the impact of ASP pharmacist participation in microbiology rounds.

Methods

This was a single-center retrospective descriptive study including inpatient and ambulatory adults ( ≥18 years) with a susceptibility request requiring review during microbiology rounds between October 2018 and 3/2019. During daily microbiology rounds, susceptibility or workup requests were reviewed with the multidisciplinary microbiology team. The ASP pharmacist was called for their clinical expertise in assessing complicated or nonstandard susceptibility requests. Number and types of interventions made by ASP pharmacist were recorded (e.g., approval rate, education, ASP referral, ID consult referral). Additionally, number and types of intervention outcomes (unnecessary susceptibility prevented, optimized susceptibility request, treatment recommendation, improved clinician understanding, etc.) were analyzed.

Results

There were 66 susceptibility requests reviewed by an ASP pharmacist from October 2018 to 3/2019, of which 84.8% were inpatient. An ID provider was the requestor for 35% of requests. ASP pharmacists completed chart reviews for 92.4% of patients and contacted the requester/primary team 72.7% of the time. Thirty-three (50%) susceptibility requests were approved and, notably, 65.2% of requests from an ID provider were approved. Intervention rates for education provided, ASP referral, and ID consult referral were 50%, 1%, and 7%, respectively. ASP pharmacists were able to impact multiple intervention outcomes, including preventing unnecessary susceptibility requests (45.5%) and improving clinician understanding (39.4%) (Table 1).

Conclusion

ASP pharmacists are an important part of the microbiology team and are able to use their clinical expertise to help approve or deny susceptibility requests, make potential recommendations to optimize antimicrobial therapy, and provide education to other healthcare professionals.

Disclosures

All authors: No reported disclosures.

534. Active Screening for Carbapenemase Producing Enterobacteriaceae: Yield and Cost Considerations

Background

During 2016, our hospital experienced an outbreak with carbapenemase-producing Enterobacteriaceae (CPE) in our solid-organ transplant (SOT) population. Since this outbreak and until now, our hospital has implemented active CPE screening of patients admitted to SOT units and point prevalence surveillances in any unit with a known CPE patient. The present study evaluates the yield of these screening tests and their cost since implementation.

Methods

This retrospective cohort was performed in a 600-bed hospital in Milwaukee, WI. CPE screening tests were retrieved from the clinical microbiology laboratory dataset from January 2016 to April 2019. CPE tests are performed on rectal swabs or stool samples using the CDC broth enrichment method followed by MIC confirmation using Etest. CPE patients were placed on enhanced precautions (gowns, gloves, booties) and were cohorted geographically and to 1:1 nursing and nurse aid staff.

Results

A total of 6,684 samples belonging to 3,383 patients were processed (1.9 samples/patient). Two hundred thirty (3.44%) had carbapenem-resistant Enterobacteriaceae, although only 33 isolates (0.49%) were confirmed as either KPC (n = 31) or NDM (n = 2) positive. Out of the 3,383 patients tested, 121 were identified as carriers of carbapenem-resistant isolates but only 11 (0.32%) were CPE (KPC = 11; NDM = 2). The incidence of new CPE patients during 2016 was 0.82% but decreased to 0.28% and 0.33% in 2017 and 2018, respectively. The units with the highest number of CPE patients were the transplant intensive care unit (n = 6) and the step-down SOT unit (n = 3). Negative cultures were quoted at $8.49 per sample but culture plates with colonies increased the cost per test to $28.44. The total cost for all the 6,684 screening tests was calculated at $61,335. The cost of CPE screening per positive CPE patient identified comes up to $5,575 (not including RN collection time).

Conclusion

In an institution with staff and CPE patient cohorting, active screening of CPE positive patients was relatively expensive given our low -level of transmission. In the near future, we plan to stop staff and patient cohorting due to the high stress that these interventions place on our hospital staff. This might ensue in increase transmission, which will be detected by CPE screening tests.

Disclosures

All authors: No reported disclosures.

2339. Clostridioides difficile: Impact of Active Screening of Asymptomatic Carriers and Testing Stewardship

Background

We recently implemented a hospital-wide C. difficile testing algorithm and screening/isolation of C. difficile asymptomatic carriers primarily in heme-onc units. We aim to evaluate the impact of these interventions on the epidemiology of C. difficile + tests.

Methods

This retrospective cohort was performed in a 600-bed hospital in Milwaukee, WI, from January 1, 2016 to March 31, 2019. All clinical C. difficile tests included nucleic acid amplification (NAAT; Xpert C. difficile, Cepheid). On February 2017, all NAAT+ tests had toxin (tox) checked (Quick check complete, Alere). Testing algorithm (Figure 1) started mid 2016 until now. Screening phases included: Phase 1 (September 2016–May 2017): C. difficile screening cultures shared with units but not placed in electronic medical records (EMR). Patients + placed on enteric precautions (gown, gloves, hand hygiene). Phase 2 (May 2017–January 2018): C. difficile screening (NAAT) performed on admission and weekly thereafter, results placed in EMR, NAAT+ patients placed on enteric precautions. Phase 3 (January 2018–present): C. difficile screening (NAAT) on admission, results placed in EMR, NAAT+ patients placed on enteric precautions. Federal reporting changed to only reporting NAAT+tox+. Tests (NAAT+, NAAT+tox+, and NAAT+tox-) were analyzed using Poisson regression offsetting for log of patient-days using SAS, v9.4.

Results

Hospital-wide C. difficile tests decreased from 21 to 10.9 tests per 1,000 patient-days (P < 0.0001; Figure 2). This effect was seen in heme-onc units (41 to 15.7; P < 0.0001; Figure 3) and in all other units (18.9 to 9.9; P < 0.0001). All NAAT+ results decreased from 2.99 to 1.94 per 1,000 patient-days hospital wide (P < 0.0001) but remained unchanged in heme-onc units (4.6 to 3.7, P > 0.05). NAAT+tox+ results remained unchanged hospital wide and in heme-onc units (0.8 to 0.7 and 1.1 to 1.2, respectively; both P > 0.05); however, the frequency of NAAT+tox− tests decreased hospital wide (1.8 to 1.3; P = 0.0003) and in heme-onc units (3.8 to 2.4; P = 0.05).

Conclusion

A C. difficile testing algorithm was successful decreasing the number of C. difficile tests performed and had a hospital-wide reduction of NAAT+tox− tests. The rate of NAAT+tox+ cases in heme-onc units and hospital wide remained unchanged despite active screening and isolation in selected units.

Disclosures

All authors: No reported disclosures.

2399. Ribotype Diversity of Clostridioides difficile strains obtained during screening tests

Background

Clostridioides difficile is an organism acquired not only in healthcare settings but also in community settings. For the past several years our hospital has performed screening tests to detect asymptomatic carriage of C. difficile. We now aim to better understand the ribotypes and degree of diversity among these C. difficile strains obtained in a systematic screening.

Methods

This study was performed at a 600 bed teaching affiliated hospital in Milwaukee, WI, where surveillance testing is performed in selected units upon admission and weekly thereafter using nucleic acid amplification test (NAAT; Xpert® C. difficile; Cepheid, Sunnyvale, CA). Screening tests are obtained regardless of symptoms. NAAT positive samples underwent anaerobic cultures in C. difficile selective broth (CCMB-TAL) for 24–48 hr and then to Brucella blood agar plates (BA) for 48–72 hr to confirm C. difficile presence. PCR-ribotyping was performed as previously described by Stubbs et al. with minor modifications. The results were compared with a database containing >3,000 clinical isolates including C. difficile reference strains from the Cardiff ribotype collection.

Results

A total of 104 strains belonging to 93 unique patients were processed. Patients had a mean age of 60 years (range: 18 - 89) and 49% were females. Most patients were hospitalized in the hematology oncology units (55.7%) or in the solid-organ transplant step down unit (9.6%). A total of 25 different ribotypes were identified. The most common ribotype was 014/020 (23; 22%), followed by ribotype 56 (13; 12.5%), 106 (12; 11.5%), 027 (11; 10.5%), 002 (6; 5.7%), and 078/126 (5; 4.81).

Regarding the timing of admission, 70 strains were obtained within 4 days from hospital admission and the remaining 34 were obtained afterwards. Both groups had ribotype 014/020 as the most frequently detected ribotype but 027 were the second most commonly detected at the time of admission (table). A total of 7 patients had more than one stool sample processed and 5 of them had discordant ribotypes at different time points.

Conclusion

Systematic screening tests for C. difficile carriage in a single center showed a large heterogeneity of ribotypes with the majority not being 027. Additionally, most patients tested more than once carried different ribotypes.

Disclosures

All authors: No reported disclosures.

Multicenter Study Demonstrates Standardization Requirements for Mold Identification by MALDI-TOF MS

Objectives

Rapid and accurate mold identification is critical for guiding therapy for mold infections. MALDI-TOF MS has been widely adopted for bacterial and yeast identification; however, few clinical laboratories have applied this technology for routine mold identification due to limited database availability and lack of standardized processes. Here, we evaluated the versatility of the NIH Mold Database in a multicenter evaluation.

Methods

The NIH Mold Database was evaluated by eight US academic centers using a solid media extraction method and a challenge set of 80 clinical mold isolates. Multiple instrument parameters important for spectra optimization were evaluated, leading to the development of two specialized acquisition programs (NIH method and the Alternate-B method).

Results

A wide range in performance (33–77%) was initially observed across the eight centers when routine spectral acquisition parameters were applied. Use of the NIH or the Alternate-B specialized acquisition programs, which are different than those used routinely for bacterial and yeast spectral acquisition (MBT_AutoX), in combination with optimized instrument maintenance, improved performance, illustrating that acquisition parameters may be one of the key limiting variable in achieving successful performance.

Conclusion

Successful mold identification using the NIH Database for MALDI-TOF MS on Biotyper systems was demonstrated across multiple institutions for the first time following identification of critical program parameters combined with instrument optimization. This significantly advances our potential to implement MALDI-TOF MS for mold identification across many institutions. Because instrument variability is inevitable, development of an instrument performance standard specific for mold spectral acquisition is suggested to improve reproducibility across instruments.

The relevance of sink proximity to toilets on the detection of Klebsiella pneumoniae carbapenemase inside sink drains

We report a higher prevalence of bla_KPC in patient room sink drains located next to toilets (87.0%) when compared with sink drains located farther away from toilets (21.7%) using direct polymerase chain reaction assay. However, culture methods were only able to recover bla_KPC-positive isolates from 16% of polymerase chain reaction-positive drains.

Multicenter evaluation of the Alere™ i influenza A&B assay using respiratory specimens collected in viral transport media

Rapid and accurate detection of influenza virus is critical for proper patient management. The Alere™ i Influenza A&B assay is an isothermal nucleic acid amplification test capable of detecting influenza A and B viruses directly from respiratory specimens. In this multicenter clinical trial conducted in the US, we evaluated the clinical performance of the Alere™ i Influenza A&B assay against that of the Prodesse ProFlu+ assay. A total of 1243 fresh, leftover nasal or nasopharyngeal swabs eluted in viral transport medium were tested by both assays. Sensitivity and specificity of the Alere™ i Influenza A&B assay were 97.8% (95% CI 94.6-99.2) and 96.6% (95% CI 95.2-97.5) for influenza A and 92.9% (95% CI 85.5-96.9) and 98.3% (95% CI 97.4-98.0) for influenza B. The Alere™ i Influenza A&B assay is an ideal molecular assay for influenza virus detection due to its high sensitivity and specificity with minimal hands-on and turn-around-time.

Effective utilization of C. difficile PCR and identification of clinicopathologic factors associated with conversion to a positive result in symptomatic patients

OBJECTIVES

We assess the diagnostic yield of repeat testing for C. difficile using molecular methods within 7days of a negative test and identify specific factors associated with conversion from negative to positive test result within a 7-day period to aid in selective test utilization.

METHODS

A retrospective chart review of 20,866 laboratory test orders for C. difficile PCR was conducted. The test result, clinicopathologic patient features, and previous test results were recorded. Univariate and multivariate analysis was conducted to compare patients with initial and repeat negative results (n=248) to a group of patients with conversion from negative to positive results within 7days.

RESULTS

Univariate analysis demonstrated a history of C. difficile infection, receipt of antibiotics within 14days, and duration of hospital stay as factors significantly different between patients with repeat negative and conversion to positive C. difficile test result. Only history of C. difficile infection was significantly different upon multivariate analysis.

CONCLUSIONS

Identification of prior C. difficile infection as the only factor significantly correlated with conversion from negative to positive C. difficile test result within 7days aids in selective test utilization and reduces the costs associated with unnecessary laboratory testing.

A Novel Protocol Obviates Endoscope Sampling for Carbapenem-Resistant Enterobacteriaceae: Experience of a Center with a Prior Outbreak

BACKGROUND

Numerous published outbreaks, including one from our institution, have described endoscope-associated transmission of multidrug-resistant organisms (MDROs). Individual centers have adopted their own protocols to address this issue, including endoscope culture and sequestration. Endoscope culturing has drawbacks and may allow residual bacteria, including MDROs, to go undetected after high-level disinfection.

AIM

To report the outcome of our novel protocol, which does not utilize endoscope culturing, to address our outbreak.

METHODS

All patients undergoing procedures with elevator-containing endoscopes were asked to permit performance of a rectal swab. All endoscopes underwent high-level disinfection according to updated manufacturer's guidance. Additionally, ethylene oxide (EtO) sterilization was done in the high-risk settings of (1) positive response to a pre-procedure risk stratification questionnaire, (2) positive or indeterminate CRE polymerase chain reaction (PCR) from rectal swab, (3) refusal to consent for PCR or questionnaire, (4) purulent cholangitis or infected pancreatic fluid collections. Two endoscopes per weekend were sterilized on a rotational basis.

RESULTS

From September 1, 2015 to April 30, 2016, 556 endoscopy sessions were performed using elevator-containing endoscopes. Prompted EtO sterilization was done on 46 (8.3%) instances, 3 from positive/indeterminate PCR tests out of 530 samples (0.6%). No CRE transmission was observed during the study period. Damage or altered performance of endoscopes related to EtO was not observed.

CONCLUSION

In this pilot study, prompted EtO sterilization in high-risk patients has thus far eliminated endoscope-associated MDRO transmission, although no CRE infections were noted throughout the institution during the study period. Further studies and a larger patient sample will be required to validate these findings.

Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts

OBJECTIVES

A report on the multicenter evaluation of the Bruker MALDI Biotyper CA System (MBT-CA; Bruker Daltonics, Billerica, MA) for the identification of clinically important bacteria and yeasts.

METHODS

In total, 4,399 isolates of medically important bacteria and yeasts were assessed in the MBT-CA. These included 2,262 aerobic gram-positive (AGP) bacteria, 792 aerobic gram-negative (AGN) bacteria 530 anaerobic (AnA) bacteria, and 815 yeasts (YSTs). Three processing methods were assesed.

RESULTS

Overall, 98.4% (4,329/4,399) of all bacterial and yeast isolates were correctly identified to the genus and species/species complex level, and 95.7% of isolates were identified with a high degree of confidence. The percentage correctly identified and the percentage identified correctly with a high level of confidence, respectively, were as follows: AGP bacteria (98.6%/96.5%), AGN bacteria (98.5%/96.8%), AnA bacteria (98.5%/97.4%), and YSTs (97.8%/87.6%). The extended direct transfer method was only minimally superior to the direct transfer method for bacteria (89.9% vs 86.8%, respectively) but significantly superior for yeast isolates (74.0% vs 48.9%, respectively).

CONCLUSIONS

The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization.

Multicenter Evaluation of MRSASelect II Chromogenic Agar for Identification of Methicillin-Resistant Staphylococcus aureus from Wound and Nasal Specimens

Hospitals strive to reduce methicillin-resistant Staphylococcus aureus (MRSA) prevalence via active surveillance of inpatient populations. Rapid and inexpensive screening methods are utilized when molecular methods are not operationally feasible. In this multisite clinical trial, the utility of Bio-Rad's MRSASelect II was evaluated for MRSA identification from remnant nares and wound swabs. The prevalence of MRSA was 11.1% (n = 1,384) from nares samples and 18.1% (n = 842) from wound samples. MRSASelect II had an overall concordance of 95.4% (confidence interval [CI] = 94.5% to 96.2%) compared to a broth-enriched reference standard. Comparisons between results, stratified by examination times, exhibited a nonsignificant trend toward increased positivity at prolonged incubation times. Cefoxitin screening of colonies directly from MRSASelect II was 96.7% (95.8% to 97.3%) concordant compared to testing of colonies following broth enrichment. A comparison of MRSASelect and MRSASelect II revealed no statistical differences; however, the latter exhibited earlier positivity, greater selectivity, and more intense indicator staining, which resulted in facilitated differentiation of positive results. MRSASelect II agar is a simple, rapid, and robust method to routinely screen patients for MRSA colonization without the need for additional testing.

Detection of multi-drug resistant Escherichia coli in the urban waterways of Milwaukee, WI

Urban waterways represent a natural reservoir of antibiotic resistance which may provide a source of transferable genetic elements to human commensal bacteria and pathogens. The objective of this study was to evaluate antibiotic resistance of Escherichia coli isolated from the urban waterways of Milwaukee, WI compared to those from Milwaukee sewage and a clinical setting in Milwaukee. Antibiotics covering 10 different families were utilized to determine the phenotypic antibiotic resistance for all 259 E. coli isolates. All obtained isolates were determined to be multi-drug resistant. The E. coli isolates were also screened for the presence of the genetic determinants of resistance including ermB (macrolide resistance), tet(M) (tetracycline resistance), and β-lactamases (bla OXA, bla SHV, and bla PSE). E. coli from urban waterways showed a greater incidence of antibiotic resistance to 8 of 17 antibiotics tested compared to human derived sources. These E. coli isolates also demonstrated a greater incidence of resistance to higher numbers of antibiotics compared to the human derived isolates. The urban waterways demonstrated a greater abundance of isolates with co-occurrence of antibiotic resistance than human derived sources. When screened for five different antibiotic resistance genes conferring macrolide, tetracycline, and β-lactam resistance, clinical E. coli isolates were more likely to harbor ermB and bla OXA than isolates from urban waterway. These results indicate that Milwaukee's urban waterways may select or allow for a greater incidence of multiple antibiotic resistance organisms and likely harbor a different antibiotic resistance gene pool than clinical sources. The implications of this study are significant to understanding the presence of resistance in urban freshwater environments by supporting the idea that sediment from urban waterways serves as a reservoir of antibiotic resistance.

Implementation of Polymerase Chain Reaction to Rule Out Clostridium difficile Infection Is Associated With Reduced Empiric Antibiotic Duration of Therapy

PURPOSE

The polymerase chain reaction (PCR) test has higher sensitivity and a faster turnaround time than the enzyme immunoassay (EIA) for identification of Clostridium difficile, although the clinical implications of these variables are not well described.

METHODS

Inpatients with a negative EIA (n = 79) or PCR (n = 87) test were retrospectively evaluated. Patients were excluded if they had a positive EIA or PCR test during the same hospitalization or if they were currently receiving treatment for C. difficile infection (CDI) prior to admission. The primary outcome was empiric CDI antibiotic duration of therapy associated with each test method.

RESULTS

Empiric CDI antibiotic duration of therapy was 2.31 (95% confidence interval [CI], 1.48-3.15) days for the EIA group and 0.88 (0.45-1.33) days for the PCR group (P = .007). Number of diagnostic laboratory tests performed per patient were 2.73 (2.64-2.83) and 1.16 (1.04-1.28) tests, respectively (P < .001).

CONCLUSION

Use of the PCR test to rule out CDI was associated with reduced duration of empiric CDI antibiotic therapy and fewer diagnostic laboratory tests performed per patient. When combined with fewer diagnostic laboratory tests performed per patient and shorter duration of contact isolation, the higher acquisition cost of the PCR test was offset, resulting in cost neutrality. These findings provide additional data to support the routine use of the PCR test.

Antimicrobial activity of ceftaroline and other anti-infective agents against microbial pathogens recovered from the surgical intensive care patient population: a prevalence analysis

BACKGROUND

Ceftaroline is a new parenteral cephalosporin agent with excellent activity against methicillin-sensitive (MSSA) and resistant strains of Staphylococcus aureus (MRSA). Critically ill surgical patients are susceptible to infection, often by multi-drug-resistant pathogens. The activity of ceftaroline against such pathogens has not been described.

METHODS

Three hundred thirty-five consecutive microbial isolates were collected from surgical wounds or abscesses, respiratory, urine, and blood cultures from patients in the surgical intensive care unit (SICU) of a major tertiary medical center. Using Clinical and Laboratory Standards Institute (CLSI) standard methodology and published breakpoints, all aerobic, facultative anaerobic isolates were tested against ceftaroline and selected comparative antimicrobial agents.

RESULTS

All staphylococcal isolates were susceptible to ceftaroline at a breakpoint of ≤1.0 mcg/mL. In addition, ceftaroline exhibited excellent activity against all streptococcal clinical isolates and non-ESBL-producing strains of Enterobacteriaceae (93.5%) recovered from SICU patients. Ceftaroline was inactive against ESBL-producing Enterobacteriaceae, Pseudomonas aeruginosa, vancomycin-resistant enterococci, and selective gram-negative anaerobic bacteria.

CONCLUSIONS

At present, ceftaroline is the only cephalosporin agent that is active against community and healthcare-associated MRSA. Further studies are needed to validate the benefit of this novel broad-spectrum anti-infective agent for the treatment of susceptible serious infections in the SICU patient population.

Comparison of MALDI-TOF MS with HPLC and nucleic acid sequencing for the identification of Mycobacterium species in cultures using solid medium and broth

OBJECTIVES

The genus Mycobacterium contains over 150 species including pathogenic and nonpathogenic strains. Accurate species level identification can aid in differentiating environmental contamination from true infection, and also can aid in selection of antimicrobial therapy.

METHODS

We evaluated the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the routine identification of clinical isolates of mycobacteria using 2 commercially available spectral reference libraries, and also assessed the impact of mycobacterial culture using solid medium and broth on MALDI-TOF MS-based identification.

RESULTS

All results were compared with those obtained on high-pressure liquid chromatography and nucleic acid sequencing. Optimal results were obtained with a mycobacterium-specific reference library (Mycobacterium Library v1.0). The identification rate was 89.8% (79/88) for isolates cultured on solid medium and 98.8% (85/86) for isolates analyzed directly from broth. Among these, the proportion identified with a high confidence level was 50.0% (44/88) for isolates cultured on solid medium and 80.2% (69/86) for isolates cultured in broth.

CONCLUSIONS

Agreement with nucleic acid sequencing for species present in Mycobacterium Library v1.0 was 97.6% (81/83) for isolates cultured on solid medium and 97.5% (79/81) for those cultured in broth.

Comparison of BD Phoenix and bioMérieux Vitek 2 automated systems for the detection of macrolide-lincosamide-streptogramin B resistance among clinical isolates of Staphylococcus

Two automated systems, BD Phoenix and bioMérieux Vitek 2, were compared to a double-disk diffusion method for the detection of inducible resistance to clindamycin in Staphylococcus spp. Analysis of 524 clinical isolates revealed sensitivity and specificity of 100% and 99.6%, respectively, for Phoenix and 91.1% and 99.8%, respectively, for Vitek 2.

Evaluation of a microarray-based genotyping assay for the rapid detection of cytochrome P450 2C19 *2 and *3 polymorphisms from whole blood using nanoparticle probes

Numerous drugs such as clopidogrel have been developed to reduce coagulation or inhibit platelet function. The hepatic cytochrome P450 (CYP) pathway is involved in the conversion of clopidogrel to its active metabolite. A recent black-box warning was included in the clopidogrel package insert indicating a significant clinical link between specific CYP2C19 genetic variants and poor metabolism of clopidogrel. Of these variants, *2 and *3 are the most common and are associated with complete loss of enzyme activity. In patients who are carriers of a CYP2C19 *2 or *3 allele, the conversion of clopidogrel to its active metabolite may be reduced, which can lead to ischemic events and negative consequence for the patient. We examined the ability of the Verigene CLO assay (Nanosphere, Northbrook, IL) to identify CYP2C19 *2 and *3 polymorphisms in 1,286 unique whole blood samples. The Verigene CLO assay accurately identified homozygous and heterozygous *2 and *3 phenotypes with a specificity of 100% and a final call rate of 99.7%. The assay is fully automated and can produce a result in approximately 3.5 hours.

Identification of two borderline oxacillin-resistant strains of Staphylococcus aureus from routine nares swab specimens by one of three chromogenic agars evaluated for the detection of MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of nosocomial infections that result in extended hospital stays and increased mortality. Therefore, rapid, cost-effective techniques for surveillance and detection of MRSA are critical to the containment and prevention of the spread of MRSA within the health care environment. We examined the ability of 3 chromogenic media (Spectra MRSA, Remel, Lenexa, KS; MRSA Select, Bio-Rad, Redmond, WA; and ChromID MRSA, bioMerieux, Marcy l'Etoile, France) to detect MRSA from routine surveillance specimens following 18, 24, and 48 hours of incubation. Our results indicate that detection of MRSA using all 3 chromogenic media is optimal following 24 hours of incubation. Early examination reduced sensitivity, while extended incubation reduced specificity. In addition, Spectra MRSA identified 2 borderline oxacillin-resistant strains of S aureus that were not detected by the other 2 chromogenic agars evaluated. These strains demonstrate increased basal and inducible resistance to β-lactam antibiotics.

Epidemiologic Observations from Passive and Targeted Surveillance during the First Wave of the 2009 H1N1 Influenza Pandemic in Milwaukee, WI

The first wave of the 2009 influenza H1N1 pandemic (H1N1pdm) in Milwaukee, WI has been recognized as the largest reported regional outbreak in the United States. The epidemiologic and clinical characteristics of this large first wave outbreak from April 28(th) 2009-July 25(th) 2009, studied using both passive and targeted surveillance methodologies are presented. A total of 2791 individuals with H1N1pdm infection were identified; 60 % were 5-18 years old. The 5-18 year and 0-4 year age groups had high infection (1131 and 1101 per 100,000) and hospitalization (49 and 12 per 100,000) rates respectively. Non-Hispanic blacks and Hispanics had the highest hospitalization and infection rates. In targeted surveillance, infected patients had fever (78%), cough (80%), sore throat (38%), and vomiting or diarrhea (8%). The "influenza like illness" definition captured only 68 % of infected patients. Modeling estimates that 10.3 % of Milwaukee population was infected in the first wave and 59% were asymptomatic. The distinct epidemiologic profile of H1N1pdm infections observed in the study has direct implications for predicting the burden of infection and hospitalization in the next waves of H1N1pdm. Careful consideration of demographic predictors of infection and hospitalization with H1N1pdm will be important for effective preparedness for subsequent influenza seasons.

Introduction of a Novel Swine-Origin Influenza A (H1N1) Virus into Milwaukee, Wisconsin in 2009

On 17 April 2009, novel swine origin influenza A virus (S-OIV) cases appeared within the United States. Most influenza A diagnostic assays currently utilized in local clinical laboratories do not allow definitive subtype determination. Detailed subtype analysis of influenza A positive samples in our laboratory allowed early confirmation of a large outbreak of S-OIV in southeastern Wisconsin (SEW). The initial case of S-OIV in SEW was detected on 28 April 2009. All influenza A samples obtained during the 16 week period prior to 28 April 2009, and the first four weeks of the subsequent epidemic were sub typed. Four different multiplex assays were employed, utilizing real time PCR and end point PCR to fully subtype human and animal influenza viral components. Specific detection of S-OIV was developed within days. Data regarding patient demographics and other concurrently circulating viruses were analyzed. During the first four weeks of the epidemic, 679 of 3726 (18.2%) adults and children tested for influenza A were identified with S-OIV infection. Thirteen patients (0.34%) tested positive for seasonal human subtypes of influenza A during the first two weeks and none in the subsequent 2 weeks of the epidemic. Parainfluenza viruses were the most prevalent seasonal viral agents circulating during the epidemic (of those tested), with detection rates of 12% followed by influenza B and RSV at 1.9% and 0.9% respectively. S-OIV was confirmed on day 2 of instituting subtype testing and within 4 days of report of national cases of S-OIV. Novel surge capacity diagnostic infrastructure exists in many specialty and research laboratories around the world. The capacity for broader influenza A sub typing at the local laboratory level allows timely and accurate detection of novel strains as they emerge in the community, despite the presence of other circulating viruses producing identical illness. This is likely to become increasingly important given the need for appropriate subtype driven anti-viral therapy and the potential shortage of such medications in a large epidemic.

Linezolid for the treatment of drug-resistant infections

Multidrug-resistant pathogens have become increasingly common in contemporary healthcare. Specific to Gram-positive pathogens, methicillin-resistant Staphylococcus aureus (MRSA) is of particular concern, as it has been associated with increased hospital length of stay, higher healthcare expenditures and poorer outcomes. To date, linezolid is the first and only oxazolidinone approved by the US FDA for the treatment of infections caused by Gram-positive pathogens, including MRSA. This article will serve as a comprehensive review of linezolid, including an overview of the current market and its in vitro activity, with an in-depth review of its pharmacokinetic and pharmacodynamic profile. Emphasis will be placed on clinical data for the drug, both on- and off-label. The article will conclude with a brief overview of linezolid's pharmacoeconomic implications and safety profile, followed by a commentary and 5-year prospective analysis remarking on the future of the antimicrobial field as it relates to MRSA.

A new chromogenic agar medium, chromID VRE, to screen for vancomycin-resistant Enterococcus faecium and Enterococcus faecalis

We compared the performance of a chromogenic agar medium chromID VRE (bioMérieux, Marcy-l'Etoile, France) designed to recover and identify vancomycin-resistant enterococci (VRE) from clinical specimens with bile esculin azide vancomycin (BEAV) agar. For this study, 120 stool specimens were plated on chromID VRE and BEAV and examined after 24 and 48 h. At 24 h, the sensitivity and specificity were as follows: BEAV, 90.2% and 73%, respectively; chromID VRE, 86.3% and 100.0%, respectively. Furthermore, we determined that the sensitivity and specificity of chromID VRE for Enterococcus faecium were 85.4% and 100%, respectively, and for Enterococcus faecalis, 90% and 100%, respectively. We conclude that chromID VRE provides an equivalent sensitivity for the recovery of VRE from stool specimens, with improved specificity, and the added advantage of providing differentiation between vancomycin-resistant E. faecium and E. faecalis.

Tigecycline for Treatment of Pneumonia and Empyema Caused by Carbapenemase-ProducingKlebsiella pneumoniae

Strains of Klebsiella pneumoniae that produce one of three possible carbapenemases--KPC--have recently been identified with increasing frequency among isolates recovered from patients residing along the East Coast of the United States, particularly within the New York City metropolitan region. These strains have exhibited resistance to multiple antibiotic classes, including carbapenem agents. We report a case of nosocomial pneumonia and empyema caused by a KPC-producing isolate of K. pneumoniae at a large midwestern U.S. tertiary care facility in which the patient was treated with tigecycline. Although the pneumonia was treated successfully, the empyema recurred in association with a treatment-emergent tigecycline minimum inhibitory concentration (MIC) increase from 0.75 to 2 microg/ml. Clinicians should be aware of the potential occurrence of this treatment-emergent MIC increase, especially in the setting of sustained tigecycline therapy. In addition, the emergence of carbapenem-resistant Enterobacteriaceae reinforces the importance of antibiotic stewardship and strict infection control practices.

Evaluation of a novel chromogenic agar medium for isolation and differentiation of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis isolates

The development of reliable and rapid methods for the identification of patients colonized with vancomycin-resistant enterococci (VRE) is central to the containment of this agent within a hospital environment. To this end, we evaluated a prototype chromogenic agar medium (VRE-BMX; bioMérieux, Marcy l'Etoile, France) used to recover VRE from clinical specimens. This medium can also identify isolated colonies as either vancomycin-resistant Enterococcus faecium or Enterococcus faecalis, based on distinct colony colors. We compared the performance of VRE-BMX with bile esculin azide agar supplemented with vancomycin (BEAV). For this study, 147 stool samples were plated on each test medium and examined after 24 and 48 h of incubation. At 24 h, the sensitivity and specificity of each medium were as follows: BEAV, 90.9% and 89.9%, respectively; VRE-BMX, 96.4% and 96.6%, respectively. The positive predictive values (PPV) of VRE-BMX and BEAV at 24 h were 89.8% and 80.7%, respectively. VRE-BMX provided the identification of 10 isolates of vancomycin-resistant E. faecalis and 4 isolates of vancomycin-resistant E. faecium that were not recovered by BEAV. Further, VRE-BMX was capable of identifying patients colonized with both E. faecium and E. faecalis, a feature useful for infection control purposes that is not a function of BEAV. In terms of the recovery of vancomycin-resistant E. faecium and E. faecalis, the sensitivity and PPV were as follows: BEAV, 75.7% and 74.6%, respectively; VRE-BMX, 95.5% and 91.3%, respectively. In this initial evaluation, we found that VRE-BMX provided improved recovery of VRE from stool specimens, with the added advantage of being able to differentiate between vancomycin-resistant E. faecalis and E. faecium. Extending the incubation period beyond 24 h did not significantly improve the recovery of VRE and resulted in decreased specificity.

Salmonella enterica serovar Typhimurium requires the Lpf, Pef, and Tafi fimbriae for biofilm formation on HEp-2 tissue culture cells and chicken intestinal epithelium

Recent work has demonstrated that Salmonella enterica serovar Typhimurium forms biofilms on HEp-2 tissue culture cells in a type 1 fimbria-dependent manner. To investigate how biofilm growth of HEp-2 tissue culture cells affects gene expression in Salmonella, we compared global gene expression during planktonic growth and biofilm growth. Microarray results indicated that the transcription of approximately 100 genes was substantially altered by growth in a biofilm. These genes encode proteins with a wide range of functions, including antibiotic resistance, central metabolism, conjugation, intracellular survival, membrane transport, regulation, and fimbrial biosynthesis. The identification of five fimbrial gene clusters was of particular interest, as we have demonstrated that type 1 fimbriae are required for biofilm formation on HEp-2 cells and murine intestinal epithelium. Mutations in each of these fimbriae were constructed in S. enterica serovar Typhimurium strain BJ2710, and the mutants were found to have various biofilm phenotypes on plastic, HEp-2 cells, and chicken intestinal tissue. The pef and csg mutants were defective for biofilm formation on each of the three surfaces tested, while the lpf mutant exhibited a complete loss of the ability to form a biofilm on chicken intestinal tissue but only an intermediate loss of the ability to form a biofilm on tissue culture cells and plastic surfaces. The bcf mutant displayed increased biofilm formation on both HEp-2 cells and chicken intestinal epithelium, while the sth mutant had no detectable biofilm defects. In all instances, the mutants could be restored to a wild-type phenotype by a plasmid carrying the functional genes. This is the first work to identify the genomic responses of Salmonella to biofilm formation on host cells, and this work highlights the importance of fimbriae in adhering to and adapting to a eukaryotic cell surface. An understanding of these interactions is likely to provide new insights for intervention strategies in Salmonella colonization and infection.

Exopolysaccharide sugars contribute to biofilm formation by Salmonella enterica serovar typhimurium on HEp-2 cells and chicken intestinal epithelium

Recently, we demonstrated that Salmonella enterica serovar Typhimurium can form biofilm on HEp-2 cells in a type 1 fimbria-dependent manner. Previous work on Salmonella exopolysaccharide (EPS) in biofilm indicated that the EPS composition can vary based upon the substratum on which the bacterial biofilm forms. We have investigated the role of genes important in the production of colanic acid and cellulose, common components of EPS. A mutation in the colanic acid biosynthetic gene, wcaM, was introduced into S. enterica serovar Typhimurium strain BJ2710 and was found to disrupt biofilm formation on HEp-2 cells and chicken intestinal tissue, although biofilm formation on a plastic surface was unaffected. Complementation of the wcaM mutant with the functional gene restored the biofilm phenotype observed in the parent strain. A mutation in the putative cellulose biosynthetic gene, yhjN, was found to disrupt biofilm formation on HEp-2 cells and chicken intestinal epithelium, as well as on a plastic surface. Our data indicate that Salmonella attachment to, and growth on, eukaryotic cells represent complex interactions that are facilitated by species of EPS.