Comparison of the Simplexa GBS Direct and ARIES GBS assays for the detection of S. agalactiae in broth-enriched swab specimens

We conducted a comparative evaluation of the FDA-cleared Simplexa GBS Direct and ARIES GBS molecular assays for the detection of Streptococcus agalactiae (Group B Streptococcus, GBS) in 386 prospectively collected, broth-enriched vaginal/rectal swab specimens. The sensitivity of each test was 96.2% and specificity was ≥98.7% when compared to a combined direct and enriched culture method using chromogenic culture medium. A total of four specimens were called positive by both molecular assays but negative by culture, likely representing specimens with a low burden of GBS in these specimens. Two specimens were reported positive by culture but negative by both molecular assays. One of these specimens demonstrated atypically colored colonies on chromogenic agar; the other yielded typically colored colonies only observed after broth enrichment. Our data demonstrate equivalent performance of Simplexa and ARIES molecular assays for the detection of GBS in clinical specimens.IMPORTANCEClinical laboratories often face decisions regarding which of the multiple available molecular platforms would best fit their needs based on cost, workflow, menu, and diagnostic performance. Therefore, objective clinical comparisons of similar molecular tests are valuable resources to aid these decisions. We provide a clinical comparison of two FDA-cleared tests to routine culture and to each other that can be used by clinical laboratories when determining which of the available molecular platforms would best fit their laboratory in terms of workflow, cost, and performance.

Multiplexed high-definition PCR assay for the diagnosis of tick-borne infections in children

Background

Ixodes scapularis ticks can carry Borrelia species as well as other pathogens that cause human disease. The frequency of tick-borne infections and co-infections in children with suspected Lyme disease is unknown, creating clinical uncertainty about the optimal approach to diagnosis.

Methods

We enrolled children aged 1 to 21 years presenting to one of eight Pedi Lyme Net emergency departments for evaluation of Lyme disease. We selected cases with serologically or clinically diagnosed Lyme disease (erythema migrans or early neurologic disease) matched by symptoms, age, gender and center to control subjects without Lyme disease. We tested whole blood samples collected at the time of diagnosis using a high-definition multiplex polymerase chain reaction (HDPCR) panel to identify 9 bacterial or protozoan pathogens associated with human disease. We compared the frequency of tick-borne co-infections in children with Lyme disease to matched controls.

Results

Of the 612 selected samples, 594 (97.1%) had an interpretable multiplex HDPCR result. We identified the following non-Borrelia tick-borne infections: Anaplasma phagocytophilum (2), Ehrlichia chaffeensis (1) and Babesia microti (12). Children with Lyme disease were more likely to have another tick-borne pathogen identified than matched controls [15/297 (5.1%) Lyme cases vs. 0/297 (0%); difference 5.1% 95% CI 2.7, 8.2%).

Conclusions

Although a substantial minority of children with Lyme disease had another tick-borne pathogen identified, either first-line Lyme disease antibiotics provided adequate treatment or the coinfection was subclinical and did not require specific treatment. Further studies are needed to establish the optimal approach to testing for tick-borne co-infections in children.

539. Impact of a Rapid Diagnostic Assay for the Detection of Bacterial and Viral Agents on Antimicrobial use in Critically Ill Patients with Pneumonia

Background

Conventional diagnostic methods for pneumonia have a long turnaround time, and a pathogen is isolated in only 33% of cases. As a result, empiric therapy with broad-spectrum antimicrobials often becomes definitive therapy. Rapid molecular diagnostics paired with antimicrobial stewardship intervention have the potential to improve outcomes for patients with lower respiratory tract infections (LRTIs). However, data to support this hypothesis are scarce. This study examined the influence of a rapid multiplex polymerase-chain-reaction (PCR) test on antimicrobial use in critically ill patients with LRTIs.

Methods

This single-center study consisted of pre-implementation (PrIP, December 1, 2018, to February 28, 2019) and post-implementation periods (PoIP, December 1, 2021, to February 28, 2022). Both groups included intensive-care unit (ICU) patients with respiratory cultures from bronchoalveolar lavage (BAL), mini-BAL, or tracheal aspirates. Interventions during the PoIP included concurrent testing of specimens with the BioFire® Pneumonia Panel and clinical decision support tools to streamline treatment recommendations from ICU pharmacists. The primary outcome was the difference in time to optimal therapy (TTOT). Secondary outcomes included time to effective therapy (TTET) and duration of therapy (DOT) for antipseudomonal and anti-MRSA agents.

Results

A total of 163 patients were included (n = 80, PrIP; n = 83, PoIP). The mean age was 57 + 16 years, and medical ICU patients accounted for 60% (n = 97) of cases. The median APACHE II score was the only significant baseline difference between the two arms (22 vs. 18, interquartile range [IQR] 16, 28 vs. 12, 25, p = 0.01). The median TTOT was 38 hours in the PrIP and 21 hours in the PoIP (p < 0.001). TTET was 5.7 hours in the PrIP and 4.9 hours in the PoIP (p = 0.106). The median DOT for antipseudomonal agents decreased by 52% (4.4 days in the PrIP and 2.1 days in the PoIP, p < 0.001), and anti-MRSA agent DOT was 53% shorter in the PoIP (1.9 days vs. 0.9 days, p < 0.001).

Conclusion

Implementation of a rapid multiplex PCR panel for lower respiratory-tract pathogens significantly reduced the time to optimal therapy in critically ill patients with pneumonia. Clinically meaningful reductions in anti-MRSA and anti-pseudomonal agent duration were also noted.

Disclosures

Blake W. Buchan, PhD, Accelerate: Advisor/Consultant|Accelerate: Honoraria|BioFire: Honoraria|ChromaCode: Advisor/Consultant|ChromaCode: Honoraria|Pattern: Advisor/Consultant|Pattern: Honoraria.

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.

Molecular Diagnosis of Pneumonia (Including Multiplex Panels)

Background

Pneumonia is a common illness, accounting for a staggering amount of worldwide morbidity and mortality. The diagnosis of pneumonia is challenging given the variety of responsible pathogens. Diagnostic testing for bacterial pneumonia has traditionally relied on time-consuming culture-based methods, though recently multiplexed molecular approaches have been described. Multiplexed molecular assays for pneumonia have the potential to provide broad diagnostic information in a rapid timeframe. Much has yet to be learned about these assays regarding analytical performance, potential impact, and optimal implementation strategy.

Content

Herein we provide a summary of what is known and what has yet to be learned about multiplexed molecular pneumonia assays. We provide a comparison of the different commercially available assays and summarize the most current performance data for each. We further describe outcome data and lessons learned from those who have implemented these assays worldwide. Finally, based on the current state of performance and outcome data, we provide informed strategies and considerations for laboratories contemplating implementation.

Summary

Multiplexed molecular assays for the diagnosis of pneumonia boast high accuracy though the diagnostic information gained from these assays is inherently different from culture and must be interpreted in cultural context. Despite this, these assays can be powerful and effective diagnostic tools with a potential to positively impact patient care. The extent to which this is realized varies from setting to setting, though is dependent on thoughtful implementation and a focus on delivering clear, rapid, and actionable results that can be interpreted in the appropriate context.

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.

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.

Severe Acute Respiratory Syndrome Coronavirus 2: The Emergence of Important Genetic Variants and Testing Options for Clinical Laboratories

Monitoring the spread of emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants relies on rapid genetic testing of the viral genome. The sequencing method commonly called next-generation sequencing can identify virus variants. At times, for target-specific mutation detection, reverse transcriptase polymerase chain reaction is used to identify specific variants. The Centers for Disease Control and Prevention's national SARS-CoV-2 Strain Surveillance Program is a comprehensive, population-based U.S. surveillance system to monitor SARS-CoV-2 genes, identifying emerging SARS-CoV-2 variants to determine implications for coronavirus disease 2019 (COVID-19) diagnostics, therapy, and vaccines. This review describes the main viral variants of concern and their potential impacts and briefly describes testing strategies.

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.

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.

Responding to the Challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Perspectives from the Association for Molecular Pathology Infectious Disease Subdivision Leadership

Clinical molecular laboratory professionals are at the frontline of the response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team, we review how our members have risen to these challenges, provide recommendations for managing the current pandemic, and outline the steps we can take as a community to better prepare for future pandemics.

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.

1225. How Frequently Should Sink Drains Be Disinfected?

Background

New evidence shows the relevance of sink drains in the horizontal transmission of multidrug-resistant organisms. We recently demonstrated that a peroxide-based disinfectant (product B) was better than bleach at disinfecting sink drains; however, we did not determine the duration of this effect. In this study, we evaluate the duration of bacterial reduction in sink drains treated with product B and compared it to an enhanced hydrogen peroxide agent (product A).

Methods

Testing was performed in a 26-bed medical intensive care unit at a 566-bed tertiary care hospital in Milwaukee, WI. Two disinfectants were compared: product A (hydrogen peroxide, octanoic acid, and peroxyacetic acid; Virasept, Ecolab) and product B (hydrogen peroxide-based disinfectant; Peroxide Multi Surface Cleaner and Disinfectant, Ecolab). Sinks were randomly assigned to product A, product B, and control (no disinfection). On day 0, baseline cultures were obtained and disinfectant agents were applied. On post-intervention days 1, 3, 5, and, 7, samples from each drain were collected using E-swabs (Copan, Italy). Quantitation of Gram-negative burden was determined by serial dilution in saline plated to MacConkey agar and dilutions that contained 20–200 colonies were used for bacterial colony-forming units (CFU).

Multivariate multiple linear regression and analysis of variance were used to compare mean Ln(1+CFU) between groups using R v3.5.0. Environmental sampling, cultures, and statistical analyses were performed blinded to the disinfected used.

Results

All three groups had similar CFU counts at baseline (P > 0.05). On day 1, a statistically significant reduction in bacterial CFUs was observed in the group treated with product A compared with sinks treated with product B (P = 0.04) or the control group (P < 0.01). The same differences were observed on day 3 post-intervention. There were no significant reductions on days 5 and 7.

Conclusion

Product A was the most effective product at disinfecting sink drains but its effect disappeared at 5 days post-disinfection. These results suggest that treating sink drains every 5 days with a hydrogen peroxide mixture would be ideal for healthcare facilities dealing with sink drain contamination.

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.

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.

Campylobacter culture fails to correctly detect Campylobacter in 30% of positive patient stool specimens compared to non-cultural methods

Campylobacter diagnosis is hampered because many laboratories continue to use traditional stool culture, which is slow and suffers false-negative results. This large multi-site study used a composite reference method consisting of a new FDA-cleared immunoassay and four molecular techniques to compare to culture. Prospectively collected patient fecal specimens (1552) were first preliminarily categorized as positive or negative by traditional culture. All specimens were also tested by EIA, and any EIA-positive or culture-discrepant results were further characterized by 16S rRNA qPCR, eight species-specific PCR assays, bidirectional sequencing, and an FDA-cleared multiplex PCR panel. The five non-culture methods showed complete agreement on all positive and discrepant specimens which were then assigned as true-positive or true-negative specimens. Among 47 true-positive specimens, culture incorrectly identified 13 (28%) as negative, and 1 true-negative specimen as positive, for a sensitivity of 72.3%. Unexpectedly, among the true-positive specimens, 4 (8%) were the pathogenic species C. upsaliensis. Culture had a 30% false result rate compared to immunoassay and molecular methods. More accurate results lead to better diagnosis and treatment of suspected campylobacteriosis.

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.

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.

Elizabethkingia anophelis: Clinical Experience of an Academic Health System in Southeastern Wisconsin

In late 2015 and early 2016, 11 patients were identified with cultures positive for Elizabethkingia anophelis in our health system. All patients had positive blood cultures upon admission. Chart review showed that all had major comorbidities and recent health care exposure. The attributable mortality rate was 18.2%.

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.

Treatment of Paecilomyces variotii pneumonia with posaconazole: case report and literature review

The fungi Paecilomyces variotii is a potential pathogen in immunocompromised and immunocompetent patients. Their rare association with clinical disease results in scarce literature regarding susceptibility and treatment. Here, we discuss a case involving successful treatment of probable P. variotii pneumonia with posaconazole after treatment failure with voriconazole. The current literature related to antifungal susceptibility profiles, microbiological identification methods and clinical management of infections caused by this organism is also reviewed.

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.

Clinical evaluation of a real-time PCR assay for identification of Salmonella, Shigella, Campylobacter (Campylobacter jejuni and C. coli), and shiga toxin-producing Escherichia coli isolates in stool specimens

Enteric illness affects millions of individuals annually in the United States and results in >50,000 hospitalizations. The rapid and accurate identification of bacterial pathogens associated with gastroenteritis can aid acute patient management decisions, including the use of antibiotic therapy and infection control. This study compared the ProGastro SSCS multiplex real-time PCR assay (Gen-Probe Prodesse, San Diego, CA) to culture for the identification of Campylobacter spp. (Campylobacter jejuni and Campylobacter coli), Salmonella spp., and Shigella spp. and to broth enrichment followed by an FDA-cleared enzyme immunoassay (EIA) for the identification of Shiga toxin-producing Escherichia coli (STEC) isolates in stool specimens. Stool samples submitted in preservatives for routine culture and EIA were prospectively enrolled and tested at four clinical centers. Discrepancies between the ProGastro SSCS assay and culture or EIA were resolved using bidirectional sequencing. The overall prevalence of the pathogens as detected by culture was 5.6% (1.8% Campylobacter, 1.8% Salmonella, 1.3% Shigella, and 0.8% STEC). When results based on the ProGastro SSCS assay and bidirectional sequencing were applied, the overall prevalence increased to 8.3% (2.3% Campylobacter, 2.6% Salmonella, 1.8% Shigella, and 1.6% STEC). Following resolution of the discrepant results, the sensitivity of the ProGastro SSCS assay was 100% for all pathogens, and the specificities ranged from 99.4% to 100%. The sensitivity of culture compared to sequence-confirmed ProGastro SSCS results ranged from 52.9% to 76.9%, with the specificities ranging from 99.9% to 100%. Overall, these results suggest that the ProGastro SSCS assay is highly sensitive and specific in a clinical setting.

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.

Cutting edge: mutation of Francisella tularensis mviN leads to increased macrophage absent in melanoma 2 inflammasome activation and a loss of virulence

The mechanisms by which the intracellular pathogen Francisella tularensis evades innate immunity are not well defined. We have identified a gene with homology to Escherichia coli mviN, a putative lipid II flippase, which F. tularensis uses to evade activation of innate immune pathways. Infection of mice with a F. tularensis mviN mutant resulted in improved survival and decreased bacterial burdens compared to infection with wild-type F. tularensis. The mviN mutant also induced increased absent in melanoma 2 inflammasome-dependent IL-1beta secretion and cytotoxicity in macrophages. The compromised in vivo virulence of the mviN mutant depended upon inflammasome activation, as caspase 1- and apoptosis-associated speck-like protein containing a caspase recruitment domain-deficient mice did not exhibit preferential survival following infection. This study demonstrates that mviN limits F. tularensis-induced absent in melanoma 2 inflammasome activation, which is critical for its virulence in vivo.

Multiple mechanisms of NADPH oxidase inhibition by type A and type B Francisella tularensis

Ft is a facultative intracellular pathogen that infects many cell types, including neutrophils. In previous work, we demonstrated that the type B Ft strain LVS disrupts NADPH oxidase activity throughout human neutrophils, but how this is achieved is incompletely defined. Here, we used several type A and type B strains to demonstrate that Ft-mediated NADPH oxidase inhibition is more complex than appreciated previously. We confirm that phagosomes containing Ft opsonized with AS exclude flavocytochrome b(558) and extend previous results to show that soluble phox proteins were also affected, as indicated by diminished phosphorylation of p47(phox) and other PKC substrates. However, a different mechanism accounts for the ability of Ft to inhibit neutrophil activation by formyl peptides, Staphylococcus aureus, OpZ, and phorbol esters. In this case, enzyme targeting and assembly were normal, and impaired superoxide production was characterized by sustained membrane accumulation of dysfunctional NADPH oxidase complexes. A similar post-assembly inhibition mechanism also diminished the ability of anti-Ft IS to confer neutrophil activation and bacterial killing, consistent with the limited role for antibodies in host defense during tularemia. Studies of mutants that we generated in the type A Ft strain Schu S4 demonstrate that the regulatory factor fevR is essential for NADPH oxidase inhibition, whereas iglI and iglJ, candidate secretion system effectors, and the acid phosphatase acpA are not. As Ft uses multiple mechanisms to block neutrophil NADPH oxidase activity, our data strongly suggest that this is a central aspect of virulence.

Identification of migR, a regulatory element of the Francisella tularensis live vaccine strain iglABCD virulence operon required for normal replication and trafficking in macrophages

Francisella tularensis, the etiological agent of tularemia, is capable of infecting a wide range of animals and causes a severe, lethal disease in humans. The pathogen evades killing by cells of the innate immune system utilizing genes encoding a pathogenicity island, including iglABCD, and instead utilizes these cells as a niche for replication and dissemination to other organs within the host. Regulators of the igl genes (e.g., MglA, SspA, FevR and PmrA) have been identified, but environmental stimuli and mechanisms of regulation are as yet unknown and are likely to involve additional gene products. In this work, we more closely examine the roles that environmental iron and the ferric uptake repressor protein (Fur) play in the regulation of the iglABCD operon. We also used a genetic approach to identify and characterize a new regulator of the igl operon, designated migR (macrophage intracellular growth regulator; FTL_1542). Quantitative real-time reverse transcription-PCR in a site-directed migR mutant confirmed the reduction in the number of iglC transcripts in this strain and also demonstrated reduced expression of fevR. Comparison of the migR and fevR mutants in monocyte-derived macrophages (MDMs) and epithelial cell lines revealed a reduced ability for each mutant to grow in MDMs, yet only the fevR mutant exhibited impaired replication in epithelial cell lines. Confocal analysis of infected MDMs revealed that although neither mutant reached the MDM cytosol, the fevR mutant was trapped in lamp-1-positive phagosomes, whereas the migR mutant resided in mature phagolysosomes enriched with both lamp-1 and cathepsin D. Disruption of migR and fevR also impaired the ability of F. tularensis to prevent neutrophil oxidant production. Thus, we have identified migR, a gene that regulates expression of the iglABCD operon and is essential for bacterial growth in MDMs and also contributes to the blockade of neutrophil NADPH oxidase activity.

Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium

Protocols have been developed and applied in the high-throughput production of selenomethionine labeled fusion proteins using the conditional Met auxotroph Escherichia coli B834. The large-scale growth and expression uses a chemically defined auto-induction medium containing 125 mg L(-1) selenomethionine, salts and trace metals, other amino acids including 10 mg L(-1) of methionine, vitamins except vitamin B12, and glucose, glycerol, and alpha-lactose. A schematic for a shaker rack that can hold up to twenty-four 2-L polyethylene terephthalate beverage bottles in a standard laboratory refrigerated floor shaker is provided. The growth cycle from inoculation of the culture bottle through the growth, induction, and expression was timed to take approximately 24 h. Culture growth in the auto-induction medium gave an average final optical density at 600 nm of approximately 6 and an average wet cell mass yield of approximately 14 g from 2 L of culture in greater than 150 expression trials. A simple method for visual scoring of denaturing electrophoresis gels for total protein expression, solubility, and effectiveness of fusion protein proteolysis was developed and applied. For the favorably scored expression trials, the average yield of purified, selenomethionine-labeled target protein obtained after proteolysis of the fusion protein was approximately 30 mg. Analysis by mass spectrometry showed greater than 90% incorporation of selenomethionine over a approximately 8-fold range of selenomethionine concentrations in the growth medium, with higher growth rates observed at the lower selenomethionine concentrations. These protein preparations have been utilized to solve X-ray crystal structures by multiwavelength anomalous diffraction phasing.