Multicenter evaluation of the BIOFIRE Joint Infection Panel for the detection of bacteria, yeast, and AMR genes in synovial fluid samples.

The bioMérieux BIOFIRE Joint Infection (JI) Panel is a multiplex in vitro diagnostic test for the simultaneous and rapid (~1 h) detection of 39 potential pathogens and antimicrobial resistance (AMR) genes directly from synovial fluid (SF) samples. Thirty-one species or groups of microorganisms are included in the kit, as well as several AMR genes. This study, performed to evaluate the BIOFIRE JI Panel for regulatory clearance, provides data from a multicenter evaluation of 1,544 prospectively collected residual SF samples with performance compared to standard-of-care (SOC) culture for organisms or polymerase chain reaction (PCR) and sequencing for AMR genes. The BIOFIRE JI Panel demonstrated a sensitivity of 90.9% or greater for all but six organisms and a positive percent agreement (PPA) of 100% for all AMR genes. The BIOFIRE JI Panel demonstrated a specificity of 98.5% or greater for detection of all organisms and a negative percent agreement (NPA) of 95.7% or greater for all AMR genes. The BIOFIRE JI Panel provides an improvement over SOC culture, with a substantially shorter time to result for both organisms and AMR genes with excellent sensitivity/PPA and specificity/NPA, and is anticipated to provide timely and actionable diagnostic information for joint infections in a variety of clinical scenarios.

Clinical comparison and agreement of PCR, antigen, and viral culture for the diagnosis of COVID-19: Clinical Agreement Between Diagnostics for COVID19.

The aim of this study is to compare the COVID-19 nasopharyngeal PCR (NP PCR) to antigen, nasal PCR, and viral culture. One-hundred-and-fourteen risk-stratified patients were tested by culture, nasal PCR, NP PCR, and Ag testing. Twenty (48%) of the high risk and 23 (32%) of the low risk were NP PCR positive. Compared with NP PCR, the sensitivity of nasal PCR, Sofia Ag, BinaxNOW Ag, and culture were 44%, 31%, 37%, and 15%. In the high risk group, the sensitivity of these tests improved to 71%, 37%, 50%, and 22%. Agreement between tests was highest between nasal PCR and both antigen tests. Patients who were NP PCR positive but antigen negative were more likely to have remote prior COVID-19 infection (p<0.01). Nasal PCR and antigen positive patients were more likely to have symptoms (p = 0.01).

Microbiology of bile aspirates obtained at ERCP in patients with suspected acute cholangitis.

BACKGROUND: The cornerstone of treatment for acute cholangitis is source control with biliary drainage and early antibiotics. The primary aim of this study was to describe the microbiology of bile aspirate pathogens obtained at the time of endoscopic retrograde cholangiopancreatography (ERCP) in patients suspected of having acute cholangitis. METHODS: In this single-center retrospective study, patients were included if a bile aspirate was collected at ERCP for suspicion of acute cholangitis, from 1 January 2010 to 31 December 2016. RESULTS: There were 721 ERCP procedures for suspected acute cholangitis with bile culture results, with 662 positive bile cultures (91.8 %). Pathogens included: Enterococcus species (spp.) 448 (67.7 %); Klebsiella spp. 295 (44.6 %); Escherichia coli 269 (40.6 %); Pseudomonas spp. 52 (7.9 %); and anaerobes 64 (9.7 %). Susceptibility of Klebsiella pneumoniae and E.coli isolates to ciprofloxacin was 88 % and 64 %, respectively. Extended-spectrum beta-lactamases and carbapenem resistance were found in 7.9 % and 3.6 % of Enterobacteriaceae, respectively. There were 437 concurrent blood cultures, of which 174 were positive (39.8 % of cultures drawn). Prior biliary endoscopic sphincterotomy (ES) was evident in 459 ERCP cases (63.7 %), and was associated with increased frequency of Klebsiella spp., Pseudomonas aeruginosa, Enterobacter spp., and Enterococcus spp. Prior biliary ES significantly increased the probability of vancomycin-resistant Enterococcus (VRE). CONCLUSIONS: The vast majority of bile cultures (91.8 %) were positive. The susceptibilities of E.coli and K.pneumoniae to ciprofloxacin are lower than historically noted. A notable portion of cultures contained pathogenic drug-resistant organisms. Prior biliary ES is associated with a higher frequency of certain organisms and higher frequency of VRE.

Evaluation of T2Candida Panel for detection of Candida in peritoneal dialysates.

Fungal 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.

A Multicenter Study of the Revogene C. difficile System for Detection of the Toxin B Gene from Unformed Stool Specimens.

Clostridioides difficile is the leading cause of diarrhea in hospitalized U.S. patients and results in over 400,000 cases of C. difficile infection per year. C. difficile infections have mortality rates of 6 to 30% and significantly increase health care costs, because of increased length of stay and increased frequency of readmissions due to recurrences. Efforts to reduce the spread of C. difficile in hospitals have led to the development of rapid sensitive diagnostic methods. A multicenter study was performed to establish the performance characteristics of the Revogene C. difficile test (Meridian Bioscience, Cincinnati, OH, USA) for use in detection of the toxin B (tcdB) gene from toxigenic C. difficile The Revogene instrument is a new molecular platform that uses real-time PCR to detect nucleic acids in up to 8 specimens at a time. A total of 2,461 specimens from symptomatic patients that had been submitted for C. difficile testing were enrolled at 7 sites throughout the United States and Canada for evaluation of the assay. Each stool specimen was tested for the presence of the tcdB gene using the Revogene C. difficile test, and results were compared with those of the reference method, a combination of direct and enriched culture methods. Overall, the Revogene C. difficile test demonstrated a sensitivity of 85.0% (95% confidence interval, 80% to 88%) and a specificity of 97.2% (95% confidence interval, 96% to 98%). The Revogene C. difficile test, using clinical stool specimens for detection of tcdB in C. difficile, demonstrated acceptable sensitivity and specificity, with a short turnaround time.

Direct antimicrobial susceptibility testing of positive blood cultures: a comparison of the Accelerate Pheno™ and VITEK® 2 systems.

OBJECTIVES: 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 93.4% and 97.4%, respectively, compared to V2. Postadjudication, 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 ASTs are fast and reliable, which may have significant antimicrobial stewardship implications.

Performance of the T2Bacteria Panel for Diagnosing Bloodstream Infections: A Diagnostic Accuracy Study.

Background: Blood cultures, the gold standard for diagnosing bloodstream infections (BSIs), are insensitive and limited by prolonged time to results. The T2Bacteria Panel (T2 Biosystems) is a direct-from-blood, nonculture test that identifies the most common ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli). Objective: To assess performance of the T2Bacteria Panel in diagnosing suspected BSIs in adults. Design: Prospective patient enrollment (8 December 2015 through 4 August 2017). Setting: Eleven U.S. hospitals. Patients: 1427 patients for whom blood cultures were ordered as standard of care. Intervention: Paired blood culture and T2Bacteria testing. Measurements: Performance of T2Bacteria compared with a single set of blood cultures in diagnosing proven, probable, and possible BSIs caused by T2Bacteria-targeted organisms. Results: Blood culture and T2Bacteria results were positive for targeted bacteria in 3% (39 of 1427) and 13% (181 of 1427) of patients, respectively. Mean times from start of blood culture incubation to positivity and species identification were 38.5 (SD, 32.8) and 71.7 (SD, 39.3) hours, respectively. Mean times to species identification with T2Bacteria were 3.61 (SD, 0.2) to 7.70 (SD, 1.38) hours, depending on the number of samples tested. Per-patient sensitivity and specificity of T2Bacteria for proven BSIs were 90% (95% CI, 76% to 96%) and 90% (CI, 88% to 91%), respectively; the negative predictive value was 99.7% (1242 of 1246). The rate of negative blood cultures with a positive T2Bacteria result was 10% (146 of 1427); 60% (88 of 146) of such results were associated with probable (n = 62) or possible (n = 26) BSIs. If probable BSIs and both probable and possible BSIs were assumed to be true positives missed by blood culture, per-patient specificity of T2Bacteria was 94% and 96%, respectively. Limitation: Low prevalence of positive blood cultures, collection of a single set of culture specimens, and inability of T2Bacteria to detect nontargeted pathogens. Conclusion: The T2Bacteria Panel rapidly and accurately diagnoses BSIs caused by 5 common bacteria. Primary Funding Source: T2 Biosystems.

Susceptibility Provision Enhances Effective De-escalation (SPEED): utilizing rapid phenotypic susceptibility testing in Gram-negative bloodstream infections and its potential clinical impact.

Objectives: We evaluated the performance and time to result for pathogen identification (ID) and antimicrobial susceptibility testing (AST) of the Accelerate Pheno™ system (AXDX) compared with standard of care (SOC) methods. We also assessed the hypothetical improvement in antibiotic utilization if AXDX had been implemented. Methods: Clinical samples from patients with monomicrobial Gram-negative bacteraemia were tested and compared between AXDX and the SOC methods of the VERIGENE® and Bruker MALDI Biotyper® systems for ID and the VITEK® 2 system for AST. Additionally, charts were reviewed to calculate theoretical times to antibiotic de-escalation, escalation and active and optimal therapy. Results: ID mean time was 21 h for MALDI-TOF MS, 4.4 h for VERIGENE® and 3.7 h for AXDX. AST mean time was 35 h for VITEK® 2 and 9.0 h for AXDX. For ID, positive percentage agreement was 95.9% and negative percentage agreement was 99.9%. For AST, essential agreement was 94.5% and categorical agreement was 93.5%. If AXDX results had been available to inform patient care, 25% of patients could have been put on active therapy sooner, while 78% of patients who had therapy optimized during hospitalization could have had therapy optimized sooner. Additionally, AXDX could have reduced time to de-escalation (16 versus 31 h) and escalation (19 versus 31 h) compared with SOC. Conclusions: By providing fast and reliable ID and AST results, AXDX has the potential to improve antimicrobial utilization and enhance antimicrobial stewardship.

A double-reprocessing high-level disinfection protocol does not eliminate positive cultures from the elevators of duodenoscopes.

BACKGROUND AND STUDY AIM: Duodenoscopes have been the source of serious infection, despite correct performance of high-level disinfection (HLD). This study aimed to observe the impact of performing HLD twice on the rate of positive cultures from duodenoscope elevators. METHODS: We performed double HLD (DHLD; i. e. complete manual cleaning followed by automated reprocessing, with the entire process repeated) and then randomly cultured the elevators of our duodenoscopes on about 30 % of occasions. RESULTS: DHLD was associated with positive elevator cultures for any microorganism in 9.4 % of cases, with a 0.8 % rate of known pathogens (627 cultures) between May 2015 and February 2016. After February 2016, and in association with changing the precleaning fluid, as well as use of a new FDA-recommended cleaning brush, the rate of positive cultures for any microorganism after DHLD was 4.8 % and 0.2 % for known pathogens (420 cultures). In a third phase, characterized by a change in personnel performing DHLD and retirement of a duodenoscope with a high rate of positive cultures, the rate of positive cultures for any microorganism was 4.9 % (783 cultures) and the rate of positive culture for known pathogens was 0.3 %. To our knowledge, no duodenoscope transmission of infection occurred during the study interval. CONCLUSIONS: DHLD resulted in a low rate of positive cultures for known pathogens and for organisms of low pathogenic potential, but did not eliminate these, from duodenoscope elevators. Additional improvements in HLD protocols and/or duodenoscope design are needed.

Induction of ß-Lactamase Activity and Decreased ß-Lactam Susceptibility by CO2 in Clinical Bacterial Isolates.

Antimicrobial susceptibility testing of clinical isolates is a crucial step toward appropriate treatment of infectious diseases. The clinical isolate Francisella philomiragia 14IUHPL001, recently isolated from a 63-year-old woman with atypical pneumonia, featured decreased susceptibility to ß-lactam antibiotics when cultivated in 5% CO2. Quantitative ß-lactamase assays demonstrated a significant (P < 0.0001) increase in enzymatic activity between bacteria cultivated in 5% CO2 over those incubated in ambient air. The presence of ß-lactamase genes blaTEM and blaSHV was detected in the clinical isolate F. philomiragia 14IUHPL001 by PCR, and the genes were positively identified by nucleotide sequencing. Expression of blaTEM and blaSHV was detected by reverse transcription-PCR during growth at 5% CO2 but not during growth in ambient air. A statistically significant alkaline shift was observed following cultivation of F. philomiragia 14IUHPL001 in both ambient air and 5% CO2, allowing desegregation of the previously reported effects of acidic pH from the currently reported effect of 5% CO2 on blaTEM and blaSHV ß-lactamases. To ensure that the observed phenomenon was not unique to F. philomiragia, we evaluated a clinical isolate of blaTEM-carrying Haemophilus influenzae and found parallel induction of blaTEM gene expression and ß-lactamase activity at 5% CO2 relative to ambient air. IMPORTANCE ß-Lactamase induction and concurrent ß-lactam resistance in respiratory tract pathogens as a consequence of growth in a physiologically relevant level of CO2 are of clinical significance, particularly given the ubiquity of TEM and SHV ß-lactamase genes in diverse bacterial pathogens. This is the first report of ß-lactamase induction by 5% CO2.

Detection of the Dimorphic Phases of Mucor circinelloides in Blood Cultures from an Immunosuppressed Female.

Mucormycosis 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.

Performance of the FilmArray® blood culture identification panel utilized by non-expert staff compared with conventional microbial identification and antimicrobial resistance gene detection from positive blood cultures.

Utilization of commercially available rapid platforms for microbial identification from positive blood cultures is useful during periods of, or in laboratories with, limited expert staffing. We compared the results of the FilmArray® BCID Panel performed by non-expert technologists to those of conventional methods for organism identification performed by skilled microbiologists. Within 8 h of signalling positive by a continuous monitoring blood culture system, positive bottles were analysed by the FilmArray BCID Panel. Data from these analyses were compared to standard-of-care testing, which included conventional and automated methods. To gauge the ease of use of the BCID Panel by non-expert staff, technologists unfamiliar with diagnostic bacteriology performed the testing without prior knowledge of the Gram stain results, or even whether organisms were detected. Identifications of 172/200 (86 %) positive blood cultures using the BCID Panel were consistent with identifications provided by standard-of-care methods. Standard-of-care testing identified organisms in 20 positive blood cultures, which were not represented on the BCID Panel. Seven (3.5 %) blood cultures demonstrated a discrepancy between the methods, which could not be attributed to either a lack of representation on the panel or unclear separate detection of organisms in a mixed blood culture of a shared genus or grouping of organisms, e.g. Staphylococcus or Enterobacteriaceae . One (0.5 %) blood culture yielded invalid results on two separate panels, so it was eliminated from the study. The easy-to-use FilmArray® technology shows good correlation with blood culture identification and antibiotic resistance detection performed by conventional methods. This technology may be particularly useful in laboratories with limited staffing or limited technical expertise.

Schwanniomyces etchellsii: an unusual cause of fungemia in a patient with cholecystitis.

Schwanniomyces species are largely unrecognized as being pathogenic, and a paucity of published reports exist regarding their role as infectious agents. Here, for the first time, we describe a case of human infection caused by Schwanniomyces etchellsii in a patient with cholecystitis.

An unusual presentation of leishmaniasis in a human immunodeficiency virus-positive individual.

INTRODUCTION: Leishmaniasis is a neglected tropical disease caused by vector-borne protozoa of the genus Leishmania. Cutaneous and mucocutaneous forms result in disfiguration or mutilation, whilst visceral leishmaniasis (VL) affects multiple organs and is fatal if untreated. Notably, Leishmania are capable of establishing a chronic infection, which may reactivate years after initial infection when the host becomes immune-suppressed. CASE PRESENTATION: A 24-year-old human immunodeficiency virus (HIV)-positive male presented for excision of anal condylomas. At the time of his current condyloma excision, the patient had no additional symptoms or cutaneous findings, but was noted to have been only intermittently compliant with his antiretroviral therapy. Microscopic examination of the haematoxylin and eosin-stained anal condyloma tissue revealed koilocytic change, ulceration and brisk histiocytic inflammation containing numerous small intracellular bodies suggestive of Leishmania amastigotes. A bone marrow biopsy was performed and demonstrated similar intracellular forms. Anal condyloma tissue and bone marrow aspirate were sent to the Centers for Disease Control and Prevention's Parasitic Diseases Branch for confirmation of Leishmania and speciation. Specific immunohistochemical staining for Leishmania in the tissue section was positive and the species was confirmed as Leishmania donovani by PCR. Subsequently, the patient resumed highly active antiretroviral therapy and received anti-Leishmania therapy. CONCLUSION: Whilst the presentation of VL in HIV-positive patients is often similar to those without HIV, here we describe an unusual initial presentation of leishmaniasis in an HIV-positive patient where the parasite was found in an anal condyloma. VL is a critical diagnosis that should be considered and pursued when leishmaniasis is encountered in seemingly illogical clinical settings.

Nonimpact of Decolonization as an Adjunctive Measure to Contact Precautions for the Control of Methicillin-Resistant Staphylococcus aureus Transmission in Acute Care.

This was an observational study comparing methicillin-resistant Staphylococcus aureus (MRSA) transmission with no decolonization of medical patients to required decolonization of all MRSA carriers during two consecutive periods: baseline with no decolonization of medical patients (16 months) and universal MRSA carrier decolonization (13 months). The setting was a one-hospital, 156-bed facility with 9,200 annual admissions. Regression models were used to compare rates of MRSA acquisition. The chi-square test was used to compare event frequencies. We used rates of MRSA clinical disease as an outcome monitor of the program. Analysis was done on 15,666 patients who had admission and discharge tests; 27.9% of inpatient days were occupied by a MRSA-positive patient (colonized patient-days) who received decolonization while hospitalized during the baseline period (this 27.9% represented those who had planned surgery) compared to 76.0% during the intervention period (P < 0.0001). The rate of MRSA transmission was 97 events (1.0%) for 9,415 admissions (2.0 transmission events/1,000 patient-days) during baseline and was 87 (1.4%) for 6,251 admissions (2.7 transmission events/1,000 patient-days) during intervention (P = 0.06; rate ratio, 0.74; 95% confidence interval [CI], 0.55 to 1.00). The MRSA nosocomial clinical disease rate was 5.9 infections/10,000 patient-days in the baseline period and was 7.2 infections/10,000 patient-days for the intervention period (rate ratio, 0.82; 95% CI, 0.46 to 1.45; P = 0.49). Decolonization of MRSA patients does not add benefit when contact precautions are used for patients colonized with MRSA in acute (hospital) care.

Malassezia Pneumonia: A Rare Complication of Parenteral Nutrition Therapy.

Malassezia species (formerly known as Pityrosporum) are part of normal human skin flora and have been associated with benign dermatologic conditions, such as seborrheic dermatitis and tinea versicolor. In rare cases, however, Malassezia has been associated with systemic disease in immunocompromised patients and infants in the neonatal intensive care unit. Malassezia species require long-chain fatty acids for growth and therefore have a known predilection for individuals receiving lipid containing intravenous parenteral nutrition (PN). Systemic infections are characterized by prolonged fevers and illness but can include nonspecific signs and symptoms. We present the diagnosis and management of a rare case of an immunocompetent, nonneonatal, PN-dependent child with Malassezia furfur pneumonia.

Francisella philomiragia Bacteremia in a Patient with Acute Respiratory Insufficiency and Acute-on-Chronic Kidney Disease.

Francisella philomiragia is a very uncommon pathogen of humans. Diseases caused by it are protean and have been reported largely in near-drowning victims and those with chronic granulomatous disease. We present a case of F. philomiragia pneumonia with peripheral edema and bacteremia in a renal transplant patient and review the diverse reports of F. philomiragia infections.

Blastomycosis in Indiana: Clinical and Epidemiologic Patterns of Disease Gleaned from a Multicenter Retrospective Study.

BACKGROUND: To better understand clinical and epidemiologic patterns of blastomycosis, we report on a large series of blastomycosis in Indiana. METHODS: All microbiologically and histopathologically confirmed cases of blastomycosis from four hospitals serving Central Indiana from 1985 to 2014 were identified. Available data were collected. Data on population estimates, annual precipitation, and construction in Indiana were evaluated for correlations with incidence rates of blastomycosis. RESULTS: A total of 114 patients were identified. The mean age was 44.4 years; 27% had diabetes mellitus, and 16% were immunosuppressed. Most presented with pneumonia (90%); 48% had extrapulmonary disease (CNS involvement in 9%), and 15% developed ARDS. Cultures, cytopathology, and histopathology were positive in 86%, 27%, and 85% of the sample, respectively, and fungal antigen was positive in 76%. Amphotericin B was administered in 49%, and 87% received an azole. Total mortality was 12%. Immunosuppression (OR = 3.0), diabetes mellitus (OR = 2.9), and multilobar pneumonia (OR = 2.9) were associated with increased likelihood of ICU admission. There was a significant increase in incidence over time in Marion County. There was no correlation with amount of precipitation, but the rise in incidence coincided with a 2005 state initiative to expand Indiana's highway infrastructure. CONCLUSIONS: The incidence of blastomycosis in Central Indiana may be on the rise. Physicians in endemic areas should be aware of the potentially fulminant consequences of the disease.