Assessment of the human microbiome associated with enteric diseases among deployed military personnel

Gastrointestinal (GI) illness is the most prevalent illness encountered by deployed military personnel and has a major impact on military operations. Frequently, the etiology of GI illness is unknown and with underreporting of cases it is difficult to accurately assess the impact. An increasing number of ailments include an altered or aberrant gut microbiome with potentially short or long-term health effects. To better understand the impact of long-term military deployment and deployment-related GI on the gut microbiome of military personnel, we initiated a longitudinal cohort surveillance study of 67 individuals followed during two nine-month deployment cycles in 2015-2016 to Central America and monitored how the fecal microbiome was affected through deployment cycle. After enrollment and collection of baseline samples, subjects were contacted weekly to track illness and, if ill, were asked to complete a case report form and submit a stool sample for testing. There were 17 episodes of GI illness over 568.8 person-months with an incidence rate of 2.99 per 100 person-months. Using a Biofire Filmarray GI panel along with bacterial culture, we identified diarrheagenic E. coli as the primary etiology with 7/16 (43.8%) EPEC, 7/16 (43.8%) EAEC, and 6/16 (37.5%) ETEC as the most prevalent pathogens detected. We simultaneously conducted a passive surveillance study of all cases of diarrhea reporting to the clinic with 152 total cases and a similar pattern of etiology with 52/152 (34.2%) EAEC, 50/152 (32.9%) ETEC, and 35/152 (23.0%) EPEC as the most prevalent pathogens was detected. 1173 personnel completed surveys during medical outprocessing at the end of their deployment to collect additional data on the prevalence of diarrhea and impact on duty. Additionally, 11 subjects were recruited into a nested substudy to specifically examine gut microbiome changes associated with deployment and illness, with these participants voluntarily submitting stool samples weekly regardless of illness and submitting a daily diet, activity, and well-being log. Gut microbiome analysis showed differentially abundant taxa for subjects who contracted TD versus those who did not, as well as detection of taxa positively associated with self-reported GI distress. Disrupted microbiota was also observable for weeks preceding and following the incidents of TD for a subject with persistent TD. These findings illustrate the complex etiology of diarrhea among military personnel in deployed settings and the impacts on performance, short and long term health, and potential factors of susceptibility that provide a foundation for future clinical trials for prevention and treatment strategies.