Abstract The global dissemination of antimicrobial resistance is increasingly driven by bacterial clones combining antimicrobial resistance with enhanced virulence and environmental adaptability. Escherichia coli sequence type 131 (ST131) has historically been regarded as a major disseminator of the extended-spectrum β-lactamase (ESBL) bla CTX-M-15 . However, the emergence of E. coli ST1193 carrying bla CTX-M-15 may represent an ongoing shift in the epidemiology of this resistance determinant. Here, we investigated the prevalence, genomic characteristics, virulence and antimicrobial resistance potential of ST1193 in comparison with ST131. A total of 1,136 E. coli isolates were recovered from touristic and non-touristic environments, hospital-associated samples, and aircraft toilets in Guadeloupe. Isolates were whole-genome sequenced and analysed for antimicrobial resistance and virulence determinants. Additionally, publicly available genomic data comprising 1,215 bla CTX-M-15 -positive ST131 and ST1193 isolates were analysed to assess temporal and geographical trends. ST1193 was significantly associated with aircraft-associated samples and exhibited a higher antimicrobial resistance gene burden than ST131, while maintaining a comparable virulence factor content. Analysis of publicly available genomes revealed similar temporal emergence patterns for bla CTX-M-15 -positive ST1193 and ST131, with ST1193 showing a more recent distribution and a higher number of deposited isolates in recent years, consistent with a potential ongoing clonal replacement. Comparative genomic analysis identified numerous virulence and adaptation-associated genes shared between both sequence types, while ST1193 additionally carried distinct determinants, including components of the transmissible locus of stress tolerance. Furthermore, quinolone resistance-associated mutations were strongly linked to bla CTX-M-15 carriage, particularly among ST1193 isolates. Together, these findings identify E. coli ST1193 as an emerging high- risk clone with substantial potential for bla CTX-M-15 dissemination. Its association with aircraft- associated samples further highlights the potential role of air travel in long-distance transmission and underscores the need to reconsider current surveillance strategies focused predominantly on ST131.

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.

Background:The global health threat of antimicrobial resistance involves the human, animal and environmental sectors. Data from Cameroon are scarce. Objectives:This study aimed to define extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) rates and associated risk factors across the three sectors in Douala, Cameroon, and to define molecular characteristics of isolates. Methods:From June 2022 to May 2023, we collected blood cultures from hospitalized patients, rectal swabs from healthy pregnant women, caeca from broiler chickens and environmental wastewater. Samples were screened for ESBL-Ec using CHROMAgar™ ESBL and cefotaxime-supplemented Tryptone Bile X-glucuronide agar. Antimicrobial susceptibility testing was performed by disk diffusion following EUCAST guidelines. Whole-genome sequencing was carried out using Illumina technology. Results:Of 628 samples, 374 yielded ESBL-Ec. Prevalence was 54.6% (131/240) in pregnant women, 70.4% (169/240) in chickens and 93.1% (67/72) in wastewater. The proportion of ESBL-Ec among E. coli-positive-blood cultures was 9.2% (7/76). Multi-family household living was independently associated with ESBL-Ec carriage among pregnant women (adjusted odds ratio = 1.7, 95% CI 1.0-3.1, P = 0.03). High co-resistance (>70%) was observed for tetracycline, ciprofloxacin and trimethoprim/sulfamethoxazole. Sequencing of 32 isolates revealed 45 distinct resistance genes, including blaCTX-M-15 (n = 13, 40.6%), blaCTX-M-55 (n = 11, 34.4%) and last-resort antibiotic resistance genes mcr-1 and bla OXA-181. High-risk sequence types included ST131 (pregnant women) and ST10 (chickens). Notably, ST48 was shared between pregnant women and chickens, and ST155 between pregnant women and wastewater. Conclusion:Cross-sectoral ESBL-Ec in Douala exhibits high genomic diversity and alarming resistance. The occurrence of last-resort genes requires immediate One Health surveillance and coordinated interventions.

Wastewater treatment plants (WWTPs) are global hotspots for disseminating antibiotic resistance genes (ARGs). Chemical compounds commonly found in wastewater, including antibiotics, biocides, non-steroidal anti-inflammatory drugs (NSAIDs), and heavy metals, along with climate variables and physicochemical factors can select for antibiotic-resistant bacteria even at low concentrations, promoting ARG proliferation. Since WWTPs can vary in their removal efficiency and influent compositions, we assessed their impact on ARGs and pollutant concentrations in Guadeloupe, French Caribbean. Using 96 samples collected across four campaigns (September 2021-January 2023) from three urban wastewater continuums (hospital-based, urban non-touristic, urban touristic), we profiled resistome and exposome in influent and effluent and applied machine learning (random forest, lasso) to identify variables most affected by treatment and factors associated with ARG patterns. Overall, ARG reduction was lower than anticipated. Among 16 clinically relevant genes targeted, aph(3’)-III, blaOXA, blaSHV, blaTEM, ermB, intI1, qnrS, and tetM decreased by 59.8% to 89.9% across WWTPs, while mcr-1 increased 9.52-fold in hospital effluent. Of nine antibiotics, most remained unchanged, and eight biocides were not effectively removed. Heavy-metal reductions occurred only in the non-touristic continuum (Cd -32.5%, Cu -21.1%, and Hg -36.2%). We found continuum-specific associations between ARGs and co-selective stressors including biocides, erythromycin, selected heavy metals (As, Cd, Cu, Cr, Hg), and water temperature. Upstream source was identified as a primary driver of effluent profiles. These results align with the EU’s revised Urban Wastewater Treatment Directive and reveal how co-occurring pollutants, and environmental factors shape ARG distributions in unique settings and regions with limited wastewater treatment management.

ABSTRACT Wastewater is a key reservoir and transmission route for antibiotic resistance genes (ARGs), enabling their spread from influent to effluent and into receiving environments. However, how combined selective pressures (antibiotics, biocides, heavy metals, pharmaceuticals) influence resistant bacteria and ARG persistence over space and time remains poorly understood. Likewise, the role of the wastewater microbiome in ARG dynamics is still unclear, as few studies integrate microbiome shifts with chemical and environmental drivers. Here, we investigated how microbiome dynamics, chemical exposures, and environmental conditions shape clinically relevant ARG dynamics from sewage to receiving environments in Guadeloupe, French Caribbean. We analysed data collected from three wastewater continuums, (hospital-based, domestic, touristic) over four campaigns (September 2021–February 2023). We characterised ARG and microbiome composition spatiotemporal patterns and used a mixed-effect model to investigate ARG associations with potential drivers, including exposome factors, microbiome dissimilarity and environmental factors. Several ARGs were negatively associated with microbiome dissimilarity (Bray–Curtis distances) ( aac(6’)-Ib, aph(3’)-III, bla SHV , bla TEM , intI1, qnrS, sul1 and tetM ). Negative associations were also observed between upstream–downstream differences in anti-inflammatory drug concentrations and the abundance of aac(6’)-Ib , aph(3’)-III , bla CTX-M , ermB , intI1 , and tetM . In contrast, ARG relative abundance was positively associated with upstream–downstream differences in antibiotic concentrations, suggesting selection along the continuum. These findings indicate that ARG dissemination along wastewater-to-coastal pathways is shaped by opposing processes, with microbiome turnover potentially limiting ARG persistence while chemical gradients promote specific gene enrichment. The outcome is ARG-specific, with implications for antimicrobial resistance risks associated with recreational waters, seafood consumption, and coastal ecosystem interactions.

Background:Bone and joint infections (BJIs) are increasingly reported worldwide, but data on their epidemiology remain limited in tropical settings. We aimed to characterize the causative agents of BJIs and their resistance patterns, in order to inform empirical antibiotic in our tropical setting. Methods:This 6-year retrospective study included all adults with a first microbiologically confirmed episode of BJI between January 2019 and December 2024 at the Guadeloupe University Hospital, a tertiary care center in the Caribbean. Results:A total of 312 patients with BJI were included. Among the 449 isolates recovered, Gram-negative bacilli (GNB) were predominant (41%), including AmpC β-lactamase-producing Enterobacterales (13%, 59/449) and Pseudomonas aeruginosa (9%, 39/449). Methicillin-resistant Staphylococcus aureus accounted for 3% (13/449). At least one GNB was identified in 31% of native septic arthritis (27/88), 33% of spondylodiscitis (9/27), 38% of prosthetic joint infections (27/71), 47% of osteosynthesis-associated infections (48/103), and 52% of osteomyelitis (12/23). Factors independently associated with GNB infection were a history of bite/scratch wound, contact with soil/vegetation and lower limb infection. Cefazolin provided limited likelihood of in vitro adequacy against causal pathogens in native septic arthritis episodes (74%, as compared to 92% for both cefepime and piperacillin-tazobactam). Lower rates were observed in cases of osteosynthesis-associated and prosthetic joint infections (48%-68%, as compared to 62%-75% for third-generation cephalosporins, 79%-80% for cefepime and 80%-86% for piperacillin-tazobactam). Conclusions:Our findings highlight the prominent role of GNBs in tropical BJI and support the implementation of local surveillance systems to guide empirical treatment strategies.

Introduction Les infections ostéoarticulaires (IOA) sont de plus en plus rapportées à travers le monde, mais les données épidémiologiques restent limitées en contexte tropical. L’objectif de notre étude était de décrire les micro-organismes responsables des infections ostéoarticulaires et leurs profils de résistance, afin d’orienter la prise en charge antibiotique probabiliste dans ce type d’environnement. Méthodologie Cette étude rétrospective sur cinq ans a inclus tous les patients adultes présentant un premier épisode d’infection ostéoarticulaire confirmé microbiologiquement entre janvier 2019 et décembre 2024 au Centre Hospitalier Universitaire de la Guadeloupe. Résultats Au total, 312 patients avec IOA ont été inclus. Parmi les 449 microorganismes isolés, les bacilles à Gram négatif étaient prédominants (41 %), incluant des entérobactéries du groupe 3 (13 %, 59/449) et Pseudomonas aeruginosa (9 %, 39/449). Les Staphylococcus aureus résistants à la méticilline représentaient 3 % (13/449), tandis que les entérobactéries productrices de bêta-lactamases à spectre étendu ne représentaient que 2 % des isolats (8/449). Au moins un bacille à Gram négatif a été identifié dans 31 % des arthrites septiques sur articulation native (27/88), 33 % des spondylodiscites (9/27), 38 % des infections sur prothèse articulaire (27/71), 47 % des infections sur matériel d’ostéosynthèse (48/103) et 52 % des ostéomyélites (12/23). Les morsures ou griffures, le contact avec le sol ou les végétaux, ainsi qu’une localisation au membre inférieur étaient des facteurs indépendamment associés à l’identification d’un bacille à Gram négatif. Dans les arthrites septiques, l’activité estimée de la céfazoline (74 %) était inférieure à celle du céfépime (92 %) et de la pipéracilline–tazobactam (92 %). Les infections sur prothèse et sur matériel d’ostéosynthèse présentaient une sensibilité plus faible à la céfazoline et aux céphalosporines de troisième génération (68–70 % et 48–49 %, respectivement), comparativement à la céfépime et à la pipéracilline–tazobactam (80–86 % et 79–83 %). Toutes les combinaisons de céfépime ou pipéracilline–tazobactam avec un glycopeptide montraient des taux de sensibilité ≥ 90 %. Conclusion Nos résultats mettent en évidence l’émergence des bacilles à Gram négatif dans les IOA en contexte tropical, soulignant la nécessité d’une surveillance locale pour orienter la prise en charge antibiotique probabiliste.

Background: Bioinformatics is increasingly used in various scientific works. Large amounts of heterogeneous data are being generated these days. It is difficult to interpret and analyze these data effectively. Several software tools have been developed to facilitate the handling and analysis of biological data, based on specific needs. Methods: The Galaxy web platform is one of these software tools, allowing free access to users and facilitating the use of thousands of tools. Other software tools, such as Bioconda or Jupyter Notebook, facilitate the installation of tools and their dependencies. In addition to these tools, RStudio can be mentioned as a powerful interface that facilitates the use of the R programming language for data analysis and statistics. Results: The aim of this study is to provide the scientific community with guides on how to perform bioinformatics/biostatistical analyses in a simpler manner. With this work, we also try to democratize well-documented software tools to make them suitable for both bioinformaticians and non-bioinformaticians. We believe that user-friendly guides and real-life/concrete examples will provide end-users with suitable and easy-to-use methods for their bioinformatics analysis needs. Furthermore, tutorials and usage examples are available on our dedicated GitHub repository. Conclusions: These tutorials/examples (In English and/or French) could be used as pedagogical tools to promote bioinformatics analysis and offer potential solutions to several bioinformatics needs. Special emphasis is placed on microbial omics data analysis.

Scarce epidemiological data are available regarding necrotizing soft tissue infections (NSTIs) in tropical areas. Here we aimed to describe the clinical and biological features, and outcomes, of critically ill patients with NSTIs admitted to an intensive care unit (ICU) in a tropical setting. Furthermore, we analyzed these findings to identify distinct clinical phenotypes and explore their associations with patient outcomes. This retrospective observational study included all patients with NSTIs admitted to the ICU of the University Hospital of Guadeloupe between January 2014 and December 2023. Subgroups of patients having similar clinical profiles were identified through unsupervised clustering (factor analysis for mixed data, and hierarchical clustering on principal components). Univariate and multivariate analyses identified factors associated with 90-day mortality. During the study period, 91 NSTI patients were admitted to the ICU. The median Simplified Acute Physiology Score (SAPS) II was 45 [IQR 40–66], and the median time between hospital admission and first surgical debridement was 8 h [IQR 6–10 h]. While in the ICU, 65

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OBJECTIVES:Antimicrobial resistance (AMR) is a major public health concern worldwide. International travel is a risk factor for acquiring antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). Therefore, understanding the transmission of ARB and ARGs is instrumental in tackling AMR. This longitudinal study aimed to assess the benefit of wastewater monitoring in Guadeloupe to evaluate the role of tourism in the spread of AMR. METHODS:A wastewater-based surveillance (WBS) study was conducted to monitor AMR in Guadeloupe in 2022 during dry and wet seasons. We characterized the resistome, microbiome and exposome of water samples collected in wastewater treatment facilities of two cities with different levels of tourism activities, in the content of aircraft toilets, and the pumping station receiving effluents from hotels. RESULTS:The results show that the WBS approach facilitates the differentiation of various untreated effluents concerning exposome, microbiome, and resistome, offering insights into AMR dissemination. Additionally, the findings reveal that microbiome and exposome are comparable across sites and seasons, while resistome characterisation at specific locations may be pertinent for health surveillance. The microbiome of aircraft was predominantly composed of anaerobic bacteria from human intestinal microbiota, whereas the other locations exhibited a blend of human and environmental bacteria. Notably, individuals arriving by air have not introduced clinically significant resistance genes. Exposome compounds have been shown to influence the resistome's variance. CONCLUSIONS:Clear differences were seen between the aircraft and the local sampling sites, indicating that the contribution of tourism to the observed resistance in Guadeloupe is not significant.

ImportanceIn low- and middle-income countries (LMICs), neonatal bacterial infections are mainly caused by Enterobacterales species and Staphylococcus aureus, which are also the leading causes of mortality directly attributable to antimicrobial resistance. As bacterial colonization often precedes infection, better knowledge of colonization is crucial to prevent antibiotic-resistant neonatal sepsis.ObjectiveTo synthesize current evidence on the prevalence of and factors associated with colonization with third-generation cephalosporin–resistant Enterobacterales (3GCRE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant S aureus (MRSA) during the first 3 months of life in LMICs.Data SourcesPubMed, Scopus, Web of Science, and the World Health Organization Global Index Medicus were searched for articles published from January 1, 2000, through July 29, 2024.Study SelectionIncluded studies were conducted in LMICs and reported prevalence rates or factors associated with colonization with 3GCRE, CRE, or MRSA in neonates and infants up to 3 months of age. Outbreak reports were excluded.Data Extraction and SynthesisData extraction and risk-of-bias assessment using a Joanna Briggs Institute tool were performed by 2 independent reviewers. Pooled prevalence for each pathogen was computed using a random-effects model. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline.Main Outcomes and MeasuresPrevalence of and factors associated with 3GCRE, CRE, and MRSA colonization.ResultsOf the 3147 articles identified in the search, 67 studies (51 for 3GCRE and CRE and 16 for MRSA) including 17 152 individuals were eligible. The pooled prevalence of 3GCRE colonization was 30.2% (95% CI, 21.4%-40.7%; τ2 = 1.48; I2 = 95.1%), varying from 18.2% (95% CI, 10.8%-29.1%) in nonhospitalized individuals to 48.2% (95% CI, 36.4%-60.2%) in hospitalized individuals. The prevalence of CRE colonization was 2.6% (95% CI, 0.7%-8.8%; τ2 = 7.79; I2 = 95.6%), while it was 2.7% (95% CI, 1.0%-6.7%; τ2 = 2.58; I2 = 93.5%) for MRSA. Increased risk of colonization with 3GCRE was associated with hospital birth (odds ratio [OR], 1.87; 95% CI, 1.33-2.64), neonatal antibiotic use (OR, 2.96; 95% CI, 1.43-6.11), and prolonged rupture of membranes (OR, 3.86; 95% CI, 2.19-6.84).Conclusions and RelevanceIn this systematic review and meta-analysis of antibiotic-resistant pathogen carriage in individuals aged 0 to 3 months, the pooled prevalence was substantial despite a limited exposure period. Although high heterogeneity between studies limited extrapolation of results, the findings highlight the need for further investigation to identify transmission routes and to design targeted and effective preventive measures.

Background Melioidosis is an emerging infectious disease caused by the soil-dwelling bacterium Burkholderia pseudomallei that affects both humans and animals. It is endemic in South and Southeast Asia, and northern Australia, causing an estimated 165,000 human cases annually worldwide. Human cases have been reported in the French West Indies (Martinique and Guadeloupe) since the 1990s. Conversely, no human cases have been reported in French Guiana, a French territory in South America. Our study aimed to investigate whether B. pseudomallei is locally established in Guadeloupe and French Guiana. We assessed animal exposure by serology and examined the presence of B. pseudomallei in the environment of seropositive animals. Methodology/Principal findings Blood samples were collected from domestic animals in two goat farms in Les Saintes, Guadeloupe (n=31), and in 56 farms in French Guiana (n=670) and tested by ELISA. Serological follow up was performed on selected farms. Soil, water and goat rectal swabs were collected and analysed by culture and PCR. In French Guiana, the highest prevalence rates were observed in equids (24%) and cattle (16%), while in Les Saintes, a prevalence of 39% was observed in goats. The longitudinal study in Les Saintes revealed consistent high seropositivity in goats. A B. pseudomallei strain was isolated from the soil from one of the farms and detected in goat rectal swabs from the other farm. Conclusions/Significance Our environmental investigation prompted by the serologic data confirms the presence of B. pseudomallei in Les Saintes, consistent with documented human cases of melioidosis on this island. In French Guiana, our serologic results call for environmental surveys and a re-evaluation of human infections with melioidosis-like symptoms. The approach developed in this study may help to identify high-risk areas that warrant further investigation. Author summary Burkholderia pseudomallei , an environmental bacterium, is the causative agent of melioidosis in humans and animals. If the disease has been historically reported to be endemic in South Asia and northern Australia, recent studies reveal its presence outside of these territories, both in the environment and among patients who have not travelled to endemic areas. Furthermore, the projected increase in extreme climatic events in the near future could increase the prevalence of the disease as well as cause its emergence in new territories. For these reasons, it is important to identify new areas at risk. Our study aimed to investigate the presence of the pathogen in French West Indies. We combined surveys in domestic animals (cattle, goats, horses, sheep, and pigs) and in the environment. The identification of seropositive animals without clinical signs, together with the isolation of B. pseudomallei in the environment of a goat farm in Guadeloupe, underscores the importance of including melioidosis in animal surveillance programs. The use of serologic methods can help identify animal exposure to the pathogen, thereby helping to identify areas where the pathogen may be present in the environment. ### Competing Interest Statement The authors have declared no competing interest.

Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.

Background Melioidosis, an emerging infectious disease that affects both humans and animals, is caused by the soil-dwelling bacterium Burkholderia pseudomallei. It is endemic in South and Southeast Asia, and northern Australia, causing an estimated 165,000 human cases annually worldwide. Human cases have been reported in the French West Indies (Martinique and Guadeloupe) since the 1990s. Conversely, no human cases have been reported in French Guiana, a French territory in South America. Our study aimed to investigate whether B. pseudomallei is locally established in Guadeloupe and French Guiana using animals as a proxy. Methodology/principal findings Blood samples were collected from different animals from 56 farms in French Guiana (n = 670) and from two goat farms in Les Saintes (n = 31), part of the Guadeloupe archipelago and tested by enzyme-linked immunosorbent assay (ELISA). In Les Saintes, a serological follow-up was performed, and soil, water and goat rectal swabs were collected and analyzed by culture and PCR. The highest seroprevalence rates (39%) were observed in goats in Les Saintes, followed by horses (24%) and cattle (16%) in French Guiana. In the two goat farms, supplementary analyses detected B. pseudomallei from one goat rectal swab, and a B. pseudomallei strain was isolated from the soil. Conclusions/significance Our animal serological data suggest the presence of B. pseudomallei in Les Saintes and French Guiana. In Les Saintes, environmental surveys confirmed the endemicity of the bacteria, which is consistent with documented human cases of melioidosis on the island. We did not conduct an environmental survey in French Guiana. Nevertheless, our serological results call for local environmental surveys and a retrospective reassessment of human infections with melioidosis-like symptoms.

Dengue virus (DENV), mainly transmitted by Aedes aegypti mosquitoes, is the most prevalent arbovirus worldwide, representing a public health problem in tropical and subtropical countries. In these areas, antibiotic consumption rises which may impact both mosquito microbiota and dengue transmission. Here, we assessed how the ingestion by Ae. aegypti of therapeutic concentrations of amoxicillin-clavulanic Acid association (Amox/Clav), a broad-spectrum antibiotic used to treat febrile symptoms worldwide, impacted its microbiota. We also evaluated whether simultaneous ingestion of antibiotic and DENV impacted Ae. aegypti ability to transmit this virus. We found that Amox/Clav ingestion impacted microbiota composition in Ae. aegypti and we confirmed such impact in field-collected mosquitoes. Furthermore, we observed that Amox/Clav ingestion enhanced DENV dissemination and transmission by this mosquito at 21 days post-DENV exposure. These findings increase our understanding of factors linked to human hosts that may influence dengue transmission dynamics in regions with mass-drug administration programs.

Importance In low- and middle-income countries (LMICs), neonatal bacterial infections are mainly caused by Enterobacterales species and Staphylococcus aureus, which are also the leading causes of mortality directly attributable to antimicrobial resistance. As bacterial colonization often precedes infection, better knowledge of colonization is crucial to prevent antibiotic-resistant neonatal sepsis. Objective To synthesize current evidence on the prevalence of and factors associated with colonization with third-generation cephalosporin-resistant Enterobacterales (3GCRE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant S aureus (MRSA) during the first 3 months of life in LMICs. Data Sources PubMed, Scopus, Web of Science, and the World Health Organization Global Index Medicus were searched for articles published from January 1, 2000, through July 29, 2024. Study Selection Included studies were conducted in LMICs and reported prevalence rates or factors associated with colonization with 3GCRE, CRE, or MRSA in neonates and infants up to 3 months of age. Outbreak reports were excluded. Data Extraction and Synthesis Data extraction and risk-of-bias assessment using a Joanna Briggs Institute tool were performed by 2 independent reviewers. Pooled prevalence for each pathogen was computed using a random-effects model. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline. Main Outcomes and Measures Prevalence of and factors associated with 3GCRE, CRE, and MRSA colonization. Results Of the 3147 articles identified in the search, 67 studies (51 for 3GCRE and CRE and 16 for MRSA) including 17 152 individuals were eligible. The pooled prevalence of 3GCRE colonization was 30.2% (95% CI, 21.4%-40.7%; tau 2 = 1.48; I2 = 95.1%), varying from 18.2% (95% CI, 10.8%-29.1%) in nonhospitalized individuals to 48.2% (95% CI, 36.4%-60.2%) in hospitalized individuals. The prevalence of CRE colonization was 2.6% (95% CI, 0.7%-8.8%; tau 2 = 7.79; I2 = 95.6%), while it was 2.7% (95% CI, 1.0%-6.7%; tau 2 = 2.58; I2 = 93.5%) for MRSA. Increased risk of colonization with 3GCRE was associated with hospital birth (odds ratio [OR], 1.87; 95% CI, 1.33-2.64), neonatal antibiotic use (OR, 2.96; 95% CI, 1.43-6.11), and prolonged rupture of membranes (OR, 3.86; 95% CI, 2.19-6.84). Conclusions and Relevance In this systematic review and meta-analysis of antibiotic-resistant pathogen carriage in individuals aged 0 to 3 months, the pooled prevalence was substantial despite a limited exposure period. Although high heterogeneity between studies limited extrapolation of results, the findings highlight the need for further investigation to identify transmission routes and to design targeted and effective preventive measures.

OBJECTIVES:To identify distinct phenotypes of critically ill leptospirosis patients upon ICU admission and their potential associations with outcome. DESIGN:Retrospective observational study including all patients with biologically confirmed leptospirosis admitted to the ICU between January 2014 and December 2022. Subgroups of patients with similar clinical profiles were identified by unsupervised clustering (factor analysis for mixed data and hierarchical clustering on principal components). SETTING:All patients admitted to the ICU of the University Hospital of Guadeloupe on the study period. PATIENTS:One hundred thirty critically ill patients with confirmed leptospirosis were included. INTERVENTIONS:None. MEASUREMENTS AND MAIN RESULTS:At ICU admission, 34% of the patients had acute respiratory failure, and 26% required invasive mechanical ventilation. Shock was observed in 52% of patients, myocarditis in 41%, and neurological involvement in 20%. Unsupervised clustering identified three clusters-"Weil's Disease" (48%), "neurological leptospirosis" (20%), and "multiple organ failure" (32%)-with different ICU courses and outcomes. Myocarditis and neurological involvement were key components for cluster identification and were significantly associated with death in ICU. Other factors associated with mortality included shock, acute respiratory failure, and requiring renal replacement therapy. CONCLUSIONS AND RELEVANCE:Unsupervised analysis of critically ill patients with leptospirosis revealed three patient clusters with distinct phenotypic characteristics and clinical outcomes. These patients should be carefully screened for neurological involvement and myocarditis at ICU admission.

Purpose: A simplified therapeutic guideline (STG) was established in our urology ward in 2019 for urinary infections. Our aim was to describe the level of physician adherence to STG and the impact of a limited number of antibiotic compounds on the rate of multidrug-resistant (MDR) bacteria. As guidelines should improve patient care, unfavorable outcomes were also reported.Methods: The STG for community-acquired and nosocomial urinary infections, including six antibiotics, was established in November 2019 and has been officially applied since January 2020. Treatment duration has to be <= 14 days. We conducted a before-after study to measure physician adherence to the STG for bacteremia treatment between January 2017 and December 2022. Adherence was defined as exclusive use of STG antibiotics. All isolated bacteria from blood cultures were recorded, including MDR Enterobacterales, defined as AmpC b-lactamase- or ESBL-producing strains. Unfavorable outcomes were defined as uncontrolled infection, a second surgical procedure, ICU requirement, and/or death.Results: Seventy-six cases of bacteremia occurred between January 2017 and December 2019, and ninety between January 2020 and December 2022. The main comorbid condition was urological cancer (46%). The main reason for surgery was ureteral stent (32%). Antibiotic management in accordance with STG increased from 18% to 52%, p < 0.001, and treatments > 14 days decreased from 53% to 28%, p < 0.001. MDR Enterobacterales bacteremia was reduced from 52% to 35%, p = 0.027. The rate of unfavorable outcomes was unchanged. Conclusion: STG adherence in urology was satisfactory and associated with reduced MDR Enterobacterales bacteremia.

Objectives The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment. Data description ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species.