Enteric pathogen detection among children discharged from outpatient treatment for severe acute malnutrition and associations with subsequent relapse in South Sudan

Severe acute malnutrition (SAM) affects millions of children each year, putting them at increased risk of death and disease. Many children relapse to acute malnutrition (AM) or SAM following community-based management of acute malnutrition (CMAM) programmes. Enteric infection is hypothesized to be a risk factor for relapse. We collected rectal swabs from children recently recovered from uncomplicated SAM in South Sudan and tested them for a suite of enteric pathogens using a TaqMan Array Card. We estimated enteric pathogen prevalence and examined associations between pathogen detection and risk of relapse to AM and SAM within three and six months of recovery. One or more enteric pathogen was detected in 82% of children (389/476). Bacterial and protozoan pathogens were the most frequently detected pathogen types, with each detected in 57% of children, followed by enteric viruses (10%) and helminths (4.4%). Detection of one or more enteric pathogen, protozoan pathogen, or viral pathogen was not associated with relapse to AM or SAM at either time point. Detection ≥1 helminth was associated with increased risk of relapse to SAM, and ≥1 bacterial pathogen was associated with decreased risk of relapse to AM. Both enterotoxigenic E. coli and enteroaggregative E. coli were associated with decreased risk of relapse to SAM and/or AM at three- or six-months post-recovery. Shigella was the only individual pathogen associated with increased risk of relapse to AM and SAM. In this setting, most children suffering from SAM were exposed to enteric pathogens during treatment. However, we found no consistent relationship between pathogen detection at treatment discharge and risk of relapse to AM or SAM within three or six months of recovery. Despite this, limiting pathogen exposures during this vulnerable period remains important given the high risk of serious adverse health effects. These results highlight the lack of access to safe water, sanitation, and hygiene and reinforce the potential importance of anthelmintics as part of CMAM.