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Introduction. Infectious gastroenteritis is a common reason for consulting a physician. Although most cases of gastrointestinal illness are self-limiting, the identification of the etiologic pathogen by stool specimen analysis is important in cases of more severe illness and for epidemiological reasons.Due to the broad range of causative pathogens, the conventional examination of a stool specimen is labour-intensive and usually requires different diagnostic methods. Multiplex PCR tests [e.g. BioFire Gastrointestinal (GI) Panel] allow the rapid detecting of up to 22 pathogens in one test.Hypothesis. Using a multiplex PCR panel to test stool specimens for infectious gastroenteritis pathogens can improve the detection rate, reduce the time-to-result and hands-on time and lower the costs of a microbiology laboratory.Aim. This study was aimed at evaluating the detection rate, the workflow and associated costs of stool specimen management using the BioFire GI Panel versus conventional methods.Methodology. Stool specimens were evaluated prospectively during the routine operation. Pathogen detection rate, hands-on time, time-to-result and material and personnel costs were determined for the BioFire GI Panel and conventional methods-the latter based on physician request and excluding viral testing.Results. Analysing 333 specimens collected between 2019 and 2020, the detection rate of enteropathogens was significantly higher with a positivity rate of 39.9â% using the multiplex PCR panel compared with 15.0â% using the conventional methods. The BioFire GI Panel presented results in a median time of 2.2 h compared with 77.5 h for culture and 22.1 h for antigen testing, noting that no tests were performed at weekends except for toxinogenic Clostridioides difficile. Based on list prices, the BioFire GI Panel was nine times more expensive compared with conventional methods, whereas hands-on-time was significantly lower using the BioFire GI Panel.Conclusion. Multiplex PCR panels are valuable tools for laboratory identification of infectious agents causing diarrhoea. The higher costs of such a multiplex PCR panel might be outweighed by the higher detection rate, ease of handling, rapid results and most likely improved patient management. However, these panels do not provide information on antimicrobial susceptibility testing. Therefore, if this is necessary for targeted therapy or if outbreak monitoring and control is required, specimens must still be cultured.
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Gastroenteritis , Reacción en Cadena de la Polimerasa Multiplex , Humanos , Flujo de Trabajo , Técnicas de Diagnóstico Molecular/métodos , Gastroenteritis/diagnóstico , Gastroenteritis/microbiología , Diarrea , Heces/microbiologíaRESUMEN
The diagnosis of acute gastroenteritis is an ongoing clinical challenge in terms of identification of the etiologic agent, time to results, and appropriate treatment. Rapid detection of gastrointestinal pathogens is needed to improve patient care. This study evaluates the performance of the QIAstat-Dx gastrointestinal panel (Q-GP; Investigational Use Only) compared to the Luminex xTAG gastrointestinal pathogen panel (L-GPP; US-IVD). Using 245 stool specimens, we evaluated 10 different targets including rotavirus, norovirus, Salmonella, Shigella, Campylobacter, Giardia, Cryptosporidium, Escherichia coli O157, enterotoxigenic E. coli (ETEC), and Shiga toxin-producing E. coli (STEC). For the viral targets, the percent positive agreement (PPA) for rotavirus was 100% (n = 19) and that for norovirus was 91% (20/22). For the parasitic targets, the PPA was 100% for Giardia and Cryptosporidium (n = 18 and n = 23, respectively). The PPA was 96% for Salmonella (22/23) and Campylobacter (22/23), and the PPA for Shigella was 100% (n = 23). For the E. coli targets, a PPA of 94% was achieved for STEC (32/34) and 96% for ETEC (24/25). We did not assess PPA for the E. coli O157 target as the Q-GP O157 call is stx dependent. The negative percent agreement across all targets was 99.1%. Our study suggests that QIAstat-Dx GP provides comparable results to Luminex GPP based on the analysis of targets found on both panels.
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Campylobacter , Criptosporidiosis , Cryptosporidium , Escherichia coli O157 , Gastroenteritis , Norovirus , Rotavirus , Humanos , Gastroenteritis/diagnóstico , HecesRESUMEN
Fecal culture for isolation and identification of Shigella may take days. The BioFire FilmArray Gastrointestinal (GI) panel (bioMérieux, France) is a PCR-based assay that detects enteric pathogens including Shigella/enteroinvasive Escherichia coli (EIEC) in about an hour. The aim of this study was to evaluate the impact of GI panel detection of Shigella in a pediatric emergency department (ED) during an outbreak. Stool samples from children with acute gastroenteritis were tested by the GI panel. Test results were either withheld in preintervention (PRE) or reported to clinicians/families in the postintervention (POST) period. The impact of the GI panel testing on patient management and outcomes was measured. Shigella/EIEC was identified by the GI panel in the PRE (n = 30) and POST (n = 21) phase. The GI panel detected more Shigella infections than did culture; six of 31 (19.4%) Shigella GI panel-positive patients who also had stool cultures were missed by culture. Azithromycin therapy was prescribed for 20% of subjects in the PRE phase and 71.4% of subjects in the POST phase (P < 0.001). Time from the clinical encounter until starting azithromycin therapy was shorter in the POST phase (n = 9), 8.25 h (range, 6.37 to 52.37 h), than in the PRE phase (n = 1), 72 h. Six subjects in the PRE phase visited additional providers compared with one in the POST phase. Prompt diagnosis of shigellosis with the GI panel may provide the opportunity for prompt antimicrobial therapy and avoid additional visits to providers due to early definitive diagnosis. Prompt diagnosis of Shigella at an ED visit may optimize patient management and reduce transmission.
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Disentería Bacilar , Shigella , Humanos , Niño , Azitromicina , Heces , Disentería Bacilar/diagnóstico , Disentería Bacilar/tratamiento farmacológico , Disentería Bacilar/epidemiología , Escherichia coli , Brotes de EnfermedadesRESUMEN
INTRODUCTION: It is common among microbiology laboratories to blind the Clostridioides difficile (C. difficile) BioFire FilmArray GI Panel result in fear of overdiagnosis. METHODS: We examined the rate of missed community-onset C. difficile infection (CDI) diagnosis and associated outcomes. Adult patients with FilmArray GI Panel positive for C. difficile on hospital admission who lacked dedicated C. difficile testing were included. RESULTS: Among 144 adults with a FilmArray Panel positive for C. difficile, 18 did not have concurrent dedicated C. difficile testing. Eight patients were categorized as possible, 5 as probable and 4 as definite cases of missed CDI diagnosis. We observed associated delays in initiation of appropriate therapy, intensive care unit admissions, hospital readmissions, colorectal surgery and death/discharge to hospice. Five out of 17 lacked risk factors for CDI. CONCLUSION: The practice of concealing C. difficile FilmArray GI Panel results needs to be reconsidered in patients presenting with community-onset colitis.
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Clostridioides difficile , Infecciones por Clostridium/diagnóstico , Infecciones por Clostridium/microbiología , Reacción en Cadena de la Polimerasa Multiplex/métodos , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Cohortes , Femenino , Hospitales , Humanos , Masculino , Persona de Mediana Edad , Estudios RetrospectivosRESUMEN
INTRODUCTION: Traveler's diarrhea (TD) is the most common illness among people traveling from resource-rich regions to resource-limited regions, although the precise microbial etiology is unclear in many cases. METHODS: Stool specimens were prospectively collected from 106 consecutive patients with TD and 16 healthy controls without TD, and were tested using both the FilmArray gastrointestinal panel (BioFire Diagnostics) and conventional stool cultures. RESULTS: The 106 patients had traveled to Southeast Asia (55 cases), South Asia (22 cases), Africa (11 cases), and East Asia (7 cases). Among the 106 specimens, 95 specimens (89.6%) were positive for pathogens during the FilmArray testing. The FilmArray testing also identified multiple pathogens in 75.8% of the specimens from positive cases. Conventional stool cultures only detected pathogens in 23.6% of the specimens. CONCLUSION: The FilmArray gastrointestinal panel significantly improved the detection of enteropathogens and allowed for a rapid assessment of the TD's etiology. In addition, conventional stool cultures are likely to underestimate co-infections with multiple infectious pathogens.
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Diarrea , Viaje , Asia , Diarrea/epidemiología , Heces , Humanos , Japón/epidemiologíaRESUMEN
Infectious diarrhea is a global pediatric health concern; therefore, rapid and accurate detection of enteropathogens is vital. We evaluated the BioFire® FilmArray® Gastrointestinal (GI) Panel with that of comparator laboratory tests. Stool samples of pediatric patients with diarrhea were prospectively collected and tested. As a comparator method for bacteria, culture, conventional PCR for diarrheagenic E. coli, and Allplex GI-Bacteria(I) Assay were tested. For discrepancy analysis, BD MAX Enteric Bacterial Panel was used. As a comparator method for virus, BD MAX Enteric Virus Panel and immunochromatography was used and Allplex GI-Virus Assay was used for discrepancy analysis. The "true positive" was defined as culture-positive and/or positive results from more than two molecular tests. Of the 184 stool samples tested, 93 (50.5%) were true positive for 128 pathogens, and 31 (16.9%) were positive for multiple pathogens. The BioFire GI Panel detected 123 pathogens in 90 of samples. The BioFire GI Panel demonstrated a sensitivity of 100% for 12 targets and a specificity of >95% for 16 targets. The overall positive rate and multiple pathogen rate among patients in the group without underlying diseases were significantly higher than those in the group with hematologic disease (57.0% vs. 28.6% (p = 0.001) and 20.4% vs. 4.8% (p = 0.02), respectively). The BioFire GI Panel provides comprehensive results within 2 h and may be useful for the rapid identification of enteropathogens.
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Though the FilmArray GI Panel has a reported aggregate specificity and reproducibility of >97% andâ¯>â¯99%, respectively, the reproducibility is less understood in clinical practice. We measured the reproducibility of positive results for low-prevalence pathogens. Samples with positive results for selected targets were repeated using a different FilmArray module. Overall, 331 of 373 (89%) results were reproducible. Giardia lamblia (57/57, 100%), Cryptosporidium spp. (61/63, 97%), Cyclospora cayetanensis (34/35, 97%), Plesiomonas shigelloides (17/18, 94%), and Rotavirus A (76/77, 99%) were highly reproducible, while Adenovirus F40/41 (38/54, 70%), Vibrio spp. (8/10, 80%), V. cholerae (3/8, 37.5%), and Yersinia enterocolitica (36/50, 72%) were poorly reproducible. Review of 38 patients with nonreproducible results showed that 19 (50%) had evidence of gastroenteritis and only 6 (16%) had possible infection with the organism that showed a nonreproducible result. Higher false-positive rates with certain targets on FAGP emphasize the need for diagnostic stewardship.
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Gastroenteritis/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Animales , Bacterias/genética , Bacterias/aislamiento & purificación , Niño , Preescolar , Reacciones Falso Positivas , Heces/microbiología , Heces/parasitología , Heces/virología , Femenino , Hongos/genética , Hongos/aislamiento & purificación , Gastroenteritis/microbiología , Gastroenteritis/parasitología , Gastroenteritis/virología , Humanos , Lactante , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa Multiplex/normas , Parásitos/genética , Parásitos/aislamiento & purificación , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Adulto JovenAsunto(s)
Heces/microbiología , Heces/parasitología , Reacción en Cadena de la Polimerasa , Adulto , Anciano , Anciano de 80 o más Años , Preescolar , Técnicas de Laboratorio Clínico/normas , Femenino , Tracto Gastrointestinal/microbiología , Tracto Gastrointestinal/virología , Humanos , Masculino , Persona de Mediana Edad , Factores de TiempoRESUMEN
The FilmArray GI panel (BioFire Diagnostics, Salt Lake City, UT) is a multiplex, on-demand, sample-to-answer, real-time PCR assay for the syndromic diagnosis of infectious gastroenteritis that has become widely adopted and, in some instances, has replaced conventional stool culture and parasite exams. Conventional testing has historically been restricted among hospitalized patients due to low diagnostic yield, but it is not known whether use of the FilmArray GI panel should be circumscribed. Cary-Blair stool samples submitted for FilmArray GI panel in adult patients admitted to an academic hospital from August 2015 to January 2017 were included in this study. Of 481 tests performed >72 h after admission, 29 (6.0%) were positive, all for a single target, excluding Clostridium difficile When follow-up tests beyond the first positive per hospitalization were excluded, 20 (4.8%) of 414 tests were positive. There was no difference in yield by immune status. Most targets detected were viral (79% of all positives [n = 23] and 70% in unique patients [n = 14]). All four cases positive for a bacterial target could not be confirmed and presentation was atypical, suggesting possible false positives. After removing potential false positives and chronic viral shedders, the yield was 3.0% (12/406). Repeat testing performed >72 h after admission and following a negative result within the first 72 h was done in 19 patients and 100% (22/22) remained negative. The FilmArray GI panel has low yield in adult patients hospitalized for >72 h, similar to conventional stool microbiology tests, and it is reasonable to restrict its use in this population.
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Pruebas Diagnósticas de Rutina/estadística & datos numéricos , Pruebas Diagnósticas de Rutina/normas , Diarrea/diagnóstico , Gastroenteritis/diagnóstico , Técnicas de Diagnóstico Molecular/estadística & datos numéricos , Adulto , Anciano , California , Reacciones Falso Positivas , Heces/microbiología , Heces/parasitología , Heces/virología , Femenino , Hospitalización/estadística & datos numéricos , Hospitales Universitarios , Humanos , Masculino , Persona de Mediana Edad , Estudios RetrospectivosRESUMEN
In the acute care hospital inpatient setting, there is a wide variety of causes for both infectious and noninfectious diarrhea. However, without molecular assays for the wide range of agents causing gastroenteritis, there is no reliable way to determine which individuals should be placed in contact precautions, as recommended by CDC. We tested 158 inpatient diarrheal stool specimens with the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, UT, USA) that had been stored at -70°C after testing negative by conventional methods for Clostridium difficile and/or rotavirus. We found that 22.2% had at least 1 other infectious agent detected, and 60% of these patients were never placed in appropriate isolation for a total of 109 patient-days. In addition, 20.3% of patients with negative GI panel results could have been removed from isolation. Use of multiplex gastrointestinal panels may improve decisions regarding patient isolation and reduce nosocomial transmission.