Children in low-resource settings carry enteric pathogens asymptomatically and are frequently treated with antibiotics, resulting in opportunities for pathogens to be exposed to antibiotics when not the target of treatment (i.e., bystander exposure). We quantified the frequency of bystander antibiotic exposures for enteric pathogens and estimated associations with resistance among children in eight low-resource settings. We analyzed 15,697 antibiotic courses from 1,715 children aged 0 to 2 y from the MAL-ED birth cohort. We calculated the incidence of bystander exposures and attributed exposures to respiratory and diarrheal illnesses. We associated bystander exposure with phenotypic susceptibility of E. coli isolates in the 30 d following exposure and at the level of the study site. There were 744.1 subclinical pathogen exposures to antibiotics per 100 child-years. Enteroaggregative Escherichia coli was the most frequently exposed pathogen, with 229.6 exposures per 100 child-years. Almost all antibiotic exposures for Campylobacter (98.8%), enterotoxigenic E. coli (95.6%), and typical enteropathogenic E. coli (99.4%), and the majority for Shigella (77.6%), occurred when the pathogens were not the target of treatment. Respiratory infections accounted for half (49.9%) and diarrheal illnesses accounted for one-fourth (24.6%) of subclinical enteric bacteria exposures to antibiotics. Bystander exposure of E. coli to class-specific antibiotics was associated with the prevalence of phenotypic resistance at the community level. Antimicrobial stewardship and illness-prevention interventions among children in low-resource settings would have a large ancillary benefit of reducing bystander selection that may contribute to antimicrobial resistance.

The use of next-generation sequencing (NGS) in blood samples is an emerging technology for clinical microbiology labs. In this work, we performed NGS on plasma samples from a well-characterized cohort, where all samples had been previously tested by PCR for 43 pathogens.

BACKGROUND: Diarrhea is a leading cause of death in children under five. Molecular methods exist for the rapid detection of enteric pathogens; however, the logistical costs of storing stool specimens limit applicability. We sought to demonstrate that dried filter paper specimen preservation can identify diarrheal diseases causing significant morbidity among children in resource constrained countries. METHODS: A sub-study was nested into cholera surveillance in Cameroon. Enrollment criteria included: enrollment between 8/1/16 - 10/1/18; age < 18 years; a stool specimen; ≥ three loose stools within 24hours with the presence of dehydration and/or blood. 7227 persons were enrolled, for which 2746 met enrollment criteria and 337 were included in this analysis using the enteric TaqMan Array Card. Bacterial pathogens were compared to severity of diarrhea, age and sex, among other variables. RESULTS: 107 were ETEC positive of which: 40.2% (N=43) LT-STh, 19.6% (N=21) LT-STp; and 49.5% (53) LT-only. Major CFs were present in 43.9% of ETEC-positives. 96 were positive for Shigella, of which 14 (14.6%) reported dysentery. Model-derived quantitative cutoffs identified 116 (34.4%) with one highly diarrhea-associated pathogen and 16 (4.7%) with ≥ two. Shigellae and rotavirus were most strongly associated with diarrhea in children with mixed infections. CONCLUSION: Dried filter paper preserved specimens eliminate the need for frozen stool specimens and will facilitate enteric surveillance and contribute to the understanding of disease burden, which is needed to guide vaccine development and introduction. This study confirms Rotavirus, Shigella and ETEC as major contributors to pediatric diarrheal disease in two regions of Cameroon.