PhD defence Lisette Mbuyi Kalonji

Supervisors

• Em. prof. dr. Jan Jacobs (ITM/KU Leuven) 

• Prof. dr. Octavie Lunguya (Institut National de Recherche Biomédicale, DRC)   

Abstract

More than 80% of iNTS infections occur in sub-Saharan Africa, with a case fatality ratio of 17%. Children under 5 years old are hugely affected, especially those suffering from P. falciparum malaria, moderate or severe anemia and malnutrition. HIV infection and schistosomiasis are also among the reported risk factors for iNTS infection and prolonged Salmonella carriage respectively.
NTS strains are worldwide spread, although they cause different disease in other parts of the world. In fact, in high-income countries, NTS are more associated with gastroenteritis (diarrheagenic NTS) and their reservoir is known as zoonotic. Conversely, NTS strains observed in sub-Saharan Africa display a different genetic signature conferring adaptation to the human host and increased virulence, with more propensity to cause invasive infections (iNTS). However, the reservoir and mode of transmission of these iNTS remain unknown.
Among the strains causing invasive disease in sub-Saharan Africa, Salmonella Typhimurium and Enteritidis are more frequent, with Typhimurium outnumbering Enteritidis, although fluctuations in time and space are described. Molecular analyses identified the major clades (lineages), Salmonella Typhimurium ST313 (Lineage 2) and Salmonella Enteritidis ST11 (Central/Eastern and Western African clades), which display increasing resistance to antibiotics, leading to difficult to treat infections.
Invasive NTS infections do not display a specific clinical picture and are difficult to distinguish from other febrile diseases. Thus, the diagnosis relies on blood cultures, which are not available or not affordable in the majority of LMICs.
DR Congo is among the countries in sub-Saharan Africa where iNTS infections were described since the 90’s, and a bloodstream infection surveillance network was implemented since 2007, which facilitated to conduct this thesis aiming to study the potential human as reservoir of iNTS.

Chapter 1 described the microbiological and epidemiological profile of iNTS bloodstream infections in DR Congo from 2011 to 2014.  The author reported iNTS as the first cause of bloodstream infections (5.9% of all suspected cases of bloodstream infections) and the first ranking pathogen isolated among children (41.2%). Variations in time, space and seasons were observed with higher proportions of iNTS during the rainy season. Among iNTS, Salmonella Typhimurium and Salmonella Enteritidis together represented more than 90% of all serotypes isolated. Almost all Salmonella Typhimurium (90.2%) and Salmonella Enteritidis (79.7%) were multidrug resistant, while less than 2.5% of them displayed decreased ciprofloxacin susceptibility (DCS). Combined resistance to third generation cephalosporin (ceftriaxone) and azithromycin was described in 11.4% of MDR Salmonella Typhimurium isolates, while it was rarely observed among the Enteritidis serotype isolates.

Chapter 2 focused on the co-presence of Salmonella intestinal carriage and Schistosoma mansoni infection among 1,108 healthy inhabitants of the Kifua 2 village (Kongo Central Province) using stool culture and microscopy (Kato-Katz method). Half of participants to the study were infected with Schistosoma mansoni and 3.4% were NTS carriers. There was no significant relation between Schistosoma mansoni infection and Salmonella intestinal carriage. The proportion of Salmonella carriage was higher among participants with a heavy Schistosoma mansoni egg load (8.7%) compared to those with light and moderate infection combined (3.2%; p = 0.012) and compared to Schistosoma negative participants (2.6%; p = 0.002). The author concluded that S. mansoni infection would not be a barrier to Salmonella vaccinations. Salmonella Typhimurium (n = 4) and Enteritidis (n = 5) were isolated from 0.8% of participants. Of these isolates, all Salmonella Typhimurium and one Salmonella Enteritidis isolates were multidrug resistant. According to the MLVA profile, 3/4 Salmonella Typhimurium and 2/5 Salmonella Enteritidis were similar to blood culture isolates from the surveillance site located at Kisantu hospital (at 66 km from Kifua 2 village). 

Chapter 3 assessed the prevalence of non-typhoidal Salmonella intestinal carriage among 2,234 healthy inhabitants of Kikonka village (at 7 km from the Kisantu hospital), the serotype distribution of the NTS isolates and the genetic relatedness with time-matched  invasive clinical isolates from the same area (patients originating from Kikonka village and admitted to Kisantu hospital) . Participants provided 3 consecutive stool samples for culture, which allowed to detect 98 Salmonella carriers (4.4%). Salmonella Typhimurium and Enteritidis carriers together accounted for 1.3% of participants living in 6.0% of households. All Salmonella Typhimurium belonged to the ST313 Lineage 2 and that the Salmonella Enteritidis isolates belonged to the ST11 Central/Eastern African and outlier clades respectively. Further, all these isolates were genetically identical to blood culture isolates. Almost 96% of Salmonella Typhimurium were multidrug resistant, while 80% showed an extensive drug resistant (XDR) profile (combined MDR, third generation cephalosporin resistance, and fluoroquinolone non-susceptibility). Collection of multiple stool samples (3 successive stool per participant) allowed increasing the Salmonella carriage detection from 1.8% to 3.2% of participants at day 2 and from 3.2% to 4.4% of participants at day 3. More than half of Salmonella carriers (56.1%, 55/98) living in 61 households were grouped in clusters of ≥ 2 isolates of identical serotype. One household had 7 Salmonella Typhimurium carriers.