Tam Thanh Tran

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.

Enterococci, commonly found in the normal intestinal flora of humans and animals, have emerged as an important human pathogen. A total of 184 isolates (88 isolates in 2015 and 96 isolates in 2016) were collected from 46 flocks. Two predominant enterococcus species were identified: Enterococcus faecalis (59%) and Enterococcus faecium (~39%). Resistance to penicillin was significantly decreased in the overall enterococci community, while it remained unchanged in the multi-class drug resistant (MDR) community. We identified the emeA and efrAB genes, which encode efflux pump systems, in 93% (26/28) of the MDR isolates with (intermediate) resistance to levofloxacin. The ermB gene was present in all MDR strains with resistance to erythromycin. The lsa gene was detected in 87% (84/97) of the MDR isolates with resistance to quinupristin/dalfopristin. About 82.2% of MDR strains in 2015 and 100% of MDR strains in 2016 carried the insertion sequence IS256, which is known to be associated with AMR genes, conferring resistance to erythromycin, gentamicin and vancomycin in enterococci. These results support the need for monitoring AMR in Gram-positive bacteria in poultry production, specifically in broiler chicken farms, to complement current AMR data, and develop a timely intervention framework.

Background/Objectives: Campylobacteriosis in human populations is an ongoing issue in both developed and developing countries. Poultry production is recognized as a reservoir for antimicrobial resistance and main source of human Campylobacter infection. Methods: In this study, sixty-five Campylobacter isolates were cultured from fecal samples collected from 17 flocks of broiler chickens in Alberta, Canada over two years (2015–2016). Susceptibility assays and PCR assays were performed to characterize resistance phenotypes and resistance genes. Conjugation assays were used to examine the mobility of AMR phenotypes. Results: Campylobacter jejuni was the predominant species recovered during both years of sampling. There were no Campylobacter coli isolates found in 2015; however, approximately 33% (8/24) of isolates collected in 2016 were Campylobacter coli. The two most frequent antimicrobial resistance patterns in C. jejuni collected in 2015 were tetracycline (39%) and azithromycin/clindamycin/erythromycin/telithromycin resistance (29%). One isolate collected in 2015 has resistance pattern ciprofloxacin/nalidixic acid/tetracycline. The tetO gene was detected in all tetracycline resistant isolates from 2015. The cmeB gene was detected in all species isolates with resistance to azithromycin/clindamycin/erythromycin/telithromycin, and from two isolates with tetracycline resistance. Alignment of the nucleotide sequences of the cmeB gene from C. jejuni isolates with different resistance patterns revealed several single nucleotide polymorphisms. A variety of multi-drug resistance patterns were observed through conjugation experiments. Conclusions: These data suggest that poultry production may serve as a potential reservoir for and source of transmission of multi-drug resistant Campylobacter jejuni and supports the need for continued surveillance.

Campylobacteriosis in human populations has been an ongoing issue in both developed and developing countries over the last 10 years. There is a grave concern whether poultry production plays an intermediate role as a reservoir and source of transmission. In this study, sixty-five broiler chicken Campylobacter isolates were isolated from fecal samples collected from 17 flocks in Alberta, Canada over two years (2015-2016). Campylobacter jejuni was the predominantly recovered Campylobacter species in both years. Approximately 33% (8/24) Campylobacter coli was identified in year 2016. The two most common antimicrobial resistance patterns in Campylobacter in year 2015 were tetracycline resistance (39%) and azithromycin/clindamycin/erythromycin/telithromycin resistance (29%). Only one isolate in 2015 displayed resistance to ciprofloxacin/nalidixic acid/tetracycline. The tetO gene was detected in all tetracycline resistant isolates in 2015. The cmeB gene was detected in all isolates with resistance to azithromycin/clindamycin/erythromycin/ telithromycin, and two isolates with resistance to tetracycline. Comparing the sequence of the cmeB genes from isolates with different resistance patterns revealed several single nucleotide polymorphisms. Transconjugants with three distinctly combined resistance patterns were obtained via in vitro conjugation. In conclusion, our study suggested that poultry can be a potential reservoir for and source of transmission of Campylobacter for human infection and requires an ongoing monitoring.

Background: Coronavirus disease 2019 (COVID-19) pandemic constituted the largest global health crisis in recent generations. It may also have disrupted the pattern of antimicrobial use (AMU) and subsequently affected the development of antimicrobial resistance (AMR) – a grave human health concern. This study aimed to give an overview of existing AMR surveillance systems and evaluate the impact of COVID-19 on AMU and AMR in the Nordics using data from these systems. Methods: Nordic AMU data (2017–2022) were extracted from national annual reports (for both humans and animals) and the European Surveillance System (TESSy) (for humans only). For humans, AMU was expressed in defined daily dose (DDD) per 1000 inhabitants per day; for animals, it was expressed in kilogram (kg). Nordic human AMR data (2017–2022) were extracted from TESSy. Multilevel linear regression and negative binomial regression models were used to fit the TESSy data. Data between 2017 and 2019 were categorised as the pre-COVID-19 time, while data between 2020 and 2022 were the per-COVID-19 time. Results: Denmark had a remarkably greater AMU in animals (about 10 times greater) than Norway, Sweden, and Finland. Iceland had the highest human AMU, while Sweden had the lowest. Drug categories, countries, and sectors were significant predictors in the model used to fit human AMU. Bacterial species and drug categories were significant predictors in the models used to fit human resistant Gram-negative and Gram-positive bacteria. The COVID-19 time was not a significant predictor in these models. Among the Nordics, Iceland had the lowest number of resistant isolates; however, high human AMU remains a great concern for Iceland. Conclusions: The study provided insight into current existing AMR surveillance systems in the Nordics. It also showed that the COVID-19 pandemic had very little impact on AMU and AMR in theses countries. This implied that strict regulations on AMU as well as well-coordinated national AMR surveillance systems in the Nordics mitigated the development of AMR crisis also during COVID-19 pandemic. However, the Nordics would still benefit further from a standardized AMR surveillance at regional level, which ultimately facilitate timely information sharing and improve our preparedness for and response to future pandemics and/or large-scale outbreaks.

Wastewater treatment plants (WWTPs) may serve as hotspots for pathogens and promote antimicrobial resistance (AMR). Plastic debris in wastewater could further contribute to AMR dissemination. The aim of this study was to investigate the impact of various microplastic types on bacterial communities and AMR gene abundance in wastewater that were obtained from two WWTPs, one in Tromsø, Norway, and the other one in Potchefstroom, South Africa. The microcosm experiments were designed as follows: Five manufactured microplastic pellet types were used for testing, and two rock aggregate types were used as controls. In addition, each material type was subjected to artificial aging treatments using either ultra-violet light or hydrogen peroxide. Each material was incubated in flasks containing inlet/outlet wastewater obtained from these two WWTPs. Nucleic acids were extracted after a one-week incubation period. The detection of the bla_FOXand bla_MOX genes was performed using quantitative PCR. Extracted DNA was sequenced using a MinION device. Non-metric multi-dimensional scaling plot on full-length 16S sequencing data at the species level showed that samples were clustered into distinct material groups, which were in line with the ANOSIM test. The Indicator Species Analysis showed a strong association between many Acinetobacter species with the plastic group than the rock group. Aging treatment using hydrogen peroxide showed some effects on microbial composition in the outlet wastewater. The abundance of bla_FOX and bla_MOX genes in the Norwegian wastewater outlet were generally lower compared to those in the inlet, though the results were contrary in South African wastewater samples. The relative abundance of AMR genes seemed to be increased on several plastic types (PET, PE, and PLA) but decreased on PVC-A. WWTP treatments in this study did not effectively reduce the abundance of AMR genes. An in-depth understanding the role of specific microplastic type on bacterial communities and AMR profiles is, therefore, needed to combat AMR threat.

Enterococci, commonly found in the normal intestinal flora of humans and animals, have emerged as an important human pathogen. A total of 184 isolates (88 isolates in 2015 and 96 isolates in 2016) were collected from 46 flocks. Two predominant enterococcus species were identified: Enterococcus faecalis (59%) and Enterococcus faecium (~39%). Resistance to penicillin was significantly decreased in the overall enterococci community, while it remained unchanged in the multi-class resistant (MCR) community. We identified emeA and efrAB genes, which encode efflux pump systems, in 93% (26/28) of the multi-class resistant (MCR) isolates with (intermediate) resistance to levofloxacin. The ermB gene was present in all MCR strains with resistance to erythromycin. The lsa gene was detected in 87% (84/97) of the MCR isolates with resistance to quinupristin/dalfopristin. About 82.2% of MCR strains in 2015 and 100% of MCR strains in 2016 carried insertion sequence IS256, which is known to be associated with AMR genes conferring resistance to erythromycin, gentamicin and vancomycin in enteroccocci. These results support the need for monitoring AMR in Gram positive bacteria in poultry production, specifically in broiler chicken farms, to complement current AMR data, and developing a timely intervention framework.