Reflex Human Immunodeficiency Virus (HIV) Type 1 RNA Testing Enables Timely Differentiation of False-Positive Results From Acute HIV Infection

Accurate, timely human immunodeficiency virus (HIV) diagnosis is critical. Routine HIV screening program data were examined before and after reflex HIV type 1 RNA testing. Reflex testing facilitated confirmation of reactive HIV screening assays (as true or false positives) (odds ratio, 23.7 [95% confidence interval, 6.7-83.4]; P < .0001), improving detection of acute HIV and reducing unconfirmed discordant results.

Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease

Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.

403. Strain Epidemiology of Clostridioides difficile across Three Geographically Distinct Medical Centers in Chicago

Background

Clostridioides difficile infections (CDI) are caused by a large and diverse group of strains with differences in prevalence and associated morbidity. Over the past 20 years the C. difficile (CD) molecular epidemiology has changed as the prevalence of the epidemic strain recognized as restriction endonuclease analysis (REA) group BI or PCR-Ribotype group (RT) 027 has decreased. The objective of this study was to determine the current epidemiology of CD in the city of Chicago.

Methods

Baseline characteristics and symptoms were compared for 81 patients who tested positive for CD by PCR (tcdB) between 9/1/2021 and 10/7/2021 at 3 hospitals in the city of Chicago. Patients were classified as having healthcare-associated CDI (HA-CDI) if symptoms began >72 hours after hospital admission, community-associated CDI (CA-CDI) if symptoms began ≤72 hours prior to admission, and community-onset healthcare-associated CDI (COHA-CDI) if they had been hospitalized ≤4 weeks prior to CDI diagnosis. Available stools were cultured and recovered CD isolates underwent REA typing. Determination of CD colonization was made by review of symptoms including chronicity of symptoms, stool frequency, and response to treatment.

Results

Among all patients, 33% (27/81) were CA-CDI, 28% (23/81) COHA-CDI, 11% (9/81) HA-CDI, and 27% (22/81) were classified as colonized. Primary CDI accounted for 66% (39/59) of the infections. Among patients with a primary CDI, 46% (18/39) of patients were classified as CA-CDI whereas COHA-CDI and HA-CDI accounted for 54% (21/39) of infections. REA group Y was the most common group strain accounting for 29% (22/75) of isolates. (Figure 1) REA group Y accounted for 26% (7/27) of CA-CDI compared to 0 REA group BI [p=0.06], and REA group Y accounted for 35% (7/20) of all colonized patients. (Figure 2) Figure 1Figure 2

Conclusion

There has been a marked change in the CD epidemiology within the city of Chicago since 2009 when REA group BI accounted for 61% of CDI (Black et al ICHE 2011; 32:897-902). REA group Y (typically identified as RT 014/020) is now the most common group strain in Chicago supplanting REA group BI (RT027). REA group Y appears to be associated primarily with CA-CDI and CD colonization. A detailed genomic analysis of REA group Y is required to determine potential reservoirs of REA group Y.

Disclosures

Mary K. Hayden, MD, Sanofi: Member, clinical adjudication panel Nicholas M. Moore, PhD, D(ABMM), Abbott Molecular: Grant/Research Support|Cepheid: Grant/Research Support Amanda Harrington, PhD, Beckman Coulter, Inc.: Clinical trial data collection funded by Beckman Coulter, Inc.|bioMeriuex/BioFire: Grant/Research Support Dale N. Gerding, MD, Destiny Pharma plc.: Advisor/Consultant Stuart Johnson, M.D., Ferring Pharmaceuticals: Membership on Ferring Publication Steering Committee|Ferring Pharmaceuticals: Employee|Summit Plc: Advisor/Consultant.

Severe COVID-19 infection is associated with aberrant cytokine production by infected lung epithelial cells rather than by systemic immune dysfunction

The mechanisms explaining progression to severe COVID-19 remain poorly understood. It has been proposed that immune system dysregulation/over-stimulation may be implicated, but it is not clear how such processes would lead to respiratory failure. We performed comprehensive multiparameter immune monitoring in a tightly controlled cohort of 128 COVID-19 patients, and used the ratio of oxygen saturation to fraction of inspired oxygen (SpO2 / FiO2) as a physiologic measure of disease severity. Machine learning algorithms integrating 139 parameters identified IL-6 and CCL2 as two factors predictive of severe disease, consistent with the therapeutic benefit observed with anti-IL6-R antibody treatment. However, transcripts encoding these cytokines were not detected among circulating immune cells. Rather, in situ analysis of lung specimens using RNAscope and immunofluorescent staining revealed that elevated IL-6 and CCL2 were dominantly produced by infected lung type II pneumocytes. Severe disease was not associated with higher viral load, deficient antibody responses, or dysfunctional T cell responses. These results refine our understanding of severe COVID-19 pathophysiology, indicating that aberrant cytokine production by infected lung epithelial cells is a major driver of immunopathology. We propose that these factors cause local immune regulation towards the benefit of the virus.

Implementation of a Sample Pooling Strategy for the Direct Detection of SARS-CoV-2 by Real-Time Polymerase Chain Reaction During the COVID-19 Pandemic

Objectives

To report our institutional experience in devising and implementing a pooling protocol and process for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing over a 3-month period in the fall of 2020.

Methods

The widespread testing implemented in the United States for detecting SARS-CoV-2 infection in response to the coronavirus disease 2019 pandemic has led to a significant shortage of testing supplies and therefore has become a major impediment to the public health response. To date, several institutions have implemented sample pooling, but publications documenting these experiences are sparse. Nasal and nasopharyngeal samples collected from low-positivity (<5%) areas were tested in pools of five on the Roche cobas 6800 analyzer system. Routine SARS-CoV-2 RT-PCR turnaround times between sample collection to result reporting were monitored and compared before and after sample pooling implementation.

Results

A total of 4,131 sample pools were tested over a 3-month period (during which 39,770 RT-PCR results were reported from the Roche system), allowing our laboratory to save 13,824 tests, equivalent to a conservation rate of 35%. A 48-hour or less turnaround time was generally maintained throughout the pooling period.

Conclusions

Sample pooling offers a viable means to mitigate shortfalls of PCR testing supplies in the ongoing pandemic without significantly compromising overall turnaround times.

Sensitive detection and quantification of SARS-CoV-2 in saliva

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

Clinical predictors of donor antibody titre and correlation with recipient antibody response in a COVID-19 convalescent plasma clinical trial

BACKGROUND

Convalescent plasma therapy for COVID-19 relies on transfer of anti-viral antibody from donors to recipients via plasma transfusion. The relationship between clinical characteristics and antibody response to COVID-19 is not well defined. We investigated predictors of convalescent antibody production and quantified recipient antibody response in a convalescent plasma therapy clinical trial.

METHODS

Multivariable analysis of clinical and serological parameters in 103 confirmed COVID-19 convalescent plasma donors 28 days or more following symptom resolution was performed. Mixed-effects regression models with piecewise linear trends were used to characterize serial antibody responses in 10 convalescent plasma recipients with severe COVID-19.

RESULTS

Donor antibody titres ranged from 0 to 1 : 3892 (anti-receptor binding domain (RBD)) and 0 to 1 : 3289 (anti-spike). Higher anti-RBD and anti-spike titres were associated with increased age, hospitalization for COVID-19, fever and absence of myalgia (all P < 0.05). Fatigue was significantly associated with anti-RBD (P = 0.03). In pairwise comparison amongst ABO blood types, AB donors had higher anti-RBD and anti-spike than O donors (P < 0.05). No toxicity was associated with plasma transfusion. Non-ECMO recipient anti-RBD antibody titre increased on average 31% per day during the first three days post-transfusion (P = 0.01) and anti-spike antibody titre by 40.3% (P = 0.02).

CONCLUSION

Advanced age, fever, absence of myalgia, fatigue, blood type and hospitalization were associated with higher convalescent antibody titre to COVID-19. Despite variability in donor titre, 80% of convalescent plasma recipients showed significant increase in antibody levels post-transfusion. A more complete understanding of the dose-response effect of plasma transfusion amongst COVID-19-infected patients is needed.

Sensitive detection and quantification of SARS-CoV-2 in saliva

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

Cording in Disseminated Mycobacterium chelonae Infection in an Immunocompromised Patient

Cording is a phenomenon in which acid fast bacilli grow in parallel and was previously used as a means of presumptive microscopic identification of Mycobacterium tuberculosis (TB). However, this process has been shown in multiple other nontuberculous mycobacterial (NTM) species. Here we present the case of an immunocompromised adult who presented with wrist pain, weight loss, and cough. A positron emission tomography scan showed uptake in the right ulna, multiple soft tissue sites, and the left lung. Biopsies and cultures were obtained from multiple sites, and the patient was ultimately diagnosed with disseminated Mycobacterium chelonae infection. The organism showed cording in culture. As seen in this patient, cording may occur in multiple NTM species and is not reliable as the sole indicator of the presence of TB.

Evaluation of the EUROIMMUN Anti-SARS-CoV-2 ELISA Assay for detection of IgA and IgG antibodies

As the Coronavirus 2019 (COVID-19) pandemic evolves, the development of immunoassays to help determine exposure and potentially predict immunity has become a pressing priority. In this report we present the performance of the EUROIMMUN enzyme-linked immunosorbent assay (ELISA) for semi-quantitative detection of IgA and IgG antibodies in serum and plasma samples using recombinant S1 domain of the SARS-CoV-2 spike protein as antigen. Specimens from patients, with and without COVID-19 infection, were tested at the University of Chicago Clinical Microbiology and Immunology Laboratory. Of 86 samples from SARS-CoV-2 PCR-negative patients, including 28 samples positive for common human coronavirus strains, 76 tested negative and 10 tested positive for IgA (88.4% agreement, 95% CI: 79.9-93.6) while 84 tested negative and 2 tested positive for IgG (97.7% agreement, 95% CI: 91.9-99.6). Of 82 samples from SARS-CoV-2 PCR-positive patients, 14 tested negative and 68 tested positive for IgA (82.9% agreement, 95% CI: 73.4-89.5) while 27 tested negative and 55 tested positive for IgG (67.1% agreement, 95% CI: 56.3-76.3). Of samples collected ≥4 days after positive PCR, 38 of 42 (90.5% agreement, 95% CI: 77.9-96.2) were positive for IgA, and 42 of 42 (100% agreement, 95% CI: 91.6-100) were positive for IgG, respectively. The EUROIMMUN Anti-SARS-CoV-2 ELISA Assay demonstrated good sensitivity for detection of IgA and excellent sensitivity for detection of IgG antibodies from samples collected ≥4 days, after COVID-19 diagnosis by PCR. This assay demonstrated good specificity for IgA and excellent specificity for IgG and demonstrated only borderline cross reaction in 2 of the 28 samples from patients with common human coronaviruses infection, types NL63 and OC43.

Clinical Sensitivity of Severe Acute Respiratory Syndrome Coronavirus 2 Nucleic Acid Amplification Tests for Diagnosing Coronavirus Disease 2019

Utilizing 34 348 severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) nucleic acid amplification test (NAAT) results from 2 health systems, we estimated the clinical sensitivity of a single SARS-CoV-2 NAAT. We found that SARS-CoV-2 NAAT has 82%-97% sensitivity for diagnosing coronavirus disease 2019 among symptomatic patients.

Rapid pathogen identification and antimicrobial susceptibility testing in in vitro endophthalmitis with matrix assisted laser desorption-ionization Time-of-Flight Mass Spectrometry and VITEK 2 without prior culture

PURPOSE

Prompt clinical diagnosis and initiation of treatment are critical in the management of infectious endophthalmitis. Current methods used to identify causative agents of infectious endophthalmitis are mostly inefficient, owing to suboptimal sensitivity, length, and cost. Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) can be used to rapidly identity pathogens without a need for culture. Similarly, automated antimicrobial susceptibility test systems (AST, VITEK 2) provide accurate antimicrobial susceptibility profiles. In this proof-of-concept study, we apply these technologies for the direct identification and characterization of pathogens in vitreous samples, without culture, as an in vitro model of infectious endophthalmitis.

METHODS

Vitreous humor aspirated from freshly enucleated porcine eyes was inoculated with different inocula of Staphylococcus aureus (S. aureus) and incubated at 37°C. Vitreous endophthalmitis samples were centrifuged and pellets were directly analyzed with MALDI-TOF MS and VITEK 2 without prior culture. S. aureus colonies that were conventionally grown on culture medium were used as control samples. Time-to-identification, minimum concentration of bacteria required for identification, and accuracy of results compared to standard methods were determined.

RESULTS

MALDI-TOF MS achieved accurate pathogen identification from direct analysis of intraocular samples with confidence values of up to 99.9%. Time from sample processing to pathogen identification was <30 minutes. The minimum number of bacteria needed for positive identification was 7.889x106 colony forming units (cfu/μl). Direct analysis of intraocular samples with VITEK 2 gave AST profiles that were up to 94.4% identical to the positive control S. aureus analyzed per standard protocol.

CONCLUSION

Our findings demonstrate that the direct analysis of vitreous samples with MALDI-TOF MS and VITEK 2 without prior culture could serve as new, improved methods for rapid, accurate pathogen identification and targeted treatment design in infectious endophthalmitis. In vivo models and standardized comparisons against other microbiological methods are needed to determine the value of direct analysis of intraocular samples from infectious endophthalmitis with MALDI-TOF MS and VITEK 2.

Comparison of 3 Nucleic Acid Amplification Tests and a Rapid Antigen Test with Culture for the Detection of Group A Streptococci from Throat Swabs

Background

Recently, the US Food and Drug Administration cleared 3 nucleic acid amplification test (NAAT) assays for detection of Streptococcus pyogenes [group A Streptococcus (GAS)] in pharyngeal specimens. However, there are limited studies evaluating the performance of these NAAT assays.

Methods

We compared the results of 3 NAATs (cobas Liat, Luminex Aries, and Cepheid Xpert Xpress) and a rapid antigen assay (Quidel QuickVue in-line strep A) with the accepted gold standard method, bacterial culture.

Results

Sixty-eight throat swab specimens collected between August and October 2017 were tested. Compared to bacterial culture, the sensitivities, specificities, positive predictive value, and negative predictive value for detecting GAS were as follows: cobas Liat: 100%, 97.4%, 96.7%, and 100%; Cepheid Xpert: 100%, 97.4%, 96.7%, and 100%; Luminex Aries: 95.2%, 100%, 100%, and 95.5%. The Quidel QuickVue in-line strep A assay showed poor sensitivity, detecting only 5.2% of culture-positive specimens.

Conclusion

The 3 NAATs have high sensitivity when compared with bacterial culture for detection of GAS. With rapid turnaround time and ease of use, these tests can be considered as reliable point-of-care tests for the diagnosis of GAS, replacing the need for back-up culture.

Antimicrobial Stewardship Review of Automated Candidemia Alerts Using the Epic Stewardship Module Improves Bundle-of-Care Adherence

Background

Antimicrobial stewardship interventions utilizing real-time alerting through the electronic medical record enable timely implementation of the bundle of care (BOC) for patients with severe infections, such as candidemia. Automated alerting for candidemia using the Epic stewardship module has been in place since July 2015 at our medical center. We sought to assess the impact of these alerts.

Methods

All adult inpatients with candidemia between April 1, 2011, and March 31, 2012 (pre-intervention), and June 30, 2016, and July 1, 2017 (post-intervention), were evaluated for BOC adherence. We also evaluated the impact on timeliness to initiate targeted therapy, length of stay (LOS), and 30-day mortality.

Results

Eighty-four patients were included, 42 in the pre- and 42 in the post-intervention group. Adherence to BOC was significantly improved, from 48% (pre-intervention) to 83% (post-intervention; P = .001). The median time to initiation of therapy was 4.8 hours vs 3.3 hours (P = .58), the median LOS was 24 and 18 days (P = .28), and 30-day mortality was 19% and 26% (P = .60) in the pre- and post-intervention groups, respectively.

Conclusions

Antimicrobial stewardship program review of automated alerts identifying patients with candidemia resulted in significantly improved BOC adherence and was associated with a 1.5-hour reduction in time to initiation of antifungal therapy. No significant change was observed with 30-day mortality or LOS.

1159. Influenza Symptoms in Vaccinated Healthcare Workers in an H3N2-Dominant Season

Background

Influenza vaccination of healthcare workers is an important component of keeping patients safe, but must be paired with exclusion of ill healthcare workers (HCW) from work. CDC recommends exclusion from work until afebrile for 24 hours, but not all HCW with influenza develop fever and may still be a risk for spreading. Half of HCW with influenza in an H1N1-dominant season (2013–2014) at our institution were afebrile.

Methods

From 1/31–4/24/18 (H3N2-dominant season), HCW with fever or cough were screened for influenza and respiratory syncytial virus by polymerase chain reaction of flocked nasopharyngeal swabs. Additional HCW were tested by their primary care providers. We collected influenza vaccination status and symptoms and calculated the proportion of influenza-positive HCWs with fever or cough. Infection control practitioners (ICPs) contacted each influenza-positive HCW to identify potential patient or HCW exposures 24 hours prior to symptom onset and offered oseltamivir prophylaxis to exposed patients and HCW.

Results

Of 186 HCW tested by UCM, 49 (26%) tested positive for influenza (35 with influenza A; 14 with influenza B) and 11 (6%) tested positive for RSV. Forty-eight HCW (98%) received influenza vaccination. Fever was reported in only 19 (54%) HCW with influenza A and three (21%) HCW with influenza B. Cough was present in the majority of HCW (34 (97%) with influenza A and 12 (86%) with influenza B). An additional 55 HCW were diagnosed with influenza by their primary care providers. ICPs performed contact investigations for 43 HCW who reported exposure to patients or other HCW between 24 hours before symptom onset through the time of diagnosis. Occupational medicine provided 138 courses of prophylactic oseltamivir to HCW.

Conclusion

Afebrile influenza illness is common; current workforce guidelines are insufficient to prevent exposure in the healthcare setting. Expanding employee influenza screening to include fever OR cough doubled the number influenza positive HCW identified. Despite excellent influenza vaccination rates, vigilance is critical to prevent influenza transmission in the hospital. HCW screening for influenza based on fever OR cough, exclusion from work, and identification of potential exposures can help keep patients and colleagues safe.

Disclosures

All authors: No reported disclosures.

526. An EMR-Based Diagnostic Stewardship Intervention for GI mPCR Aimed at Reducing Inappropriate C. difficile Tests

Background

Diagnostic stewardship is an emerging tool that can be used to prevent overuse of diagnostics. Because GI mPCR (GI multiplex PCR panel) tests can be ordered on formed stool, the test has lower pre-test probability for Clostridium difficile (C. difficile) infection than traditional singleplex PCR. Furthermore, after 48hours of admission, most other targets on the GI mPCR are no longer clinically relevant. Any C. difficile testing on inappropriate specimens may increase the rate of Lab ID events (positive C. difficile tests after 3 days of admission) without improving detection of true infections.

Methods

In January 2018, our 700-bed academic medical center implemented an informatics-based intervention that restricted ordering of the GI mPCR to the first 48 hours of hospitalization. After 48 hours, providers were required to contact microbiology to request an exception (see Figure 1). Singleplex PCR testing for C. difficile was available throughout admission. Orders for the GI mPCR test require the provider to note whether the patient had >3 loose stools in the previous day. Statistical analysis performed with STATA software.

Results

A total of 282 late (after 48 hours of admission) GI mPCR tests were ordered in the 104 days before restriction and 210 late tests were ordered in the 104 days after. Late GI mPCR tests (before and after restriction) resulted in diagnoses other than C. difficile less than 5% of the time (20 of 492 tests). 11.7% (24 of 210) of late GI mPCR tests were ordered for patients who did not have >3 loose stools in the previous day. Prior to restriction, 15% (41 of 282) of Lab ID events from GI mPCR were for patients who had already tested positive for C. difficile earlier in the same admission. Following the intervention, there was a decreased proportion of GI mPCR tests that were positive for C. difficile (from 14.5% to 11.3%, P = 0.26), as well as a significantly decreased rate of Lab ID events detected by GI mPCR, from 7.2/10,000 patient days to 4.0/10,000 patient days (P = 0.01).

Conclusion

Accurate diagnosis of C. difficile infection is important for treatment and prevention efforts, yet these data show that many rapid GI mPCR tests are inappropriately ordered on patients who may not have loose stools and who are unlikely to have an alternate diagnosis. EMR-based restriction on the GI mPCR ordering time reduced Lab ID events of C. difficile infection without missing important alternate diagnoses.

Disclosures

All authors: No reported disclosures.

The performance of Luminex ARIES® Flu A/B & RSV and Cepheid Xpert® Flu/RSV XC for the detection of influenza A, influenza B, and respiratory syncytial virus in prospective patient samples

BACKGROUND

The demand for rapid, accurate viral testing has increased the number of assays available for the detection of viral pathogens. One of the newest FDA cleared platforms is the Luminex ARIES^® Flu A/B & RSV, which is a fully automated, real-time PCR-based assay used for detection of influenza A, influenza B, and respiratory syncytial virus (RSV).

OBJECTIVES

We sought to compare the performance of Luminex ARIES^® Flu A/B & RSV assay to the Cepheid Xpert^® Flu/RSV XC assay for rapid Flu and RSV testing.

STUDY DESIGN

A series of consecutive nasopharyngeal specimens received in the clinical microbiology laboratory during peak influenza season at a major academic center in Chicago, IL, were prospectively tested, using both the ARIES^® Flu A/B & RSV and Xpert^® Flu/RSV XC assays, side by side. Discrepant results were tested on the BioFire FilmArray^® Respiratory Panel for resolution.

RESULTS

A total of 143 consecutive nasopharyngeal specimens, obtained from patients ranging from six months to ninety-three years in age were received between January 1st, 2017 and March 21st, 2017. There was 96.6% agreement between the two assays for detection influenza A, 100% agreement for detection influenza B and RSV, and 98.9% agreement for negative results. The Xpert^® Flu/RSV XC performed with an average turn-around time of approximately 60min, compared to the ARIES^® Flu A/B & RSV of approximately 120min. Both assays were equally easy to perform, with a similar amount of hands-on technologist time for each platform.

CONCLUSIONS

Overall, these results indicate that both tests are comparable in terms of result agreement and technical ease-of-use. The Xpert^® Flu/RSV XC assay did produce results with less turn-around-time, approximately 60min quicker than the ARIES^® Flu A/B & RSV.

Influenza among afebrile and vaccinated healthcare workers

Background. To prevent transmission of influenza from healthcare workers (HCWs) to patients, many hospitals exclude febrile HCWs from working, but allow afebrile HCWs with respiratory symptoms to have contact with patients. During the 2013–2014 influenza season at our hospital, an influenza-positive HCW with respiratory symptoms but no fever was linked to a case of possible healthcare-associated influenza in a patient. Therefore, we implemented a temporary policy of mandatory influenza testing for HCWs with respiratory symptoms.

Methods. From 3 January through 28 February 2014, we tested HCWs with respiratory symptoms for influenza and other respiratory pathogens by polymerase chain reaction of flocked nasopharyngeal swabs. HCWs also reported symptoms and influenza vaccination status, and underwent temperature measurement. We calculated the proportion of influenza-positive HCWs with fever and prior influenza vaccination.

Results. Of 449 HCWs, 243 (54%) had a positive test for any respiratory pathogen; 34 (7.6%) HCWs tested positive for influenza. An additional 7 HCWs were diagnosed with influenza by outside physicians. Twenty-one (51.2%) employees with influenza had fever. Among influenza-infected HCWs, 20 had previously received influenza vaccination, 18 had declined the vaccine, and 3 had unknown vaccination status. There was no significant difference in febrile disease among influenza-infected employees who had received the influenza vaccine and those who had not received the vaccine (45% vs 61%; P = .32).

Conclusions. Nearly half of HCWs with influenza were afebrile prior to their diagnosis. HCWs with respiratory symptoms but no fever may pose a risk of influenza transmission to patients and coworkers.

Community-associated methicillin-resistant Staphylococcus aureus colonization burden in HIV-infected patients

BACKGROUND

The epidemic of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has had a disproportionate impact on patients with human immunodeficiency virus (HIV).

METHODS

We evaluated CA-MRSA colonization burden (number of colonized sites per total number sampled) among HIV-infected and HIV-negative inpatients within 72 hours of hospitalization. From March 2011 through April 2012, we obtained cultures from nasal and extranasal sites (throat, axilla, inguinal, perirectal, and chronic wound if present) and collected risk factor data.

RESULTS

Of 745 patients (374 HIV-infected, 371 HIV-negative), 15.7% were colonized with CA-MRSA at any site: 20% of HIV and 11% of HIV-negative patients (relative prevalence=1.8, P=.002). HIV-infected patients had a higher prevalence of nasal, extranasal, and exclusive extranasal colonization as well as higher colonization burden. Perirectal and inguinal areas were the extranasal sites most frequently colonized, and 38.5% of colonized patients had exclusive extranasal colonization. Seventy-three percent of isolates were identified as USA300. Among HIV-infected patients, male sex, younger age, and recent incarceration were positively associated whereas Hispanic ethnicity was negatively associated with higher colonization burden. Among HIV-negative patients, temporary housing (homeless, shelter, or substance abuse center) was the only factor associated with higher colonization burden. Predictors of USA300 included HIV, younger age, illicit drug use, and male sex; all but 1 colonized individual with current or recent incarceration carried USA300.

CONCLUSIONS

HIV-infected patients were more likely to have a higher CA-MRSA colonization burden and carry USA300. In certain populations, enhanced community and outpatient-based infection control strategies may be needed to prevent CA-MRSA cross-transmission and infection.

Community-associated methicillin-resistant Staphylococcus aureus colonization in high-risk groups of HIV-infected patients

BACKGROUND

We examined the epidemiology of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) nasal colonization among 3 groups of human immunodeficiency virus (HIV)-infected and 1 group of HIV-negative outpatients.

METHODS

We determined prevalence and risk factors associated with MRSA colonization among women, recently incarcerated, and Hispanic HIV-infected patients and HIV-negative patients; isolates were typed by pulsed-field gel electrophoresis. Relative prevalence was calculated using Poisson regression, and logistic regression was used for multivariate analysis.

RESULTS

Of 601 patients, 9.3% were colonized with MRSA; 11% of HIV-infected and 4.2% of HIV-negative patients were colonized (relative prevalence, 2.6; 95% confidence interval [CI], 1.12-6.07; P = .03). Among HIV-infected patients, recently incarcerated patients had the highest colonization prevalence (15.6%) followed by women (12%); Hispanic patients had the lowest (2.8%). Eighty percent of confirmed MRSA isolates were identified as USA300. On multivariate analysis, history of incarceration or residence in alternative housing (odds ratio [OR], 2.3; 95% CI, 1.1-4.7; P = .03) was associated with MRSA colonization; Hispanic ethnicity was negatively associated (OR, 0.3; 95% CI, .11-.98; P = .045). There was a trend (OR, 1.6; 95% CI, .9-3.0; P = .097) toward geographic location of residence being associated with colonization. After controlling for incarceration, residence, and geography, HIV status was no longer significantly associated with colonization.

CONCLUSIONS

The CA-MRSA and HIV epidemics have intersected. Examination of networks of individuals released from incarceration, both HIV positive and negative, is needed to assess the role of social networks in spread of CA-MRSA and inform prevention strategies.

A two-site analytical evaluation of the BD Viper System with XTR Technology in Nonextracted Mode and Extracted Mode with seeded simulated specimens

The BD ProbeTec CT Q(x) Amplified DNA Assay and the BD ProbeTec GC Q(x) Amplified DNA Assay (both BD Diagnostics, Sparks, MD) represent two new assays developed for use with the BD Viper System with XTR Technology (BD Diagnostics). These assays were built on the foundation of the former BD ProbeTec ET assays (BD Diagnostics) and its accompanying instrumentation. The study described below compared the new assay format, Extracted Mode, to the former assay format, Nonextracted Mode, with the primary objective of examining and measuring overall time expenditures and efficiency of operation. An 80-142-min reduction in "hands-on" total processing time was observed for the Extracted Mode whether testing urines or swabs. The second objective was to assess the accuracy of performance at low simulated analytical loads for the pathogens Chlamydia trachomatis and Neisseria gonorrhoeae. Performance accuracies for simulated positive and negative urine or swab specimens were calculated to be 99.97% for Extracted Mode and 99.76% for Nonextracted Mode.

A review of sentinel laboratory performance: identification and notification of bioterrorism agents

CONTEXT

The anthrax incident of 2001 in the United States prompted the College of American Pathologists (CAP), the Association of Public Health Laboratories, and the Centers for Disease Control and Prevention to develop exercises for Laboratory Response Network (LRN) sentinel laboratories.

OBJECTIVE

To provide an overview of the results of the CAP bioterrorism Laboratory Preparedness Survey (LPS, 2007) and Laboratory Preparedness Exercise (LPX, 2008) and assist LRN sentinel laboratories and public health agencies in planning for bioterrorism events.

DESIGN

Bioterrorism agents and nonbiothreat mimic organisms were provided in 2 mailings per year (2007 and 2008, 20 total challenges). Within each mailing, 2 to 3 agents were category A or category B bioterrorism agents (total of 10 categoric challenges). Some category A/B isolates were modified/vaccine strains. The total number of laboratories participating in these exercises ranged from 1316 to 1381. Isolate characteristics used to identify the organisms were compiled along with the participants' reporting actions. Educational commentary was provided with each exercise.

RESULTS

Acceptable identification responses were as follows: Bacillus anthracis, 90% (2007) and 99.9% (2008); Yersinia pestis, 83.8% (2007) and 87.6% (2008); and Francisella tularensis subsp Holarctica, 86.6% (2007) and 91.6% (2008). The time interval between specimen receipt and notification of results to an LRN reference laboratory decreased from more than 10 days in 2007 to 3 or 4 days in 2008 for some challenges.

CONCLUSIONS

The bioterrorism challenge program (LPS, LPX) provides important comparative data from more than 1300 sentinel laboratories that can be used by individual laboratories to evaluate their identification and LRN reporting performance.

Laboratory diagnosis of mycobacterial infections

This paper reviews the recent US history of infection with Mycobacterium tuberculosis and discusses the emergence of drug-resistant strains. The paper continues with brief discussions of the clinical presentation of tuberculosis, tuberculosis in the pediatric population, and nontuberculous pulmonary disease. We discuss laboratory techniques that will rapidly identify Mycobacterium tuberculosis and provide susceptibility test results. The advances and limitations of currently available diagnostic techniques are presented. The chapter concludes with an explanation of the current strengths and limitations of molecular diagnosis of disease and resistance.

Sustained bacteremia associated with transjugular intrahepatic portosystemic shunt (TIPS)

Transjugular intrahepatic portosystemic shunt (TIPS) has become a routine procedure in patients with portal hypertension, yet there are few data concerning the incidence of bacteremia associated with this shunt. All patients who underwent TIPS placement at a university hospital from January 1992 through January 1999 were studied. Ninety-nine TIPS were placed, and 10 patients subsequently developed sustained bacteremia; 5 patients had no identifiable source of bacteremia despite rigorous evaluation and were presumed to represent TIPS infections, for an estimated annual incidence of 7 cases/1000 TIPS procedures. Case patients developed bacteremia a median of 100 days after TIPS placement (range, 6-732 days). Bacteremia resolved in all patients after treatment with appropriate intravenous antibiotics (median, 2 weeks of therapy). Although the incidence of TIPS-associated bacteremia appears low, the increasing frequency of this procedure suggests that more information is needed to define this entity and to develop appropriate treatment recommendations.

Yersinia enterocolitica and Yersinia pseudotuberculosis

Yersinia enterocolitica can cause enteritis, right lower-quadrant pain mimicking appendicitis, reactive arthritis, and erythema nodosum. This organism is transmitted through food, animal contact, and contaminated blood products. Patients with iron excess are at a higher risk for serious infection. This article describes the history, microbiology, virulence factors, epidemiology, clinical manifestations, diagnosis, and therapy of Y. enterocolitica and Y. pseudotuberculosis. In addition, the immune response of those developing reactive arthritis following infection with Y. enterocolitica is discussed.

Mycobacterial growth and bacterial contamination in the mycobacteria growth indicator tube and BACTEC 460 culture systems

The BACTEC 460 system currently provides the most rapid detection of mycobacterial growth, but the system is radiometric and requires needles to inoculate specimens through the bottle's septum. The Mycobacteria Growth Indicator Tube (MGIT) system has a liquid medium, like the BACTEC system, and does not require needles when inoculating specimens. We compared mycobacterial growth from 510 specimens in the two systems. Average time to acid-fast bacillus (AFB) detection and identification to the species level was less with the BACTEC system, but this result was statistically significant only for AFB detection in specimens containing Mycobacterium avium-M. intracellulare complex. The contamination rate with MGIT was 29%; the BACTEC rate was 5%. To investigate MGIT contamination, we initiated a second study with changes in specimen processing. The MGIT contamination rate was reduced to 12%; the BACTEC rate was not significantly affected (5.5%). The most likely explanation for the contamination in MGIT is the richness of its medium compared to the BACTEC medium. Cost analysis for the two systems in a laboratory that processes 4,500 specimens a year is presented. The data suggest that the BACTEC 460 and the MGIT systems are approximately equivalent in cost and ability to support the growth of AFB. The MGIT system appears safer and easier to use and was preferred by laboratory personnel, but it cannot currently be used for blood specimens or antituberculosis susceptibility testing.

Evaluation of automated COBAS AMPLICOR PCR system for detection of several infectious agents and its impact on laboratory management

We evaluated the COBAS AMPLICOR (CA) PCR system (Roche Diagnostic Systems) designed for automated PCR amplification and detection of nucleic acids from infectious agents in clinical samples. The Roche AMPLICOR microwell plate (MWP) PCR was the reference method. CA amplifies target nucleic acid, captures the biotinylated amplification products by using magnetic particles coated with specific oligonucleotide probes, and detects the bound products colorimetrically. For Mycobacterium tuberculosis, the correlation of the results of CA tests with those of MWP tests was 100% with 230 samples, including 20 culture-positive samples. For hepatitis C virus, the correlation was 100% with 214 samples, including 60 positive samples. MultiPlex CA analysis of 199 cervical specimens for Chlamydia trachomatis, Neisseria gonorrhoeae, and the internal control gave 100% concordance. These samples included 19 C. trachomatis and 3 N. gonorrhoeae culture-positive samples. Overall, the agreement between PCR methods for all 842 comparisons was 100%. Compared with culture, the sensitivities of the assays for C. trachomatis and M tuberculosis were > or = 95%. After spiking alternating amplification tubes in the CA system with 10(14) copies of the Chlamydia amplicon per ml, we were unable to demonstrate any carryover cross-contamination of negative samples. Using the criteria of the College of American Pathologists workload recording method, we found that the total hands-on time to produce CA PCR results was 4.4, 7.9, and 3.3 min for M. tuberculosis, hepatis C virus, and the MultiPlexed assay for chlamydia plus gonorrhea and an internal control, respectively. The CA system brings true PCR automation to laboratories. In addition to the accuracy of automated results, the CA system provides labor savings, provides containment of the amplification and detection components of PCR, and supports both MultiPlex amplification and sequential algorithm (ReFlex) detection of analytes.

Evaluation of Amplicor PCR for direct detection of Mycobacterium tuberculosis from sputum specimens

We evaluated the Amplicor PCR assay (Roche Molecular Systems, Branchburg, N.J.) for direct detection of Mycobacterium tuberculosis in sputum. A total of 532 specimens from 270 patients were decontaminated and stored at 4 or -75 degrees C until assayed by PCR. This assay used three-step sample preparation, biotinylated primer pairs, AmpErase, and a microtiter format for amplicon capture and detection. Amplicor PCR results were compared with clinical history, culture from a Lowenstein-Jensen slant, and results from the BACTEC TB-460 system. Eighty-seven cultures from 15 patients grew M. tuberculosis; of these, 83 (95%) were positive with the Amplicor PCR test. The false negatives were most likely due to sample variation and inhibitors. Of the 445 specimens from which M. tuberculosis was not isolated, 428 (96%) were negative with the Amplicor PCR test. Of the 17 M. tuberculosis culture-negative, Amplicor-positive specimens, 15 were reclassified as true positives because previous cultures grew M. tuberculosis. Of the 445 specimens which did not grow M. tuberculosis, Mycobacterium spp. other than M. tuberculosis were isolated from 150 specimens. Three of these 150 specimens were Amplicor positive; two were from a patient with a history of tuberculosis, and one specimen gave a false-positive result. We do not feel that this represents cross-reactivity, because repeated Amplicor testing of the isolate gave negative results. The microtiter plate has 96 wells. Allowing for six controls, 90 decontaminated specimens can be tested by one technologist in 7.5 h. This PCR assay took 7.5 h to complete and is a sensitive and specific, rapid method for the direct detection of M. tuberculosis from sputum.