Ciprofloxacin resistant Klebsiella pneumoniae is common or emerging in many geographies, and knowledge of local resistance rates is important for empirical therapy. While K. pneumoniae ciprofloxacin resistance determinants are known, there is a lack of systematic data on the effect of these determinants, alone and in combination, and there are no publicly accessible tools for predicting ciprofloxacin resistance from whole genome sequence data. The KlebNET-GSP AMR Genotype-Phenotype Group aggregated a matched genotype-phenotype dataset of n = 12,167 K. pneumoniae species complex (KpSC) isolates from 27 countries between 2001 and 2021. We developed a rule-based classifier to predict ciprofloxacin resistance by categorizing the number of mutations in the quinolone resistance determining regions of gyrA and parC and the number of plasmid-mediated quinolone resistance genes, including the presence/absence of aac(6')-Ib-cr (which can acetylate ciprofloxacin). Predictive performance was assessed using the discovery dataset, with the reassessment of discrepant and concordant isolates; and validated using externally contributed datasets (n = 7,030 KpSC isolates). The rule-based classifier predicted R vs S/I with categorical agreement, sensitivity, and specificity > 96
Monkeypox virus (MPXV) is a zoonotic pathogen known to be endemic to the Congo basin and West Africa, and which causes characteristic lesions disseminated on all skin surfaces of infected cases. Multiple MPXV outbreaks have been reported in the Central African Republic (CAR), a country in the Congo basin, at an increased frequency since 2020. The genomic history of these outbreaks in CAR is poorly characterized due to undersampling, with only a recent expansion in the number of sequences from CAR. Here, we report twenty-six new near-complete genomes from six prefectures of CAR, selected to represent outbreaks that occurred in the country between 2019 and 2024. Our analysis shows the sustained homogeneity of genomes in CAR, as all of them belonged to Clade Ia, but with an expansion of sub-lineages and therefore increased MPXV diversity within CAR. We highlight the introduction into CAR of a lineage previously known to occur only in Gabon and Cameroon, as well as the apparent regional clustering of MPXV genomes in CAR. Our analysis reveals limited APOBEC3-mediated activity, which is consistent with recent zoonotic origins and short human-to-human transmission chains observed in CAR. These analyses provide an in-depth view of the genomic diversity of MPXV in the Central African region.
Importance:Escherichia coli and Klebsiella pneumoniae are major causes of urinary tract infections. While antibiotic resistance in these critical pathogens is a global concern, data from Africa remain sparse, cover short time frames, and aggregate multiple specimen types. Objective:To model antimicrobial resistance trends in urinary E coli and K pneumoniae isolates from 6 African countries between 2010 and 2022 and to project future resistance patterns. Design, Setting, and Participants:Data for this retrospective cross-sectional study were obtained from Pasteur Network clinical laboratories located in the capital cities of 5 African countries (Cameroon, Central African Republic [CAR], Madagascar, Morocco, and Senegal) and from 1 university hospital in Benin. Urine samples yielding E coli or K pneumoniae collected during routine clinical care were included. Data collection spanned 2008 to 2023, with a shared observation period from October 2014 to December 2021. Data were analyzed from March through December 2025. Main Outcomes and Measures:The primary outcome was resistance in E coli and K pneumoniae urinary isolates, measured as nonsusceptibility to aminopenicillins (for E coli), fluoroquinolones, third- and fourth-generation cephalosporins, β-lactam and β-lactamase inhibitor combinations, aminoglycosides, and carbapenems. Resistance trends were analyzed using logistic regression with generalized estimating equations. Results:A total of 44 367 urinary isolates (mean [SD] age of patients, 35.8 [30.2] years; 26 935 isolates from women among 42 839 samples with sex data [62.9%]) were included. Mean (SD) age ranged from 29.1 (30.5) years among patients with K pneumoniae-positive samples in Cameroon to 54.3 (23.4) years among patients with E coli-positive samples in Morocco. E coli-positive samples were more common in women, with the highest proportions in Madagascar (11 948 women among 16 137 patients [74.0%]) and CAR (1329 women among 1893 patients [70.2%]), whereas K pneumoniae positive samples showed no clear sex pattern. At study end, amoxicillin resistance in E coli exceeded 85% across sites (eg, 96.0% [95% CI, 93.5%-97.6%] in Morocco), and amoxicillin-clavulanate resistance surpassed 50% for E coli (eg, 84.9% [95% CI, 77.7%-90.1%] in Morocco) and K pneumoniae (eg, 96.1% [95% CI, 89.4%-98.7%] in Morocco) in most countries. E coli resistance to third-generation cephalosporins (3GCs) and fluoroquinolones surpassed 35% at study end, with increasing trends in most countries (eg, 34.5% [95% CI, 27.3%-42.6%] to 59.8% [95% CI, 55.7%-63.8%] for cefotaxime in Benin and 32.4% [95% CI, 25.1%-40.7%] to 75.9% [95% CI, 72.4%-79.1%] for norfloxacin in Senegal). For K pneumoniae, resistance to 3GCs increased in Cameroon, Madagascar, CAR, and Senegal, exceeding 50% in most settings (eg, 50.7% [95% CI, 45.6%-55.9%] to 76.6% [95% CI, 71.7%-80.9%] for cefotaxime in Madagascar). Rates remained stable in Benin and Morocco. Fluoroquinolone resistance increased in Cameroon, Senegal, and CAR (eg, 38.5% [95% CI, 25.7%-53.0%] to 65.8% [95% CI, 58.8%-72.2%] for ciprofloxacin in Senegal); remained high in Benin and Morocco; and decreased in Madagascar but remained elevated (eg, 63.7% [95% CI, 58.7%-68.3%] to 59.9% [95% CI, 54.1%-65.4%] for norfloxacin). For both bacteria, carbapenem resistance remained less than 18% (eg, 17.2% [95% CI, 11.8%-24.3%] for K pneumoniae resistance to ertapenem in Senegal), but resistance to ertapenem reached 28.0% (95% CI, 25.7%-30.5%) for E coli and 27.8% (95% CI, 22.0%-34.5%] for K pneumoniae in Madagascar. Projections suggest that 3GC and carbapenem resistance could exceed 90% by 2050 in most countries (eg, 2037 [95% CI, 2032-2053] for E coli resistance to imipenem in Benin). Conclusions and Relevance:In this study, elevated and increasing resistance levels were observed, underlining the urgent need for improved measures against antimicrobial resistance in Africa.
Abstract The recent MPXV epidemic across Africa revealed extensive viral diversity and complex transmission dynamics, prompting a continent-wide genomic investigation. We analysed 3,450 high-quality MPXV virus whole genomes from 24 African Union Member States, revealing the complex and concurrent circulation of Sub-clades Ia, Ib, IIa, and IIb. Subclade Ia showed high levels of virus diversity in reservoir hosts in Central Africa, detected through zoonotic transmission and some sustained human outbreak lastly detected. In contrast, Clade Ib exhibited signatures of sustained human-to-human transmission across Eastern and Southern Africa. Clade IIa remains largely zoonotic in West Africa. Like Ia, IIb shows continued zoonotic transmission, and sustained human outbreak linked to lineage G1 and G2 circulation. Phylogeographic analyses revealed frequent cross-border transmission and interconnectedness, which was aligned with both human mobility corridors and international boundaries. For instance, the Democratic Republic of the Congo or Sierra Leone seems to emerge as a source of regional exportation, while the Cameroon–Nigeria, CAR-Cameroon or CAR-DRC interfaces reflected ongoing cross-border zoonotic spillovers. These findings underscore the need for harmonised genomic surveillance, APOBEC3-aware triage, and integrated One Health strategies to prevent local outbreaks from escalating into regional epidemics and to inform vaccine deployment and public health preparedness.
With the ongoing global resurgence of COVID-19, it is crucial to better understand past transmission dynamics to strengthen national preparedness for future surges. Since its emergence in Wuhan, China, in December 2019, SARS-CoV-2 has caused multiple waves of infection worldwide. The World Health Organization (WHO) has identified several variants of concern, including Alpha, Beta, Gamma, and Delta. At the end of 2021, the Omicron variant emerged in South Africa and rapidly spread across the globe. While many studies have explored the evolution and transmission of these variants, data from the Central African Republic remained limited. This study aimed to identify and characterize SARS-CoV-2 variants circulating in Bangui to support genomic surveillance and COVID-19 prevention strategies. Characterizing circulating variants provides essential information for the early detection of emerging lineages, the anticipation of potential epidemic waves, and the adaptation of public health strategies. We conducted a retrospective, descriptive study in Bangui, Central African Republic (CAR), from January to August 2022. A total of 102 nasopharyngeal samples positive for SARS-CoV-2 (Ct ≤ 30), selected from the biobank of the Pasteur Institute in Bangui, were reanalyzed using multiplex qPCR to confirm their Ct values. Eligible samples were then sequenced using the MinION MK1C (Oxford Nanopore Technologies) platform, following the ARTIC Network protocol at the Institut Pasteur, Paris (CIBU). Bioinformatics processing using reads mapping to a reference genome, followed by consensus sequence generation, included standard steps of basecalling, demultiplexing, quality filtering, genome alignment, primer trimming, consensus generation, and variant calling. The different variants were described using the Nexstrain web application. The results revealed that 66.7
