Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa’s most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.

Nontyphoidal Salmonella are a leading cause of community-onset bacteremia and other serious infections in sub-Saharan African countries where large studies indicate that they are an uncommon cause of moderate-to-severe diarrhea. Approximately 535 000 nontyphoidal Salmonella invasive disease illnesses and 77 500 deaths were estimated to occur in 2017; 422 000 (78.9%) illnesses and 66 500 (85.9%) deaths in countries in sub-Saharan Africa. Lineages of Salmonella enterica serovar Typhimurium sequence type (ST) 313 and lineages of Salmonella enterica serovar Enteritidis ST11 dominate as causes of invasive disease. A major reservoir for these specific strains outside of humans has not been identified to date. Human fecal shedding of such strains is common in areas where nontyphoidal Salmonella invasive disease incidence is high. The case-fatality ratio of nontyphoidal Salmonella invasive disease is approximately 15%. Early diagnosis and treatment are needed to avert fatal outcomes. Antimicrobial resistance, including multiple drug resistance, decreased fluoroquinolone susceptibility, and resistance to third-generation cephalosporins, is increasing in prevalence and is likely to further compromise patient outcomes. Naturally acquired immunity against invasive disease develops in children aged >3 years in endemic areas, likely mediated in part by the sequential acquisition of T-cell immunity, followed by antigen-specific immunoglobulin G antibodies. Vaccines in preclinical or clinical development include live-attenuated S. enterica serovar Typhimurium, nontyphoidal S. enterica core and O-polysaccharide glycoconjugates, multiple antigen-presenting system complexes, and generalized modules for membrane antigens vaccines. The latter are in phase I trials in Europe and Africa. Both vaccine use, and other effective, evidence-based nonvaccine interventions, are needed to prevent and control nontyphoidal Salmonella invasive disease.

Clinical observations and animal studies have suggested that Salmonella intestinal carriage is promoted by concurrent Schistosoma infection. The present study assessed association of Salmonella intestinal carriage and Schistosoma mansoni infection among individuals in a Schistosoma endemic area in sub-Saharan Africa. From November 2015 to March 2016, a cross-sectional community-wide study was conducted in Kifua II, a rural village in Kongo Central Province, Democratic Republic of Congo. Stool samples were collected and analyzed for Salmonella intestinal carriage (culture) and Schistosoma mansoni infection (Kato Katz microscopy with determination of egg load). Salmonella Typhimurium and Enteritidis isolates were assessed for genetic similarity with blood culture isolates obtained during the same period in a neighboring hospital using multi-locus variable-numbers tandem repeat analysis (MLVA). A total of 1,108 participants were included (median age 15 years (IQR: 7–36), male-to-female ratio of 1:1.1). The overall prevalence of Schistosoma mansoni infection and non-typhoidal Salmonella carriage was 51.2% (95% CI: 48.2–54.1) and 3.4% (95% CI: 2.5–4.7) respectively, with 2.2% (95% CI: 1.5–3.2) of participants coinfected. The proportion of Salmonella carriage tended to be higher among Schistosoma mansoni infected participants compared to non-infected participants but this difference did not reach statistical significance (4.2% versus 2.6%, p = 0.132). However, the proportion of Salmonella carriage among participants with a heavy Schistosoma mansoni infection was significantly higher compared to those with a light and moderate infection (8.7% versus 3.2%, p = 0.012) and compared to Schistosoma mansoni negatives (8.7% versus 2.6%, p = 0.002). The 38 Salmonella isolates comprised five and four Enteritidis and Typhimurium serotypes respectively, the majority of them had MLVA types identical or similar to those observed among blood culture isolates. Salmonella intestinal carriage was associated with a heavy intensity of Schistosoma mansoni infection. Further studies are needed to address causation. Salmonella intestinal carriage may be facilitated by infection with Schistosoma mansoni, which is a flatworm that lives in the small blood vessels of the human intestinal tract. This situation has been described in tropical low and middle income countries, where both pathogens are endemic. The present study aimed to assess the association of Salmonella intestinal carriage with Schistosoma mansoni infection in Kifua II village, located in the Kongo Central province of the Democratic republic of Congo. We collected stool samples from 1,108 inhabitants of the village and analysed them for Salmonella (culture) and Schistosoma mansoni eggs (microscopy). Our findings showed that 3.4% of the participants had Salmonella in their stool and 51.2% were infected with Schistosoma mansoni. There was no association between overall Schistosoma infection and Salmonella carriage but Salmonella carriage was significantly higher among participants with heavy Schistosoma infection compared to those with a light and moderate infection (8.7% versus 3.2%, p = 0.012) and compared to those without Schistosoma mansoni infection (8.7% versus 2.6%, p = 0.002). Further, we showed that some Salmonella isolates recovered from stool were very similar to isolates obtained from invasive infections (blood cultures from patients in a neighbouring hospital).

Background: Antimicrobial resistance (AMR), particularly due to extended-spectrum beta-lactamases (ESBL), is a growing threat to public health in sub-Saharan Africa. This study investigates the prevalence, epidemiological characteristics, resistance patterns and resistance dynamic over time of ESBL-producing non-typhoidal Salmonella (NTS) bacteremia in Kisantu, Democratic Republic of Congo (DRC), from 2019 to 2022. Methods: A retrospective observational study used routine bloodstream infection data from the AMR network at Saint Luc Hospital in Kisantu. Blood cultures from suspected bacteremia cases were processed using standard microbiological techniques. Bacterial identification relied on biochemical reactions. Antibiotic susceptibility testing and ESBL-producing NTS detection were performed by disk diffusion following Clinical and Laboratory Standards Institute guidelines. Associations between ESBL production and patient characteristics (age, sex) were assessed using Pearson’s Chi-square test, and annual temporal trends in ESBL-producing NTS from 2019 to 2022 were analyzed by logistic regression using 2019 as the reference year. Results: Of the 19,430 blood cultures, 1681 NTS isolates were identified, and 1568 of these were screened for ESBL. ESBL prevalence was significantly associated with age (p = 0.007), peaking in children under 2 years, but not with sex (p = 0.570). Compared with 2019, the likelihood of isolating ESBL-producing NTS increased markedly through 2022, with adjusted probabilities rising from 58% to 87%, reflecting a strong upward temporal trend. High levels of extensively drug-resistant (94.1%) were observed. No carbapenem resistance was detected. Conclusions: ESBL-producing NTS bacteremia is rising in Kisantu, DRC, mainly affecting children under 2 years. Rising resistance to key antibiotics limits treatment options and highlights the need for strengthened AMR surveillance, optimized antibiotic use, and vaccination strategies.

Background: Antimicrobial resistance (AMR), particularly due to extended-spectrum beta-lactamases (ESBL), is a growing threat in sub-Saharan Africa. This study investigates the prevalence, epidemiological characteristics, resistance patterns and over time resistance dynamics of ESBL-producing non-typhoidal Salmonella (NTS) bacteremia in Kisantu, Democratic Republic of Congo (DRC), from 2019 to 2022. Methods: A retrospective observational study used routine bloodstream infection data from the AMR network at Saint Luc Hospital in Kisantu. Blood cultures from suspected bacteremia cases were processed using standard microbiological techniques. Bacterial identification relied on biochemical reactions. Antibiotic susceptibility testing and ESBL-NTS detection were performed by disk diffusion following Clinical and Laboratory Standards Institute guidelines. Quarterly temporal trends in ESBL-positive NTS were evaluated using logistic regression. Results: Of 19,430 blood cultures, 1,681 NTS isolates were identified, 1,568 were screened for ESBL. ESBL production was detected in 1,184 isolates (75.5%), mostly from children under 5 years (1,098/1,184; 92.7%), including nearly 72% under 24 months. ESBL prevalence increased significantly over time (β = 0.139, OR = 1.15, 95% CI: 1.11–1.19, p < 0.001), rising from 14.3% in Q (Quarter) 1 2019 to 95.3% in Q3 2022. High levels of extensively drug-resistant (94.1%) and pan-drug-resistant (6.3%) isolates were observed. No carbapenem resistance was detected, and azithromycin resistance remained low (6.4%). Conclusion: ESBL-producing NTS bacteremia is rising in Kisantu, RDC, manly affecting children under 5 years. Rising resistance to key antibiotics limits treatment options and highlights the need for strengthened AMR surveillance, optimized antibiotic use, and vaccination strategies.