Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda.

Multi-drug resistant (MDR), gram-negative Enterobacteriaceae, such as Escherichia coli (E. coli) limit therapeutic options and increase morbidity, mortality, and treatment costs worldwide. They pose a serious burden on healthcare systems, especially in developing countries like Rwanda. Several studies have shown the effects caused by the global spread of extended-spectrum beta-lactamase (ESBL)-producing E. coli. However, limited data is available on transmission dynamics of these pathogens and the mobile elements they carry in the context of clinical and community locations in Sub-Saharan Africa. Here, we examined 120 ESBL-producing E. coli strains from patients hospitalized in the University Teaching Hospital of Butare (Rwanda), their attending caregivers as well as associated community members and livestock. Based on whole-genome analysis, the genetic diversification and phylogenetics were assessed. Moreover, the content of carried plasmids was characterized and investigated for putative transmission among strains, and for their potential role as drivers for the spread of antibiotic resistance. We show that among the 30 different sequence types (ST) detected were the pandemic clonal lineages ST131, ST648 and ST410, which combine high-level antimicrobial resistance with virulence. In addition to the frequently found resistance genes bla CTX-M-15 , tet(34), and aph(6)-Id, we identified csg genes, which are required for curli fiber synthesis and thus biofilm formation. Numerous strains harbored multiple virulence-associated genes (VAGs) including pap (P fimbriae adhesion cluster), fim (type I fimbriae) and chu (Chu heme uptake system). Furthermore, we found phylogenetic relationships among strains from patients and their caregivers or related community members and animals, which indicates transmission of pathogens. Also, we demonstrated the presence and potential transfer of identical/similar ESBL-plasmids in different strains from the Rwandan setting and when compared to an external plasmid. This study highlights the circulation of clinically relevant, pathogenic ESBL-producing E. coli among patients, caregivers and the community in Rwanda. Combining antimicrobial resistance with virulence in addition to the putative exchange of mobile genetic elements among bacterial pathogens poses a significant risk around the world.

Flies from a tertiary hospital in Rwanda carry multidrug-resistant Gram-negative pathogens including extended-spectrum beta-lactamase-producing E. coli sequence type 131.

Multidrug-resistant gram-negative (MRGN) bacteria are a serious threat to global health. We used genomics to study MRGN obtained from houseflies in a tertiary Rwandan hospital. Our analysis revealed a high abundance of different MRGN including E. coli pathogenic lineage ST131 suggesting the important role of flies in disseminating highly virulent pathogens in clinical settings and beyond.

Intense pre-admission carriage and further acquisition of ESBL-producing Enterobacteriaceae among patients and their caregivers in a tertiary hospital in Rwanda.

OBJECTIVES: To assess the presence and risk factors of intestinal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) among patients admitted to the University Teaching Hospital of Butare and among their attending caregivers, and to analyse the acquisition of ESBL-PE carriage during hospital stay and associated factors. METHODS: We screened 392 patients and their attending caregivers at admission and discharge for ESBL-PE carriage. Bacterial species were determined using the API-20E system, and antimicrobial susceptibility testing was performed by agar disc diffusion. Data on socio-economic status, diet, behaviour, household assets, livestock and hospital procedures were collected. RESULTS: At admission, 50% of the patients showed intestinal ESBL-PE carriage (Escherichia coli, 51%; Klebsiella pneumoniae, 39%; Enterobacter cloacae, 19%) as did 37% of their caregivers. Co-resistance was common but no carbapenem resistance was detected. At discharge, the proportion of ESBL-PE-colonised patients increased to 65% (caregivers, 47%) with almost complete carriage in paediatric patients (93%). The acquisition rate among initially non-colonised patients was 55% (or, 71/1000 patient days). Independent predictors of admission carriage included a colonised caregiver, prior antibiotic intake, egg consumption and neglecting to boil drinking water, whereas being a paediatric patient, undergoing surgery and male gender predicted acquisition during hospitalisation. CONCLUSIONS: Abundant admission carriage of ESBL-PE and a high acquisition rate in a Rwandan university hospital point to potential intrahospital transmission and community dissemination. Caregivers are an additional source of possible spread. Risk factors of colonisation such as diet and water source need to be tackled to prevent the further emergence and spread of ESBL-PE.