Serotyping, Antimicrobial Resistance Profiling and Assessment of Non-typhoidal Salmonella Risk Factors in Children Aged 5 Years and Below in Selected Study Sites in Mukuru Informal Settlement

Abstract

Non-Typhoidal Salmonella (NTS) presents a pressing global health challenge, notably in low- and middle-income countries. In Kenya, NTS contributes to a substantial proportion of bacteremia cases in both children and adults, particularly affecting children under five in urban informal settlements. Simultaneously, the emergence of antimicrobial resistance (AMR) among non-Typhoidal Salmonella strains is a concerning public health issue. This study aimed to investigate factors associated with NTS disease and characterize antimicrobial-resistant non-Typhoidal Salmonella in children under five in Nairobi's Mukuru informal settlement. Participants with fever ≥ 38° C with or without diarrhea were enrolled from four outpatient healthcare facilities. Fecal and blood samples underwent culture, serotyping, antimicrobial sensitivity testing and PCR. Out of 3,071 participants 43 tested positive for NTS, with Salmonella Enteritidis and Typhimurium isolates accounting for 1.4% of the cases. Notably, some isolates exhibited resistance to first-line antibiotics, including ampicillin and sulfamethoxazole-trimethoprim, with resistance proportions of 9.3 %( 4/43). The highest level of resistance was identified in Salmonella Typhimurium, with proportions of 16.7% for trimethoprim-sulfamethoxazole resistance and 22.2% for ampicillin resistance. Furthermore, 8% of Salmonella Enteritidis and 16.7% of Salmonella Typhimurium isolates demonstrated resistance to azithromycin. Although nalidixic acid resistance was noted in 8% of Salmonella Enteritidis isolates, these strains remained susceptible to ciprofloxacin, albeit with the potential for decreased susceptibility. Importantly, most non-Typhoidal Salmonella isolates remained susceptible to recommended third-generation cephalosporins, particularly ceftriaxone and cefotaxime. Molecular analysis of 11 isolates displaying phenotypic resistance to one or more antibiotic classes revealed the presence of the blaTEM gene responsible for β-lactam resistance in 3 out of the 11 isolates, representing 27.3%. Interestingly, all of these blaTEM-positive isolates were Salmonella Typhimurium. Demographically, the study indicated that infection rates were highest in children aged 12 to 24 months (2.1%) and in male children (1.7%). Nonetheless, statistical

analysis found no significant associations between NTS occurrence and gender, age, or contact with animals. Using drums and other open containers for water storage potentially predicted infection with NTS (2.0%; OR = 1.95, p = 0.040). Additionally, the proportion of children infected with Salmonella Enteritidis and Typhimurium was higher in households that did not treat water before drinking (1.8%) compared to those who treated their water (1.0%; OR = 0.85, p = 0.106). Lastly, having malignancy as a comorbidity was predictive of contracting NTS in children (33.3%; OR = 39.10, p = 0.003). This study highlights the importance of improving WASH infrastructure to reduce risk factors associated with transmission of non-Typhoidal Salmonella in the community. In the short-to medium-term, there is need for introduction of vaccine in the prevention and control of NTS. It also emphasizes the importance of using antibiotics prudently and continually monitoring the antimicrobial resistance of non-Typhoidal Salmonella.