Spectrum of enteropathogens detected by the FilmArray GI Panel in a multicentre study of community-acquired gastroenteritis

Abstract

The European, multicentre, quarterly point-prevalence study of community-acquired diarrhoea (EUCODI) analysed stool samples received at ten participating clinical microbiology laboratories (Austria, Finland, France, Germany, Greece, Ireland, Italy, Portugal, Romania, and the UK) in 2014. On four specified days, each local laboratory submitted samples from ≤20 consecutive patients to the Austrian Study Centre for further testing with the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, UT, USA). Of the 709 samples from as many patients received, 325 (45.8%) tested negative, 268 (37.8%) yielded only one organism, and 116 (16.4%) yielded multiple organisms. Positivity rates ranged from 41% (30 of 73 samples) in France to 74% (59 of 80 samples) in Romania. With the exception of Entamoeba histolytica and Vibrio cholerae, all of the 22 targeted pathogens were detected at least once. Enteropathogenic Escherichia coli, Campylobacter species, toxigenic Clostridium difficile, enteroaggregative E. coli, norovirus and enterotoxigenic E. coli were the six most commonly detected pathogens. When tested according to local protocols, seven of 128 positive samples (5.5%) yielded multiple organisms. Overall, the FilmArray GI Panel detected at least one organism in 54.2% (384/709) of the samples, as compared with 18.1% (128/709) when testing was performed with conventional techniques locally. This underlines the considerable potential of multiplex PCR to improve routine stool diagnostics in community-acquired diarrhoea. Classic culture methods directed at the isolation of specific pathogens are increasingly becoming second-line tools, being deployed when rapid molecular tests give positive results. This optimizes the yield from stool examinations and dramatically improves the timeliness of diagnosis.

Panel Filmarray GI® en la detección de patógenos entéricos en deposiciones: experiencia preliminar

“…Estudios recientes, encontraron que 32,9%, 54,2% y 31,5% de las muestras positivas por Filmarray presentaban más de un patógeno [7][8][9][10] . Una explicación a estos hallazgos puede asociarse a la falta de experiencia clínica en exámenes que detectan un número importante de patógenos en una misma reacción.…”

“…Desde su descubrimiento, el diagnóstico de estos patógenos se basa en la detección de genes de patogenicidad específicos para cada serotipo mediante técnicas de biología molecular, una situación que impide determinar la prevalencia de estos patotipos y su uso como una técnica de rutina 10 . Tal como se presenta en la tabla 1, de las 354 detecciones positivas en 137 (38,7%) se detectaron E. coli diarreogénicas, en su mayoría asociado a co-infecciones (≥ 70%), con alto número de detecciones positivas para los patotipos EPEC y EAEC, consistentes con reportes previos [7][8][9] . Será interesante implementar en el futuro estudios epidemiológicos destinados a establecer la prevalencia de estos patógenos de modo de diseñar estrategias que permitan su manejo y control.…”

Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis

“…19 Subgroups of interest were reported in 10 studies 11,19,20,22,25,26,29,35,36,39 and, of these, one considered travellers only 39 and two considered immunocompromised patients only. 22,26 Children aged < 5 years were not considered separately in any study, but the proportion of children aged < 5 years was reported in six studies 11,19,20,25,35,36 and ranged from 2% to 40% of the total study population. These studies did not report outcomes by setting or subgroup at the pathogen level, which is why reported outcomes should be regarded as applicable to a mixed population.…”

“…Only one study 11 differentiated between hospital-based samples (from children admitted with suspected viral gastroenteritis and children presenting to the emergency room) and community-based samples [adult and child travellers whose samples were submitted by general practitioners (GPs)]; the study population consisted of children and travellers only. Seven studies 19,22,26,27,29,35,39 reported the setting sufficiently to allow judgement on the origin of the infection (hospital vs. community). The majority of studies 11,12,20,21,[23][24][25]28,[30][31][32][33][34][36][37][38] reported recruitment of hospitalised patients, for which a mixed population should be assumed (in terms of origin of infection) as it is unclear at what point in time during hospitalisation each infection occurred.…”

“…However, one study reported study-level results for hospital-and community-acquired infections. 27 Country of study Eleven studies 11,22,[27][28][29][30]32,35,[37][38][39] included participants from European countries, including three studies from the UK. 27,30,32 One study was multinational, covering North America and Europe, 21 eight studies were from North America, 12,20,25,26,31,33,34,36 two were from Asia 23,24 and one was from Africa.…”