Genomic characterization of endemic diarrheagenic Escherichia coli and Escherichia albertii from infants with diarrhea in Vietnam

BackgroundDiarrheagenic Escherichia coli (DEC) is a group of bacterial pathogens that causes life-threatening diarrhea in children in developing countries. However, there is limited information on the characteristics of DEC isolated from patients in these countries. A detailed genomic analysis of 61 DEC-like isolates from infants with diarrhea was performed to clarify and share the characteristics of DEC prevalent in Vietnam. Principal findingsDEC was classified into 57 strains, including 33 enteroaggregative E. coli (EAEC) (54.1%), 20 enteropathogenic E. coli (EPEC) (32.8%), two enteroinvasive E. coli (EIEC) (3.3%), one enterotoxigenic E. coli (ETEC), and one ETEC/EIEC hybrid (1.6% each), and surprisingly into four Escherichia albertii strains (6.6%). Furthermore, several epidemic DEC clones showed an uncommon combination of pathotypes and serotypes, such as EAEC Og130:Hg27, EAEC OgGp9:Hg18, EAEC OgX13:H27, EPEC OgGp7:Hg16, and E. albertii EAOg1:HgUT. Genomic analysis also revealed the presence of various genes and mutations associated with antibiotic resistance in many isolates. Strains that demonstrate potential resistance to ciprofloxacin and ceftriaxone, drugs recommended for treating childhood diarrhea, accounted for 65.6% and 41%, respectively. SignificanceOur finding indicate that the routine use of these antibiotics has selected resistant DECs, resulting in a situation where these drugs do not provide in therapeutic effects for some patients. Bridging this gap requires continuous investigations and information sharing regarding the type and distribution of endemic DEC and E. albertii and their antibiotic resistance in different countries. Author summaryDiarrhea is a leading cause of morbidity and mortality in children under five years of age in developing countries, and diarrheagenic Escherichia coli (DEC) is a group of bacterial pathogens that cause a wide variety of intestinal diseases. To control the epidemic of DECs, it is necessary to understand the characteristics of prevalent strains in each region and propose appropriate treatment methods for them. This study reports detailed genomic analysis results of DEC-like strains isolated from infant diarrhea patients in Vietnam. The results suggested that many of the DECs prevalent in this country are uncommon types, and that Escherichia albertii, an emerging diarrheal pathogen, is the cause of diarrhea. Furthermore, comprehensive genome analysis revealed that these DECs are developing serious drug resistance. We believe that the results of this study will be the basis for improving treatment methods for patients with diarrhea and for tracking the evolution of this pathogenic group.