Evaluation of Anatomically Designed Flocked Rectal Swabs for the Molecular Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis in Botswana

Two-hundred and eighty matched bulk stool and anatomically-designed flocked rectal swab samples were collected from children admitted to hospital with acute diarrhea in Botswana. Parents were asked about the acceptability of the swab collection method as compared with bulk stool sampling. All samples underwent identical testing with a validated 15 target (9 bacterial, 3 44 viral, 3 parasite) commercial multiplex PCR assay. Flocked swabs had 12% higher yield for bacterial pathogen targets (241 vs. 212; p=0.003) when compared with stool samples and similar yields for viral targets (110 vs. 113; p= 0.701) and parasite targets (59 vs. 65; p= 0.345). One hundred and sixty-four of the flocked swab stool pairs were also tested with separate laboratory-developed bacterial and viral multiplex assays, and the flocked rectal swabs showed performance that was similar to that seen with commercial assay testing. Almost all parents/guardians found the swabs acceptable. Flocked rectal swabs significantly facilitate the molecular diagnosis of diarrheal disease in children.