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A total of 142 cefoxitin-resistant Escherichia coli isolates from water sources were collected across Canada. Multidrug resistance was observed in 65/142 (45.8%) isolates. The bla CMY-2 gene was identified in 110/142 (77.5%) isolates. Sequencing of the chromosomal ampC promoter region showed mutations from the wild type, previously shown to hyperproduce AmpC. CMY-2-producing plasmids predominantly belonged to replicon groups I1-I␥, A/C, and K/B. The majority of the E. coli isolates belonged to the nonvirulent phylogenetic groups A and B1.

Stool is the diagnostic specimen of choice to identify enteropathogens in pediatric gastroenteritis. However, stool collection is challenging and its diagnostic characteristics in patients with isolated vomiting are unknown. Therefore, we evaluated if oral swabs are a suitable alternative specimen to stools. In total, 738 oral swabs and 577 stool specimens were collected from 738 children with vomiting and/or diarrhea. All specimens were tested by a laboratory-developed quantitative RT-PCR Gastroenteritis Virus Panel; 150 oral swabs and 577 stool specimens were tested by the commercial gastroenteritis pathogen panel. The Gastroenteritis Virus Panel identified adenovirus (n = 38), norovirus (n = 21), and rotavirus (n = 16) commonly in oral swabs. In stool specimens, rotavirus (n = 139), norovirus (n = 86), and adenovirus (n = 69) were detected commonly. Compared with stool specimens, the specificity of oral swabs was 99% (95% CI, 96%-100%); the sensitivity of oral swabs was 18% (95% CI, 14%-22%) for the detection of enteric viruses. The Gastrointestinal Pathogen Panel identified enteric bacteria and parasites in stool but not in oral swabs. Given the lower sensitivity of oral swabs, stool remains a preferable specimen to detect enteric viruses. However, with their high specificity, oral swabs can be considered as a suitable specimen if stool specimens are unavailable. Nevertheless, negative oral swabs require a confirmative test of stool specimens.