To characterize WHO-defined transmitted HIV drug resistance mutation (TDRM) data from recently HIVinfected African volunteers, we sequenced HIV ( pol) and evaluated for TDRM the earliest available specimens from ARV-naive volunteers diagnosed within 1 year of their estimated date of infection at eight research centers in sub-Saharan Africa. TDRMs were detected in 19/408 (5%) volunteers. The prevalence of TDRMs varied by research center, from 5/26 (19%) in Entebbe, 6/78 (8%) in Kigali, 2/49 (4%) in Kilifi, to 3/106 (3%) in Lusaka. One of five volunteers from Cape Town (20%) had TDRMs. Despite small numbers, our data suggest an increase in DRMs by year of infection in Zambia ( p ¼ 0.004). The prevalence observed in Entebbe was high across the entire study. ARV history data from 12 (63%) HIV-infected sexual partners were available; 3 reported ARV use prior to transmission. Among four partners with sequence data available, transmission linkage was confirmed and two had the same TDRMs as the newly infected volunteer (both K103N). As ARV therapy continues to increase in availability throughout Africa, monitoring incident virus strains for the presence of TDRMs should be a priority. Early HIV infection cohorts provide an excellent and important platform to monitor the development of TDRMs to inform treatment guidelines, drug choices, and strategies for secondary prevention of TDRM transmission.

Bombali virus (genus Ebolavirus) was identified in organs and excreta of an Angolan free-tailed bat ( Mops condylurus ) in Kenya. Complete genome analysis revealed 98% nucleotide sequence similarity to the prototype virus from Sierra Leone. No Ebola virus–specific RNA or antibodies were detected from febrile humans in the area who reported contact with bats.

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B ombali virus (BOMV) is the sixth and most recently identified virus of the genus Ebolavirus (1), first detected in Sierra Leone in oral and rectal swab samples from 2 species of insectivorous bats, Mops condylurus and Chaerephon pumilus (2). Since then, BOMV has been found in the tissues and excreta of M. condylurus bats in southeastern Kenya (3) and Guinea (4). To explore the role of M. condylurus bats as hosts for BOMV and the geographic distribution of the virus, we trapped bats in western Kenya, screened tissues for BOMV, and conducted next-generation sequencing on positive samples. The Study Bats were trapped in mist nets at 4 sites in Busia County: 2 house roosts, 1 orchard, and 1 cave. A total of 182 bats were captured, including 113 M. condylurus and 18 C. pumilus (Table 1). Similarly, at the original location in the Taita Hills, bats were trapped at a bridge site where an infected bat had previously been identified (3), at 4 additional building roosts, and over a water hole. From these sites, 396 bats were captured, including 177 M. condylurus and 219 C. pumilus (Table 1). Captured bats were euthanized with terminal isoflurane anesthesia followed by cervical dislocation. We collected mouth swab samples, fecal and blood samples, and major organs (kidney, spleen, liver, intestine, lung, and brain) and stored them in RNAlater (Invitrogen, https://www.thermofisher.com) as described previously (3). Samples were stored at-20°C for up to 10 days in Kenya before being shipped to Helsinki, Finland, where they were stored at-70°C before processing in a Biosafety Level 3 laboratory. Tissue samples were treated with TRIzol (Invitrogen) for virus inactivation, and RNA was extracted according to the manufacturer's instructions. Because previous studies have identified the highest BOMV viral loads in bat lungs (3,4), we initially conducted reverse transcription PCR (RT-PCR) on pooled lung samples from 3 bats (same species, collection date, and location) by using the BOMV-specific RT-PCR protocol described earlier (2). Samples in positive pools were then screened individually, and other sample types (other organs, saliva, and excreta) from these bats were also tested. We conducted next-generation sequencing on positive lung samples. Before sequencing, we applied

IntroductionClostridioides difficile is a neglected pathogen in many African countries as it is generally not regarded as one of the major contributors toward the diarrheal disease burden in the continent. However, several studies have suggested that C. difficile infection (CDI) may be underreported in many African settings. The aim of this study was to determine the prevalence of CDI in hospitalized patients, evaluate antimicrobial exposure, and detect toxin and antimicrobial resistance profiles of the isolated C. difficile strains.MethodsIn this cross-sectional study, 333 hospitalized patients with hospital-onset diarrhoea were selected. The stool samples were collected and cultured on cycloserine-cefoxitin egg yolk agar (CCEY). Isolates were presumptively identified by phenotypic characteristics and Gram stain and confirmed by singleplex real-time PCR (qPCR) assays detecting the species-specific tpi gene, toxin A (tcdA) gene, toxin B (tcdB) gene, and the binary toxin (cdtA/cdtB) genes. Confirmed C. difficile isolates were tested against a panel of eight antimicrobials (vancomycin, metronidazole, rifampicin, ciprofloxacin, tetracycline, clindamycin, erythromycin, and ceftriaxone) using E-test strips.ResultsC. difficile was detected in 57 (25%) of diarrheal patients over the age of two, 56 (98.2%) of whom received antimicrobials before the diarrheal episode. Amongst the 71 confirmed isolates, 69 (97.1%) harbored at least one toxin gene. More than half of the toxigenic isolates harbored a truncated tcdA gene. All isolates were sensitive to vancomycin, while three isolates (2.1%) were resistant to metronidazole (MIC >32 mg/L). High levels of resistance were observed to rifampicin (65/71, 91.5%), erythromycin (63/71, 88.7%), ciprofloxacin (59/71, 83.1%), clindamycin (57/71, 80.3%), and ceftriaxone (36/71, 50.7.8%). Among the resistant isolates, 61 (85.9%) were multidrug-resistant.ConclusionMultidrug-resistant C. difficile strains were a significant cause of healthcare facility-onset C. difficile infections in patients with prior antimicrobial exposure in this Kenyan hospital.