Palpouguini Lompo

Environmental surveillance for human pathogen detection is crucial for safeguarding public health; however, traditional approaches are often time-consuming, equipment-intensive and workflow-complex, delaying actionable public-health decision-making. The integration of a mobile laboratory (ML) with rapid bioinformatic analysis and interactive data visualization offers a novel approach to this surveillance. The ML workflows, with a focus on metagenomic sequencing and qPCR technologies, have been specifically designed to provide real-time information in detecting epidemiological threats in environmental samples. We have adopted a minimalist strategy, avoiding complex, expensive, and energy-intensive equipment that is challenging to maintain and transport, thereby reflecting a more sustainable approach. This study details the activities and outcomes of implementing such a ML in Tanzania. During one-month ML deployment, a total of 83 samples were sequenced using long-read metagenomic sequencing, and 70 samples were analyzed by Biomeme qPCR. The deployment enabled the detection of multiple bacterial, viral, and antimicrobial resistance targets in wastewater, drinking water, surface water, and soil samples providing valuable insights into the population epidemiological information relevant to the prevention of waterborne and zoonotic infections. In addition, the ML deployment provided a rare opportunity for knowledge transfer, actively engaged local researchers, and strengthened local epidemiological capacity. After the deployment, certificates of completion were issued to twenty-five scientists from four African countries (Tanzania, Burkina Faso, Democratic Republic of Congo, and Ethiopia) and post-deployment surveys were sent out to gather their feedback. Our findings highlight the importance of combining targeted qPCR assays with metagenomic sequencing for the proper interpretation, while acknowledging the risk of false-positive detections arising from low-abundance sequencing reads, particularly when using fast taxonomic classification tools such as kraken2. Given the hardware limitations inherent to ML deployments, metagenomic pathogen detection in this context should therefore be regarded primarily as a valuable screening tool rather than a definitive diagnostic method. These observations further underscore the need for more stringent and computationally demanding bioinformatic approaches when assessing high-priority pathogens. Complementary qPCR-based assays conducted within the ML can ensure equivalent robustness to those conducted in conventional laboratory settings. This innovative approach has the potential to significantly enhance detection capabilities and support timely public health responses in resource-limited settings.

The emergence of the novel monkeypox virus (MPXV) clade Ib in the Democratic Republic of the Congo (DRC) and neighboring countries in late 2023 highlighted the need for rapid, scalable surveillance approaches to support outbreak detection and response. As part of the ODIN-Mpox project, wastewater surveillance (WWS) systems were established as an emergency public health measure in three Sub-Saharan African countries (DRC, Tanzania, and Burkina Faso) to evaluate the feasibility of wastewater-based monitoring for mpox and strengthen local surveillance capacity. Between January 2025 and April 2026, 117 wastewater samples were collected from selected sites and analyzed for MPXV DNA using targeted qPCR assays. Clinical mpox data were obtained from national surveillance systems and WHO reports to assess epidemiological linkages between wastewater detections and reported infections. Six wastewater samples tested positive for MPXV DNA. During the study period, DRC experienced the highest disease burden, with weekly reported cases peaking at about 3,000 in January 2025, while Tanzania reported a peak of 20 weekly cases in March 2025. No confirmed clinical cases were reported in Burkina Faso. No clear relationship was observed between reported case numbers and qPCR Ct values in positive wastewater samples. Despite the low detection frequency, the project demonstrated the operational feasibility of implementing MPXV wastewater surveillance in resource-limited settings and established laboratory capacity for environmental monitoring of emerging infectious diseases. Given the early stage of WWS implementation in the region, the study identified opportunities for further system strengthening, including optimization of sample processing and reporting workflows, improved access to laboratory supplies, and enhanced integration of environmental and clinical surveillance data streams. These findings highlight the value of WWS as a complementary component of integrated public health surveillance systems and emphasize the need for continued investment in laboratory capacity, harmonized methodologies, governance frameworks, and knowledge exchange to enhance outbreak preparedness and response in low-resource settings.

Mobile laboratories (MLs) offer a flexible platform for on-site wastewater and environmental surveillance, particularly in regions with limited laboratory capacity. Effective ML deployment, however, requires optimized molecular workflows that match local infrastructure, equipment, and workforce constraints. Here, we present an integrated ML workflow that combines Oxford Nanopore Technologies (ONT) sequencing for shotgun metagenomics, multiplex metabarcoding for microbial community profiling, and Biomeme-based qPCR for targeted pathogen detection. We introduce and validate a multiplexed ONT small subunit rRNA amplicon sequencing approach that enables simultaneous profiling of bacteria, archaea, and microeukaryotes in complex environmental samples. Sample pretreatment and nucleic acid extraction was tested for combined chemical–mechanical lysis followed by magnetic bead purification. Workflow performance was assessed by analyzing a known mock community (ZymoBIOMICS) and wastewater samples spiked with inactivated monkeypox virus (MPXV), demonstrating accurate taxonomic representation and sensitive MPXV detection. The multiplex metabarcoding workflow enabled rapid, high-resolution community profiling and showed stronger concordance with qPCR-based pathogen detection than whole-genome and whole-transcriptome amplification workflows. MPXV tiled amplicon sequencing was successfully incorporated into the ML protocol, supporting near-real-time genomic characterization in field settings. Across diverse environmental matrices, a multiple displacement amplification (MDA)-based metagenomic workflow combined with ML nucleic acid extraction reliably reproduced the composition of the mock community. Overall, integrating ONT sequencing, MDA-based metagenomics, multiplex metabarcoding, and mobile qPCR provides an efficient surveillance platform within a One Health framework. While key components of the workflow were validated under controlled laboratory conditions, pilot testing on environmental samples from sub-Saharan Africa demonstrates its applicability to real-world matrices. Graphical

High ESBL prevalence in MDR E. coli and Klebsiella from clinical and wastewater samples, with concerning AmpC and carbapenemase occurrence and frequent co-resistance. Multidrug-resistant (MDR) gram-negative bacteria pose a global health threat, with MDR-Escherichia coli and MDR-Klebsiella pneumoniae as the primary contributors among Enterobacterales. This study explored the prevalence of extended-spectrum beta-lactamase (ESBL), AmpC-β-lactamase and carbapenemase-encoding genes among ESBL-producing E. coli and Klebsiella spp. isolated from clinical and hospital wastewater samples in Burkina Faso. We analyzed 292 ESBL-producing E. coli and Klebsiella spp. isolates from clinical specimens (n = 218) and hospital wastewaters (n = 74) across five Burkinabe hospitals. Using the conventional PCR multiplex technique, we screened for 10 key resistance genes, covering ESBL (blaCTX-M, blaSHV and blaTEM), AmpC-β-lactamase (blaDHA and blaFOX) or carbapenemases (blaOXA-48, blaNDM, blaVIM, blaKPC and blaIMP). Resistance genes were present in both clinical and wastewater samples across all levels of healthcare facilities. ESBL-encoding genes were detected in 95.5% of the isolates, AmpC-β-lactamase genes in 11.0% and carbapenemase-encoding genes in 17.1%. Many isolates from both clinical and hospital wastewater samples harbored multiple resistance genes, spanning all three gene categories. The findings from this study underscore the urgent need for a comprehensive hospital-based AMR surveillance system and stringent antibiotic stewardship measures to limit the spread of resistant bacteria in the environment to protect public health.

Wastewater and environmental surveillance (WES) provides a complementary approach to traditional clinical surveillance, particularly in low- and middle-income countries (LMICs) where clinical coverage is variable. WES implementation across these settings can generate comparable, reliable data to inform regional and global public-health action. We implemented a WES study in Burkina Faso, the Democratic Republic of the Congo (DRC), and Tanzania, across diverse sanitation systems. Wastewater and surface water samples were collected and analysed using culture-based methods to detect and isolate faecal indicator bacteria (FIBs), toxigenic Vibrio cholerae, and Salmonella Typhi, following shared protocols where possible. Contextual information, including available clinical surveillance data and site descriptions, was incorporated to support data interpretation. Across the three countries, a total of 112 samples of wastewater and surface water were analysed during monthly sampling campaigns from January to September 2025. The presence of faecal contamination was confirmed at 12 sampling sites across the three countries, with FIB detected at least once at each site. Presumptive S. Typhi was detected at three sites in Burkina Faso and one site in Tanzania, while V. cholerae was detected at one site in Tanzania; neither pathogen was detected at any sites in the DRC. Clinical data from Burkina Faso indicated typhoid fever cases in all corresponding catchment areas, while cholera cases were absent. In the DRC, clinical data indicated the presence of both typhoid fever and cholera cases in the vicinity of all sampling locations. Implementation challenges included laboratory capacity gaps, supply-chain delays, and incomplete adherence to harmonised protocols. Lessons learned on laboratory implementation, sampling strategies, and data management were systematically documented, and active stakeholder participation facilitated site selection, interpretation, and integration of findings. Coordinated WES can complement clinical surveillance, and the study provides a further exploration of its potential role in diarrhoeal disease surveillance to support public health action in sub-Saharan Africa.

Food-borne diseases affect nearly 10% of the global population annually, with Salmonella being a major cause, particularly impacting children, the elderly, and populations in low- and middle-income countries. This study aimed to assess the prevalence, serotype distribution, antibiotic resistance profiles, and genetic determinants of resistance and virulence of Salmonella enterica in humans and poultry in the Nanoro health district. A community-based cross-sectional study involving humans and poultry was conducted in the Nanoro health district. Fresh stool samples (human and poultry cloacal/cecal) were collected, transported under sterile conditions, and processed within two hours using standard bacteriological methods. Phenotypic antibiotic resistance was determined by the Kirby–Bauer disk diffusion method, and whole-genome sequencing (Illumina) identified serotypes, resistance genes, and virulence factors. Logistic regression analyzed associations between Salmonella carriage and host or environmental factors. Salmonella enterica carriage was detected in 8.7% of humans and 7.2% of poultry. Human isolates showed 24% resistance to cephalosporins, while poultry isolates showed 36.8% resistance. Resistance genes, including fosA7, qnrB19, and a cryptic aminoglycoside resistance gene, and virulence genes encoding T3SS-1 and T3SS-2, were detected in both hosts. Logistic regression indicated that residence in Sitaon and Zimidin was associated with ~70% lower odds of carriage (aOR = 0.3), while individuals aged 11–20 and 51–60 years had 2.8-fold higher odds. Carriage was also 60% higher during the rainy season. These findings suggest possible cross-transmission of Salmonella between humans and poultry and the circulation of resistant, potentially virulent strains in the community. Seasonal and age-related variations highlight environmental and behavioral influences on asymptomatic carriage. Integrated One Health surveillance and targeted hygiene interventions are essential to reduce Salmonella transmission and antimicrobial resistance in rural settings.

Background: Antiseptics, disinfectants, and hand hygiene products can be contaminated with bacteria and cause healthcare-associated infections, which are underreported from low- and middle-income countries. To better understand the user-related risk factors, we conducted a knowledge, awareness, and practice survey among hospital staff in sub-Saharan Africa. Methods: Self-administered questionnaire distributed among healthcare workers in three tertiary care hospitals (Burkina Faso, Benin, Democratic Republic of the Congo). Results: 617 healthcare workers (85.3% (para)medical and 14.7% auxiliary staff) participated. Less than half (45.5%) had been trained in Infection Prevention & Control (IPC), and only 15.7% were trained < 1 year ago. Near two-thirds (64.2%) preferred liquid soap for hand hygiene, versus 33.1% for alcohol-based hand rub (ABHR). Most (58.3%) expressed confidence in the locally available products. Knowledge of product categories, storage conditions and shelf-life was inadequate: eosin was considered as an antiseptic (47.5% of (para)medical staff), the shelf life and storage conditions (non-transparent container) of freshly prepared chlorine 0.5% were known by only 42.6% and 34.8% of participants, respectively. Approximately one-third of participants approved using tap water for preparation of chlorine 0.5% and liquid soap. Most participants (> 80%) disapproved recycling soft-drink bottles as liquid soap containers. Nearly two-thirds (65.0%) declared that bacteria may be resistant to and survive in ABHR, versus 51.0% and 37.4% for povidone iodine and chlorine 0.5%, respectively. Depicted risk practices (n = 4) were ignored by 30 to 40% of participants: they included touching the rim or content of stock containers with compresses or small containers, storing of cotton balls soaked in an antiseptic, and hand-touching the spout of pump dispenser. Filling containers by topping-up was considered good practice by 18.3% of participants. Half (52.1%) of participants acknowledged indefinite reuse of containers. Besides small differences, the findings were similar across the study sites and professional groups. Among IPC-trained staff, proportions recognizing all 4 risk practices were higher compared to non-trained staff (35.9% versus 23.8%, p < 0.0001). Conclusions: The present findings can guide tailored training and IPC implementation at the healthcare facility and national levels, and sensitize stakeholders’ and funders’ interest.

Antiseptics, disinfectants, and hand hygiene products can act as reservoirs of Gram-negative bacteria causing healthcare-associated infections. This problem is rarely documented in low- and middle-income countries, particularly in sub-Saharan Africa. In a cross-sectional survey, we assessed the bacterial contamination of antiseptics, disinfectants, and hand hygiene products in two university hospitals in Burkina Faso and Benin. During ward visits and staff interviews, in-use products were cultured for the presence of Gram-negative bacteria. The growth of Gram-negative bacteria was absent or rare in alcohol-based products, povidone iodine, and Dakin solution. Contamination was highest (73.9% (51/69)) for liquid soap products (versus antiseptic/disinfectants (4.5%, 7/157) (p < 0.0001)), mostly used in high-risk areas and associated with high total bacterial counts (>10,000 colony-forming units/mL). Contaminating flora (105 isolates) included Enterobacterales and the Vibrio non-cholerae/Aeromonas group (17.1%) and non-fermentative Gram-negative rods (82.8%). Multidrug resistance was present among 9/16 Enterobacterales (Klebsiella and Enterobacter spp.) and 3/12 Acinetobacter spp., including carbapenem resistance (Acinetobacter baumannii: NDM, Pseudomonas stutzeri: VIM). The risk factors for contamination included the type of product (cleaning grade and in-house prepared liquid soap), use of recycled disposable containers and soft drink bottles, absence of labeling, topping-up of containers, dilution with tap water (pharmacy and ward), and poor-quality management (procurement, stock management, expiry dates, and period after opening).

This scoping review addresses bacterial contamination of antiseptics, low-level disinfectants, and hand hygiene products in healthcare settings in high-income countries. Over 70 years, 114 articles were found: 68 outbreaks, 13 pseudo-outbreaks and 33 cross-sectional surveys. Outbreaks affected median 29 (1–151) patients, extended for 26 (1–156) weeks and had a case fatality of 0.0% (0.0–60.0%). Most (72.8%) (pseudo-)outbreaks were caused by water-based chlorhexidine (CHG), quaternary ammonium compounds (QUAT) and the combination CHG–QUAT. Contaminating bacteria were nonfermentative Gram-negative rods (87.6% (pseudo-)outbreaks), mainly Burkholderia cepacia, Pseudomonas aeruginosa and Achromobacter spp.) and Enterobacterales (29.6%, 24/81), mostly Serratia spp.). Risk factors were at the level of the bacteria (natural resistance to CHG and QUAT), containers (design and functioning, presence of cork and cotton, biofilm formation), preparation (nonsterile water, overdilution) and practices (too long expiry dates, inappropriate container reprocessing, topping up of containers and deviation from procedures). Transmission occurred through direct contact (antiseptics), contact with semicritical items (disinfectants) and were handborne (soaps). During recent decades, reports of soap contaminated with Enterobacterales emerged and nationwide outbreaks of intrinsically contaminated CHG occurred. Outstanding issues comprise intrinsic contamination, implementation of antiseptic stewardship, the role of unit doses and sterile products, transmission studies, biofilm control and understanding healthcare providers’ perceptions.

We conducted a systematic review of healthcare-associated outbreaks and cross-sectional surveys related to the contamination of antiseptics, disinfectants, and hand hygiene products in healthcare settings in low- and middle-income countries (PROSPERO CRD42021266271). Risk of bias was assessed by selected items of the ORION and MICRO checklists. From 1977 onwards, 13 outbreaks and 25 cross-sectional surveys were found: 20 from Asia and 13 from Africa. Products most associated with outbreaks were water-based chlorhexidine, chlorhexidine-quaternary ammonium compound combinations (7/13), and liquid soap products (4/13). Enterobacterales (including multidrug-resistant Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens) and non-fermentative Gram-negative rods were found in 5 and 7 outbreaks and in 34.1% and 42.6% of 164 isolates, respectively, from cross-sectional surveys. Risk factors included preparation (place, utensils, or tap water high and incorrect dilutions), containers (reused, recycled, or inadequate reprocessing), and practices (topping-up or too long use). Potential biases were microbiological methods (neutralizers) and incomplete description of products’ identity, selection, and denominators. External validity was compromised by low representativeness for remote rural settings and low-income countries in sub-Saharan Africa. Outstanding issues were water quality, biofilm control, field-adapted containers and reprocessing, in-country production, healthcare providers’ practices, and the role of bar soap. A list of “best practices” to mitigate product contamination was compiled.