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Item A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel(American Society for Microbiology, 2021) Wolk, Donna M.; Young, Stephen; Whitfield, Natalie N.; Reid, Jennifer L.; Thornberg, Adam; Carroll, Karen C.; Buchan, Blake W.; Davis, Thomas E.; Salimnia, Hossein; Pathology and Laboratory Medicine, School of MedicineBacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard-of-care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with negative Gram stain results. Of these, 109 samples had false-negative and/or -positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and postdiscordant resolution sample accuracy excludes 37 Gram-negative organisms representing 20 uncommon genera, 10 Gram-positive organisms, and 1 Candida species present in 5% of samples that are not targeted by the BCID-GN. The overall weighted positive percent agreement (PPA), which averages the individual PPAs from the 27 targets (Gram-negative and ARG), was 94.9%. The limit of detection ranged from 104 to 107 CFU/ml, except for one strain of Fusobacterium necrophorum at 108 CFU/ml.Item Clinical Performance of the BD CTGCTV2 Assay for the BD MAX System for Detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis Infections(Wolters Kluwer, 2021) Van Der Pol, Barbara; Torres-Chavolla, Edith; Kodsi, Salma; Cooper, Charles K.; Davis, Thomas E.; Fife, Kenneth H.; Taylor, Stephanie N.; Augenbraun, Michael H.; Gaydos, Charlotte A.; Medicine, School of MedicineBackground: Diagnostic options to combat the increasing rates of sexually transmitted infections recorded throughout the world increasingly include multiplex assays. Here we describe the estimated sensitivity and specificity of a triplex molecular assay that simultaneously detects Chlamydia trachomatis (CT), Neisseria gonorrhoeae (or gonococci [GC]), and Trichomonas vaginalis (TV). Methods: Participants (2547 women and 1159 men) were recruited from 12 clinics in the United States. BD CTGCTV2 for BD MAX System assay (CTGCTV2) results were obtained from vaginal and endocervical swabs, endocervical samples in cytology medium, and female and male urine. Results were compared with infection standards that were sample type and pathogen dependent. Results: Female specimen sensitivity estimates ranged from 92.7% to 98.4%, 92.9% to 100%, and 86.6% to 100% for CT, GC and TV, respectively. Male urine sensitivity estimates were 96.7%, 99.2%, and 97.9% for CT, GC, and TV, respectively. Specificity estimates were >98.7% for all sample types. Conclusions: BD CTGCTV2 performed well using a variety of sample types. As a true triplex assay, performed using a benchtop instrument, BD CTGCTV2 may be useful in settings where no testing is currently performed and in settings, such as reference laboratories, where testing turnaround time may be several days. Use of this assay at local laboratories may result in greater access to testing and a shorter time to result, which are important steps for improving our ability to combat sexually transmitted infections.Item Comparison of Four Commercially Available Group B Streptococcus Molecular Assays Using Remnant Rectal-Vaginal Enrichment Broths(Elsevier, 2018) Relich, Ryan F.; Buckner, Rebecca J.; Emery, Christopher L.; Davis, Thomas E.; Pathology and Laboratory Medicine, School of MedicineThe incidence of neonatal Group B streptococcal (GBS) disease has significantly declined since the widespread implementation of prenatal screening of expectant mothers for urogenital and gastrointestinal tract GBS colonization. Screening methods have evolved from exclusively culture-based approaches to more rapid and highly sensitive molecular methods. We chose to evaluate the performance of four commercially available GBS molecular tests for detection of GBS colonization using 299 antepartum rectal-vaginal specimens submitted to our laboratory for routine GBS screening. In 97% of instances, there was agreement between all three systems. When testing 1, 6, and 12 samples simultaneously, all methods performed comparably, but the ARIES® GBS assay required the least total hands-on time and the illumigene® Group B Streptococcus assay required the most hands-on time.Item Detection of (1,3)-β-d-Glucan in Cerebrospinal Fluid in Histoplasma Meningitis(American Society for Microbiology, 2018-09-25) Myint, Thein; Chow, Felicia C.; Bloch, Karen C.; Raymond-Guillen, Luke; Davis, Thomas E.; Wright, Patty W.; Woc-Colburn, Laila; Khairy, Raed N.; Street, Alan C.; Yamamoto, Tomotaka; Albers, Amanda; Wheat, L. Joseph; Hage, Chadi A.; Medicine, School of MedicineThe diagnosis of central nervous system (CNS) histoplasmosis is often difficult. Although cerebrospinal fluid (CSF) (1,3)-β-d-glucan (BDG) is available as a biological marker for the diagnosis of fungal meningitis, there are limited data on its use for the diagnosis of Histoplasma meningitis. We evaluated CSF BDG detection, using the Fungitell assay, in patients with CNS histoplasmosis and controls. A total of 47 cases and 153 controls were identified. The control group included 13 patients with a CNS fungal infection other than histoplasmosis. Forty-nine percent of patients with CNS histoplasmosis and 43.8% of controls were immunocompromised. The median CSF BDG level was 85 pg/ml for cases, compared to <31 pg/ml for all controls (P < 0.05) and 82 pg/ml for controls with other causes of fungal meningitis (P = 0.27). The sensitivity for detection of BDG in CSF was 53.2%, whereas the specificity was 86.9% versus all controls and 46% versus other CNS fungal infections. CSF BDG levels of ≥80 pg/ml are neither sensitive nor specific to support a diagnosis of Histoplasma meningitis.Item Detection of the Dimorphic Phases of Mucor circinelloides in Blood Cultures from an Immunosuppressed Female.(Hindawi, 2016) Arroyo, Miguel A.; Schmitt, Bryan H.; Davis, Thomas E.; Relich, Ryan F.; Department of Pathology and Laboratory Medicine, IU School of MedicineMucormycosis fungemia is rarely documented since blood cultures are nearly always negative. We describe a case of Mucor circinelloides fungemia in a patient with a history of a sinus infection, sarcoidosis, and IgG deficiency. The identity of the isolate was supported by its microscopic morphology and its ability to convert into yeast forms under anaerobic conditions. The early detection, initiation of liposomal amphotericin B treatment, and reversal of underlying predisposing risk factors resulted in a good outcome.Item Direct antimicrobial susceptibility testing of positive blood cultures: A comparison of the accelerate Pheno™ and VITEK® 2 systems(Elsevier, 2019) Schneider, Jack G.; Wood, James B.; Smith, Nathan W.; Emery, Christopher L.; Davis, Thomas E.; Manaloor, John J.; Bocian, Brittany; Schmitt, Bryan H.; Medicine, School of MedicineObjectives To compare the performance and time-to-result (TTR) for antimicrobial susceptibility testing (AST) of positive blood cultures (PBC) using the Accelerate Pheno™ system (AXDX) and both a direct VITEK® 2 card inoculation workflow (DV2) and traditional FDA-approved VITEK® 2 workflow using subcultured isolates (V2). Methods Patient samples with monomicrobial Gram-negative rod bacteremia were tested on AXDX and DV2 in tandem, and compared to V2 AST results. Categorical agreement (CA) errors were adjudicated using broth microdilution. Instrumentation times and AST TTR were compared. Results AXDX and DV2 had a CA of 91.5% and 97.4%, respectively, compared to V2. Post-adjudication, AXDX, DV2, and V2 had CA of 94.7%, 95.7% and 96.5%, respectively. Instrument run times were 6.6 h, 9.4 h, and 9.2 h, and AST TTR were 8.9 h, 12.9 h and 35.5 h, respectively. Conclusions AXDX and DV2 AST is fast and reliable, which may have significant antimicrobial stewardship implications.Item Evaluation of T2Candida Panel for detection of Candida in peritoneal dialysates(Sage, 2019-01) Kouri, Anne M.; Kieffer, Theodore W.; Nailescu, Corina; Leiser, Jeffrey; Schmitt, Bryan H.; Relich, Ryan F.; Davis, Thomas E.; Manaloor, John J.; Pediatrics, School of MedicineFungal peritonitis in the peritoneal dialysis population is difficult to diagnose promptly due to the inherently slow cultivation-based methods currently required for identification of peritonitis pathogens. Because of the moderate risk for severe complications, the need for rapid diagnostics is considerable. One possible solution to this unmet need is the T2Candida Panel, a new technology designed to detect the most common pathogenic Candida spp. directly from whole blood specimens in as little as a few hours. We hypothesized that this technology could be applied to the detection of Candida in peritoneal dialysate, a matrix not currently approved by the Food and Drug Administration for testing by this system. Remnant dialysate samples from three healthy (noninfected) pediatric peritoneal dialysis patients were spiked with Candida glabrata, serially diluted, and tested in triplicate with unaltered dialysate specimens. The assay detected C. glabrata in 100% of spiked dialysate samples across the full spectrum of dilutions tested, and no assay inhibition or cross-reactivity was noted. These findings suggest one of possibly more applications of this technology. The positive clinical implications of this test will continue to be realized as its use is validated in peritoneal dialysate and other patient specimen types.Item The Incidence and Incubation Period of False Positive Cultures in Shoulder Surgery(Elsevier, 2020) McCarroll, Tyler R.; Jaggers, Ryan R.; Cagle, Robert A.; Davis, Thomas E.; Easton, Brenda L.; Curless, Chris T.; Misamore, Gary W.; Pathology and Laboratory Medicine, School of MedicineBackground Postoperative shoulder infection (PSI) is a significant complication requiring timely identification and treatment. Indolent infections such as those involving Cutibacterium acnes (C. acnes, recently reclassified from Propionibacterium acnes 1) provide a diagnostic dilemma as they present differently without the acute symptoms associated with most postoperative bone and joint infections. Furthermore, C. acnes is thought to be a common contaminant isolated from intraoperative cultures. With no consensus algorithm, long hold cultures play a major role in guiding management decisions in potential PSI. Our study seeks to determine the incidence of positive cultures in both open and arthroscopic procedures in non-infected patients as well as clarify whether or not an increase in the incubation time frame leads to an increased rate of culture growth. Method ology: One hundred patients were prospectively enrolled into either an open and arthroscopic procedure group. Patients with abnormal inflammatory labs, history of previous shoulder surgery, or corticosteroid injection within six months of surgery were excluded from the study. Three cultures were obtained for each patient (1superficial tissue culture, 2- tissue culture, and 3- “sterile” control swab). Cultures were held for 28 days and checked on regular intervals. All patients were followed clinically for 6 months to ensure no signs of postoperative infection. Results Ultimately ninety-five patients were included in the final analysis. The false-positive rate in open shoulder surgery was 17.02% and arthroscopic shoulder surgery was 10.4%. The incidence of positive C. acnes cultures was 6.4% in the open group while C. acnes was not isolated in the arthroscopic group. All positive bacterial cultures were reported within seven days of collection. One culture was positive for “mold” at 26 days. Conclusion A relatively high false-positive culture rate occurred in both open and arthroscopic shoulder surgery. C. acnes was the most commonly identified bacteria in cultures in the open surgery group. Knowledge of one’s own institutional false-positive culture rate could be important in avoiding potentially inappropriate treatment. Additionally, we found that holding cultures longer than 14 days did not lead to an increased rate of false positive culture results.Item Investigation of peptide nucleic acid fluorescence in situ hybridization for diagnosis of ventilator-associated pneumonia in bronchoalveolar lavage specimens(2014-01-03) Phillips, Aaron M.; Davis, Thomas E.; Leland, Diane S.; Relich, Ryan F.Item Multicenter Clinical Evaluation of the Xpert GBS LB Assay for Detection of Group B Streptococcus in Prenatal Screening Specimens(American Society for Microbiology, 2015-02) Buchan, Blake W.; Faron, Matthew L.; Fuller, DeAnna; Davis, Thomas E.; Mayne, Donna; Ledeboer, Nathan A.; Department of Microbiology and Immunology, IU School of MedicineNeonatal infection with Streptococcus agalactiae (group B Streptococcus [GBS]) is a leading cause of sepsis and meningitis in newborns. Recent guidelines have recommended universal screening of all pregnant women to identify those colonized with GBS and administration of peripartum prophylaxis to those identified as carriers to reduce the risk of early-onset GBS disease in neonates. Enriched culture methods are the current standard for prenatal GBS screening; however, the implementation of more sensitive molecular diagnostic tests may be able to further reduce the risk of early-onset GBS infection. We report a clinical evaluation of the Xpert GBS LB assay, a molecular diagnostic test for the identification of GBS from broth-enriched vaginal/rectal specimens obtained during routine prenatal screening. A total of 826 specimens were collected from women undergoing prenatal screening (35 to 37 weeks' gestation) and tested at one of three clinical centers. Each swab specimen was tested directly prior to enrichment using the Xpert GBS assay. Following 18 to 24 h of broth enrichment, each specimen was tested using the Xpert GBS LB assay and the FDA-cleared Smart GBS assay as a molecular diagnostic comparator. Results obtained using all three molecular tests were compared to those for broth-enriched culture as the gold standard. The sensitivity and specificity of the Xpert GBS LB assay were 99.0% and 92.4%, respectively, compared to those for the gold standard culture. The Smart GBS molecular test demonstrated sensitivity and specificity of 96.8% and 95.5%, respectively. The sensitivities of the two broth-enriched molecular methods were superior to those for direct testing of specimens using the Xpert GBS assay, which demonstrated sensitivity and specificity of 85.7% and 96.2%, respectively.