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Background  Acute diarrhea is one of the major public health problems worldwide. Most of studies on acute diarrhea have been made on infants aged below 5 years and few efforts have been made to identify the etiological agents of acute diarrhea in people over five, especially in China.    Methods  271 diarrhea cases and 149 healthy controls over 5 years were recruited from four participating hospitals between June 2014 and July 2015. Each stool specimen was collected to detect a series of enteric pathogens, involving five viruses ( Rotavirus  group A, RVA;  Norovirus , NoV;  Sapovirus , SaV;  Astrovirus , As; and  Adenovirus , Ad), seven bacteria (diarrheagenic  Escherichia coli , DEC; non-typhoidal  Salmonella , NTS;  Shigella  spp.; Vibrio cholera;  Vibrio parahaemolyticus ;  Aeromonas  spp.; and  Plesiomonas  spp.) and three protozoa ( Cryptosporidium  spp.,  Giardia lamblia, G. lamblia , and  Blastocystis hominis, B. hominis ). Standard microbiological and molecular methods were applied to detect these pathogens. Data was analyzed using Chi square, Fisher-exact tests and logistic regressions.    Results  The prevalence of at least one enteric pathogen was detected in 29.2% (79/271) acute diarrhea cases and in 12.1% (18/149) in healthy controls ( p  < 0.0001). Enteric viral infections (14.4%) were the most common in patients suffering from acute diarrhea, followed by bacteria (13.7%) and intestinal protozoa (4.8%). DEC (12.5%) was the most common causative agent in diarrhea cases, followed by NoV GII (10.0%), RVA (7.4%) and  B. hominis  (4.8%). The prevalence of co-infection was statistically higher ( p  = 0.0059) in the case group (7.7%) than in the healthy control (1.3%). RVA–NoV GII (3.0%) was the most common co-infection in symptomatic cases.    Conclusions  DEC was the most predominant pathogen in diarrhea cases, but it was largely overlooked because the lack of laboratory capacities. Because of the high prevalence of co-infections, it is recommended the urgent development of alternative laboratory methods to assess polymicrobial infections. Such methodological improvements will result in a better prevention and treatment strategies to control diarrhea illness in China.    Electronic supplementary material  The online version of this article (doi:10.1186/s13099-016-0141-1) contains supplementary material, which is available to authorized users.

Case–control study of diarrheal disease etiology in individuals over 5 years in southwest China