Salmonella bloodstream infection and concurrent intestinal colonization in children with severe acute malnutrition in Niger

Children with severe acute malnutrition (SAM) are at high risk of invasive infection. In sub-Saharan Africa, invasive non-typhoidal Salmonella enterica (iNTS) serovars are a leading cause of paediatric bloodstream infection. However, low-resource settings lack genomic data linking intestinal carriage with concurrent BSI in children presenting with SAM.

We conducted a longitudinal cohort study among children aged 0–59 months admitted for inpatient management of complicated SAM at the Madarounfa Intensive Nutritional Rehabilitation Centre, Maradi, Niger (2016–2017). Blood cultures and rectal swabs were obtained on admission (and during hospitalization if symptoms worsened). Genomic population structure of S. enterica serovars Enteritidis and Typhimurium was compared using phylogeny and clustering approaches. Among 1,371 enrolled children, 87 Salmonella isolates were recovered from 83 BSI episodes in 80 children. Invasive isolates belonged to a few globally circulating lineages, whereas carriage-only isolates demonstrated more heterogeneous genotypes. Minimum inhibitory concentrations were determined for 58 viable BSI isolates: susceptibility was retained to third-generation cephalosporins and carbapenems, while resistance to ampicillin (95%) and amoxicillin/clavulanate (90%) was common.

A nested case–control analysis of rectal swabs from 232 children (58 iNTS BSI cases; 174 non-BSI controls) was performed to test the association between gut carriage and BSI. Salmonella was detected in 44/58 (76%) cases vs. 7/174 (4%) controls, yielding a relative risk of 18.86 (CI 95% 9.00–39.53; χ²=126.7; P<0.0001). Clustering analyses confirmed close genomic relatedness within patient pairs and indicated circulation of a limited number of endemic clones. Among controls with faecal Salmonella, serovars were diverse and distinct from invasive lineages.