Publications by authors named "Kathleen G Beavis"

29 Publications

  • Page 1 of 1

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

Sci Rep 2021 06 14;11(1):12425. Epub 2021 Jun 14.

Section of Hematology and Oncology, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA.

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.
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http://dx.doi.org/10.1038/s41598-021-91835-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8203799PMC
June 2021

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.

Am J Clin Pathol 2021 06;156(1):15-23

Department of Pathology, Chicago, IL, USA.

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.
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http://dx.doi.org/10.1093/ajcp/aqab035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136033PMC
June 2021

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

medRxiv 2020 Dec 7. Epub 2020 Dec 7.

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.
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http://dx.doi.org/10.1101/2020.12.04.20241059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7743089PMC
December 2020

Clinical Performance of the Point-of-Care cobas Liat for Detection of SARS-CoV-2 in 20 Minutes: a Multicenter Study.

J Clin Microbiol 2021 01 21;59(2). Epub 2021 Jan 21.

Department of Pathology and Laboratory Medicine, University of California Davis, California, USA

Highly accurate testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the point of care (POC) is an unmet diagnostic need in emergency care and time-sensitive outpatient care settings. Reverse transcription-PCR (RT-PCR) technology is the gold standard for SARS-CoV-2 diagnostics. We performed a multisite U.S. study comparing the clinical performance of the first U.S. Food and Drug Administration (FDA)-authorized POC RT-PCR for detection of SARS-CoV-2 in 20 min, the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test, to the most widely used RT-PCR laboratory test, the cobas 68/8800 SARS-CoV-2 test. Clinical nasopharyngeal swab specimens from 444 patients with 357 evaluable specimens at five U.S. clinical laboratories were enrolled from 21 September 2020 to 23 October 2020. The overall agreement between the Liat and 68/8800 systems for SARS-CoV-2 diagnostics was 98.6% (352/357). Using Liat, positive percent agreement for SARS-CoV-2 was 100% (162/162) and the negative percent agreement was 97.4% (190/195). The Liat is an RT-PCR POC test that provides highly accurate SARS-CoV-2 results in 20 min with performance equivalent to that of high-throughput laboratory molecular testing. Rapid RT-PCR testing at the POC can enable more timely infection control and individual care decisions for coronavirus disease 2019.
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http://dx.doi.org/10.1128/JCM.02811-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111162PMC
January 2021

Universal screening for at an urban academic medical center.

Infect Control Hosp Epidemiol 2021 Mar 22;42(3):351-352. Epub 2020 Sep 22.

Section of Infectious Disease, Department of Medicine, University of Chicago, Chicago, Illinois.

We implemented universal inpatient Clostridioides difficile screening at an 800-bed hospital. Over 3 years, 2,010 of 47,048 screening tests (4.2%) were positive, with significantly higher rates of C. difficile colonization on transplant units than medical-surgical units: 5.4% (152 of 2,801) versus 4.3% (880 of 20,564), respectively (P = .005). Compliance with screening ranged from 79% to 96%.
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http://dx.doi.org/10.1017/ice.2020.428DOI Listing
March 2021

Cording in Disseminated Mycobacterium chelonae Infection in an Immunocompromised Patient.

Lab Med 2021 May;52(3):e50-e52

Department of Pathology, University of Chicago Medical Center, Chicago, Illinois.

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.
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http://dx.doi.org/10.1093/labmed/lmaa082DOI Listing
May 2021

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

Open Forum Infect Dis 2020 Aug 24;7(8):ofaa315. Epub 2020 Jul 24.

Providence St. Joseph Health, Seattle, Washington, USA.

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.
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http://dx.doi.org/10.1093/ofid/ofaa315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7423294PMC
August 2020

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

J Clin Virol 2020 08 23;129:104468. Epub 2020 May 23.

Department of Pathology, University of Chicago, Chicago, IL 60637-1470, USA. Electronic address:

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.
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http://dx.doi.org/10.1016/j.jcv.2020.104468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255182PMC
August 2020

Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays.

J Clin Microbiol 2020 Jul 23;58(8). Epub 2020 Jul 23.

Clinical Microbiology Laboratory, University of Chicago Medicine, Chicago, Illinois, USA.

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http://dx.doi.org/10.1128/JCM.00772-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383516PMC
July 2020

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.

PLoS One 2019 30;14(12):e0227071. Epub 2019 Dec 30.

Department of Ophthalmology and Visual Science, The University of Chicago Hospitals and Health System, Chicago, Illinois, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227071PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936829PMC
April 2020

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

Open Forum Infect Dis 2019 Oct 11;6(10):ofz412. Epub 2019 Oct 11.

Infectious Diseases and Global Health, The University of Chicago Medicine, Chicago, Illinois, USA.

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; = .001). The median time to initiation of therapy was 4.8 hours vs 3.3 hours ( = .58), the median LOS was 24 and 18 days ( = .28), and 30-day mortality was 19% and 26% ( = .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.
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http://dx.doi.org/10.1093/ofid/ofz412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788339PMC
October 2019

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

J Appl Lab Med 2019 09 25;4(2):164-169. Epub 2019 Jun 25.

Department of Pathology, University of Chicago, Chicago, IL.

Background: Recently, the US Food and Drug Administration cleared 3 nucleic acid amplification test (NAAT) assays for detection of [group A (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.
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http://dx.doi.org/10.1373/jalm.2018.028696DOI Listing
September 2019

Improved rates of antimicrobial stewardship interventions following implementation of the Epic antimicrobial stewardship module.

Infect Control Hosp Epidemiol 2018 08 28;39(8):980-982. Epub 2018 Jun 28.

4Infectious Diseases and Global Health,University of Chicago Medical Center,Chicago,Illinois.

We evaluated the impact of the Epic antimicrobial stewardship module (EAM) on the number of interventions, antimicrobial usage, and clinical outcomes. Use of the EAM allowed us to significantly increase the number of ASP antimicrobial reviews and interventions while maintaining a sustained impact on antimicrobial utilization.
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http://dx.doi.org/10.1017/ice.2018.130DOI Listing
August 2018

Misdiagnosis of Bordetella bronchiseptica Respiratory Infection as Bordetella pertussis by Multiplex Molecular Assay.

Clin Infect Dis 2018 11;67(12):1919-1921

Section of Infectious Diseases and Global Health, University of Chicago, Illinois.

Multiplex polymerase chain reaction (PCR) tests are useful for the rapid detection of pathogens, though diagnostic challenges may arise. We report 2 immunocompromised patients with Bordetella bronchiseptica respiratory infection misdiagnosed as Bordetella pertussis using PCR, including discussion of transmission, diagnostic testing, clinical implications, and infection control considerations.
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http://dx.doi.org/10.1093/cid/ciy469DOI Listing
November 2018

Use of the Accelerate Pheno System for Identification and Antimicrobial Susceptibility Testing of Pathogens in Positive Blood Cultures and Impact on Time to Results and Workflow.

J Clin Microbiol 2018 01 26;56(1). Epub 2017 Dec 26.

Clinical Microbiology Laboratory, Department of Pathology, University of Chicago Medicine, Chicago, Illinois, USA.

The Accelerate Pheno system uses automated fluorescence hybridization technology with morphokinetic cellular analysis to provide rapid species identification (ID) and antimicrobial susceptibility testing (AST) results for the most commonly identified organisms in bloodstream infections. The objective was to evaluate the accuracy and workflow of bacterial and yeast ID and bacterial AST using the Accelerate Pheno system in the clinical microbiology laboratory. The consecutive fresh blood cultures received in the laboratory were analyzed by the Accelerate Pheno system within 0 to 8 h of growth detection. ID/AST performance, the average times to results, and workflow were compared to those of the routine standard of care. Of the 232 blood cultures evaluated (223 monomicrobial and 9 polymicrobial) comprising 241 organisms, the overall sensitivity and specificity for the identification of organisms were 95.6% and 99.5%, respectively. For antimicrobial susceptibility, the overall essential agreement was 95.1% and categorical agreement was 95.5% compared to routine methods. There was one very major error and 3 major errors. The time to identification and the time to susceptibility using the Accelerate Pheno system were decreased by 23.47 and 41.86 h, respectively, compared to those for the standard of care. The reduction in hands on time was 25.5 min per culture. The Accelerate Pheno system provides rapid and accurate ID/AST results for most of the organisms found routinely in blood cultures. It is easy to use, reduces hands on time for ID/AST of common blood pathogens, and enables clinically actionable results to be released much earlier than with the current standard of care.
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http://dx.doi.org/10.1128/JCM.01166-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5744213PMC
January 2018

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.

J Clin Virol 2017 10 5;95:84-85. Epub 2017 Sep 5.

Department of Pathology, The University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637, USA. Electronic address:

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.
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http://dx.doi.org/10.1016/j.jcv.2017.08.018DOI Listing
October 2017

Comparison of Cepheid Xpert Flu/RSV XC and BioFire FilmArray for Detection of Influenza A, Influenza B, and Respiratory Syncytial Virus.

J Clin Microbiol 2016 07 20;54(7):1902-1903. Epub 2016 Apr 20.

Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA

The Xpert Flu/RSV XC was compared to the FilmArray respiratory panel for detection of influenza (Flu) A, Flu B, and respiratory syncytial virus (RSV), using 128 nasopharyngeal swabs. Positive agreements were 100% for Flu A and RSV and 92.3% for Flu B. The Xpert may be useful in clinical situations when extensive testing is not required and may serve an important role in laboratories already performing broader respiratory panel testing.
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http://dx.doi.org/10.1128/JCM.00084-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922080PMC
July 2016

BioFire FilmArray Respiratory Panel for Detection of Enterovirus D68.

J Clin Microbiol 2016 Feb 25;54(2):457-9. Epub 2015 Nov 25.

The University of Chicago Medicine, Department of Pathology, Chicago, Illinois, USA.

During the enterovirus D68 (EV-D68) outbreak of 2014, the BioFire FilmArray (FA) respiratory panel was used to detect rhinovirus/enterovirus in respiratory specimens; suspected EV-D68-positive specimens were sent to CDC for confirmation. Positive rhinovirus/enterovirus FA targets revealed patterns loosely associated with EV-D68 that may be useful for confirmation triaging.
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http://dx.doi.org/10.1128/JCM.02339-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733204PMC
February 2016

Influenza among afebrile and vaccinated healthcare workers.

Clin Infect Dis 2015 Jun 2;60(11):1591-5. Epub 2015 Mar 2.

Department of Medicine.

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.
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http://dx.doi.org/10.1093/cid/civ163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108074PMC
June 2015

Pseudo-outbreak of Mycobacterium gordonae Following the Opening of a newly constructed hospital at a Chicago Medical Center.

Infect Control Hosp Epidemiol 2015 Feb;36(2):198-203

3Rush University Medical Center,Chicago,IL,USA.

OBJECTIVE To identify the source of a pseudo-outbreak of Mycobacterium gordonae DESIGN Outbreak investigation. SETTING University Hospital in Chicago, Ilinois. PATIENTS Hospital patients with M. gordonae-positive clinical cultures. METHODS An increase in isolation of M. gordonae from clinical cultures was noted immediately following the opening of a newly constructed hospital in January 2012. We reviewed medical records of patients with M. gordonae-positive cultures collected between January and December 2012 and cultured potable water specimens in new and old hospitals quantitatively for mycobacteria. RESULTS Of 30 patients with M. gordonae-positive clinical cultures, 25 (83.3%) were housed in the new hospital; of 35 positive specimens (sputum, bronchoalveolar lavage, gastric aspirate), 32 (91.4%) had potential for water contamination. M. gordonae was more common in water collected from the new vs. the old hospital [147 of 157 (93.6%) vs. 91 of 113 (80.5%), P=.001]. Median concentration of M. gordonae was higher in the samples from the new vs. the old hospital (208 vs. 48 colony-forming units (CFU)/mL; P<.001). Prevalence and concentration of M. gordonae were lower in water samples from ice and water dispensers [13 of 28 (46.4%) and 0 CFU/mL] compared with water samples from patient rooms and common areas [225 of 242 (93%) and 146 CFU/mL, P<.001]. CONCLUSIONS M. gordonae was common in potable water. The pseudo-outbreak of M. gordonae was likely due to increased concentrations of M. gordonae in the potable water supply of the new hospital. A silver ion-impregnated 0.5-μm filter may have been responsible for lower concentrations of M. gordonae identified in ice/water dispenser samples. Hospitals should anticipate that construction activities may amplify the presence of waterborne nontuberculous mycobacterial contaminants.
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http://dx.doi.org/10.1017/ice.2014.28DOI Listing
February 2015

Medical care for people in transition: symptoms may point to stories.

Health Prog 2014 Mar-Apr;95(2):49-52

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May 2014

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

Clin Infect Dis 2013 Apr 16;56(8):1067-74. Epub 2013 Jan 16.

Rush University Medical Center, Stroger Hospital of Cook County, and University of Illinois at Chicago Medical Center, Chicago, Illinois 60612, USA.

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.
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http://dx.doi.org/10.1093/cid/cit010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601722PMC
April 2013

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

Clin Infect Dis 2012 May 21;54(9):1296-303. Epub 2012 Feb 21.

Rush University Medical Center, Chicago, Illinois 60612, USA.

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.
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http://dx.doi.org/10.1093/cid/cis030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404690PMC
May 2012

Phaeomycotic cysts caused by Phoma species.

Diagn Microbiol Infect Dis 2011 Aug;70(4):531-3

Section of Infectious Diseases, John H. Stroger Jr. Hospital of Cook County, The Ruth M. Rothstein CORE Center and Rush University Medical Center, Chicago, IL 60612, USA.

Phoma species are primarily phytopathogens which have been reported to sporadically cause human disease. We report a patient with phaeohyphomycotic cysts caused by Phoma species, which were initially mistaken for ganglions.
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http://dx.doi.org/10.1016/j.diagmicrobio.2011.04.009DOI Listing
August 2011

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

J Lab Autom 2011 Aug 8;16(4):271-5. Epub 2011 May 8.

Medical Affairs, BD Diagnostic Systems, 7 Loveton Circle, MC 662, Sparks, MD 21152, USA.

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.
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http://dx.doi.org/10.1016/j.jala.2011.03.001DOI Listing
August 2011

Routine, rapid HIV testing of medicine service admissions in the emergency department.

Ann Emerg Med 2011 Jul;58(1 Suppl 1):S65-70

Department of Internal Medicine, Division of Infectious Diseases, John H. Stroger, Jr Hospital of Cook County, Chicago, IL 60612, USA.

Objective: We identify undiagnosed HIV among adult emergency department (ED) patients awaiting medicine admission through rapid testing, expedite their redirection to the inpatient HIV service, and improve linkage to ambulatory HIV care.

Methods: Two ED health educators offered rapid testing to patients aged 18 to 64 years from the high-acuity ED area from which most medicine admissions originate. Heath educators obtained consent, obtained fingerstick blood, and performed point-of-care testing. Patients with reactive results received counseling, confirmatory testing, and appointments at the affiliated HIV clinic.

Results: Between March 1, 2008, and February 28, 2009, 4,755 patients received testing. Thirty patients (0.6%) had received a new diagnosis of HIV; 26 were admitted and redirected to the HIV service. Characteristics of HIV positive patients were mean age 38 years, 87% men, 64% black, and 33% Hispanic; 76% had CD4 counts less than 200 cells/mm(3); 67% had HIV-related diagnoses; and 93% reported for ambulatory HIV care in a median of 10 days. During 2 preceding years, these patients had a mean of 3 previous health system visits without testing. During a 6-month quality assurance interval of the 5,340 ED medicine admissions, 31% of patients were eligible for testing, of whom 88% received testing (1% positive) and 12% declined; 29% of the 5,340 were not approached for testing; and 40% were deemed ineligible. Common reasons for ineligibility included older age, recent previous test, and known HIV-positive status.

Conclusion: Patients who receive a diagnosis of HIV in our ED before admission are extremely ill, most having AIDS. Targeted HIV screening of ED patients awaiting hospital admission facilitated timely diagnosis and reliable linkage to inpatient and outpatient HIV care.
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http://dx.doi.org/10.1016/j.annemergmed.2011.03.027DOI Listing
July 2011

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

Arch Pathol Lab Med 2010 Oct;134(10):1490-503

Department of Laboratory Medicine, University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA.

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.
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http://dx.doi.org/10.5858/2010-0098-CP.1DOI Listing
October 2010
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