Use of a multiplex DNA extraction PCR in the identification of pathogens in travelers’ diarrhea

Journal of Travel Medicine, 2017, 1–6 doi: 10.1093/jtm/tax087 Original Article Original Article Use of a multiplex DNA extraction PCR in the identification of pathogens in travelers’ diarrhea Bradley A. Connor, MD1,2*, Marina Rogova, RN1, and Olga Whyte, RN1 The New York Center for Travel and Tropical Medicine, New York, NY, USA and 2Department of Medicine, Weill Cornell Medical College, New York, NY, USA *To whom correspondence should be addressed. Email: Submitted 19 July 2017; Revised 8 November 2017; Editorial decision 16 November 2017; Accepted 29 November 2017 Abstract Background: Diarrhea is one of the most common ailments afflicting travelers with attack rates of 30–40% for medium to high-risk destinations. As travelers’ diarrhea (TD) is syndromic and caused by a wide range of pathogens, including bacteria, parasites and viruses, multiplex deoxyribonucleic acid (DNA) extraction polymerase chain reaction (PCR) technology can be useful for determining the etiology of TD pathogens. Objective: The goal of this retrospective study was to produce clinically relevant and useful data on gastrointestinal illness related to travel identified by culture-independent methods of diagnosis—use of the multiplex DNA extraction PCR platform (BioFire FilmArray GI Panel) and to describe the use of this technology in detection of enteric pathogens. Method: We reviewed our data in returned travelers from May 2014 to March 2017, looking at demographics, country of travel, number of pathogens found and pathogens by specific region. Results: Stool analysis by DNA extraction PCR was obtained in 388 post-travel patients. Three hundred and twentyseven of these had diarrhea or other enteric symptoms. Sixty-one travelers presented with enteric symptoms and were diagnosed with post infectious irritable bowel syndrome (PI-IBS) after stool analyses were negative. Of those with diarrhea or gastrointestinal (GI) symptoms and excluding those diagnosed with PI-IBS, 207 patients tested positive for at least 1 enteric pathogen (63.4%). Eighty of those patients were found to have multiple pathogens. Viral pathogens were identified in 38 patients, 18% of the total number of cases. Conclusion: The BioFire FilmArray GI Panel was associated with better detection of pathogens than historical controls while also allowing prompt and accurate diagnosis and potential treatment. A higher proportion of viral pathogens compared with historical assumptions was identified as well as mixed infections with multiple pathogens, a phenomenon largely unknown to clinicians before this technology became available. Key words: Travelers’ diarrhea, molecular diagnostics, enteric infection, intestinal parasites, infectious diarrhea Introduction Diarrhea is one the most common ailments afflicting travelers with attack rates of 30–40% in travelers to moderate-to-high risk destination.1 Travelers’ diarrhea (TD) has historically been considered primarily a bacterial illness with diarrheagenic Escherichia coli, Campylobacter, Shigella and Salmonella being the primary pathogens.2 Community acquired diarrhea in developed countries, such as those of Western Europe and the USA have historically been caused by viral pathogens, most commonly norovirus.3,4 Traditional methods of diagnosis of enteric pathogens fail to reveal the etiology in the majority of cases of acute diarrheal infection. In TD in particular, specific etiologic agents are found in <50% of the time.5–7 There are several reasons for this. Traditional diagnostic methods such as bacterial culture often fail to reveal enteropathogens particularly in the setting of antibiotic use.8 In addition, for certain pathogens such © International Society of Travel Medicine, 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: 1 2 Methods This retrospective study was conducted at The New York Center for Travel and Tropical Medicine, a private medical practice that specializes in Travel and Tropical Medicine and Gastroenterology. Data used for the study included patient demographics, travel destination, pathogens and number of pathogens found in each patient, as well as pathogens by specific country and region. Participants Participants for this study included men, women and children. Gender and age of all participants were documented. Materials Data collection method Patients were selected based on their symptom presentation and history of travel. All participants were returning travelers who presented to the clinic with diarrhea and/or other enteric symptoms (abdominal pain, nausea/vomiting, bloating, abdominal cramping) shortly after their trip. Diarrhea was defined as a change in bowel movement frequency associated with a decrease in form of passed stool bothersome enough to seek medical attention. We studied patients with diarrhea which was acute, persistent and chronic post travel. Most patients with chronic diarrhea were negative on Film Array and diagnosed with post infectious irritable bowel syndrome (PI-IBS). PI-IBS is defined as the persistence of gastrointestinal symptoms characterized by a change in bowel habits following a bout of TD or gastroenteritis where no pathogen is identified and underlying gastrointestinal disease is excluded. All participants were required to provide information specific to age, gender, travel dates, travel destinations, detailed description of symptoms, activities during travel and date of symptom onset. Each participant was interviewed by a healthcare provider during the initial office visit. Eligibility for testing by DNA extraction PCR BioFire FilmArray was determined after complete patient examination and evaluation of onset of symptoms and their relationship to travel dates, travel destinations and severity of symptoms. Specimen collection methods Stool specimens were obtained from patients in two ways: (1) Patients provided a specimen collected in a Cary Blair transport medium vial during visit.22 (2) Specimen was collected from patients during examination by using a fecal swab that was transferred into a Cary Blair transport medium vial. Specimen inclusion criteria (1) Specimen was received in Cary-Blair transport medium. (2) Specimen volume was sufficient for testing. (at least 200 µl of stool). (3) Specimen could be tested by the BioFire FilmArray GI Panel. All specimens were tested within 4 days after collection. Equipment Each stool specimen was tested by using a high throughput DNA extraction PCR FilmArray GI Panel. The FilmArray system is integrated and includes automated sample preparation. All reagents needed for sample preparation, reverse transcription, PCR and detection are provided freeze-dried in a single-use pouch.23 Stool specimens were stored at room temperature 20–25°C until FilmArray GI Panel testing could be completed. At least 200 µl of specimen (stool specimen mixed in Cary-Blair transport medium) was subject to FilmArray GI Panel testing, according to th (...truncated)