Carriage of multidrug-resistant bacteria and encoding genes among Vietnamese children with acute diarrhea

• This work investigated both phenotypic and genetic features of MDR bacteria • 33.2% children with acute diarrhea harbored at least one MDR bacteria and/or one colistin-resistance genes • ESBL-producing E. coli was the predominant multidrug-resistant pathogen • bla CTX-M-A was the most frequent resistance gene among Enterobacteriaceae • Colistin resistance genes, especially mcr-1 and mcr-3 , were commonly detected To assess the prevalence of multidrug-resistant (MDR) bacterial carriage and resistance-encoding genes in children with acute diarrhea. A prospective study was conducted from July 2020 to July 2021 in children under five years hospitalized. Stool samples were collected at hospital admission. MDR bacteria were identified by culture, antimicrobial susceptibility patterns were assessed using the disk diffusion method and resistance genes were investigated in isolates, using real-time PCR. Colistin-resistance genes were also tested from stool samples. 451 children were included, 33.2% harbored at least one MDR bacteria and/or one colistin-resistance genes. 79 (17.6%) were positive for at least one MDR pathogen by culture. 100 isolates were identified, including 17 methicillin-resistant Staphylococcus aureus (MRSA) and 83 Enterobacteriaceae. Escherichia coli was the most common (11.8%), followed by S. aureus (3.8%) and Klebsiella pneumoniae (2.7%). High resistance levels were observed in tested isolates: 94.8% to ceftriaxone, 77.1% to cefepime, 42.2% to piperacillin–tazobactam, and 19.3% to ertapenem. Among MRSA isolates, 15/17 (88.2%) carried mecA gene. Among Enterobacteriaceae, 73/83 (88.0%) carried bla CTX-M-A , 49 (59.0%) had bla TEM , 19 (22.9%) had bla SHV , and six (7.2%) were positive for bla NDM . Additionally, 87/451 children (19.3%) carried at least one colistin-resistance gene, with 10.9% of mcr-1 . MDR bacterial carriage and resistance genes were frequently detected at hospital admission, reflecting community or prior healthcare-associated exposure rather than in-hospital antibiotic selection. These findings underscore the urgent need for strengthened antimicrobial stewardship, rational antibiotic use, improved infection control, and enhanced diagnostic capacity.