National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches

Water Research, Journal Year: 2024, Volume and Issue: 262, P. 121989 - 121989

Published: June 22, 2024

Wastewater serves as an important reservoir of antimicrobial resistance (AMR), and its surveillance can provide insights into population-level trends in AMR to inform public health policy. This study compared two common high-throughput screening approaches, namely (i) quantitative PCR (HT qPCR), targeting 73 genes, (ii) metagenomic sequencing. Weekly composite samples wastewater influent were taken from 47 treatment plants (WWTPs) across Wales, part a national programme, alongside 4 weeks daily effluent large municipal hospital. Metagenomic analysis provided more comprehensive resistome coverage, detecting 545 genes the targeted by HT qPCR. It further contextual information critical risk assessment (i.e. potential bacterial hosts). In contrast, qPCR exhibited higher sensitivity, quantifying all including those clinical relevance present at low abundance. When limited target both methods able reflect spatiotemporal dynamics complete resistome, distinguishing that hospital WWTPs. Both approaches revealed correlations between compositional shifts environmental variables like ammonium concentration, though differed their interpretation some influencing factors. Overall, metagenomics provides profiling, while permits sensitive quantification significant resistance. We highlight importance selecting appropriate methodologies aligned aims guide development effective wastewater-based monitoring programmes.

Language: Английский

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Mechanisms of Antimicrobial Resistance in Klebsiella: Advances in Detection Methods and Clinical Implications

Infection and Drug Resistance, Journal Year: 2025, Volume and Issue: Volume 18, P. 1339 - 1354

Published: March 1, 2025

Abstract: Klebsiella spp . are ubiquitous gram-negative bacteria, commonly present in natural environments and as part of the human microbiota. is involved occurrence development many diseases, effective antibiotics for it have attracted attention researchers. In recent years, its multi-drug resistance, particularly to carbapenems β-lactam antibiotics, has posed significant challenges clinical treatment. Therefore, a comprehensive understanding resistance mechanisms , along with enhancement detection methods, crucial effectively controlling spread drug-resistant strains guiding individualized This paper systematically reviews epidemiological characteristics, mechanisms, treatment strategies aiming provide new insights management this pathogen. Keywords: drug method, β-lactam,

Language: Английский

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Determinants of Campylobacter species diversity in infants and association with family members, livestock, and household environments in rural Eastern Ethiopia

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

Background Campylobacter infections pose a significant challenge in low- and middle-income countries, contributing to child mortality. is linked acute gastrointestinal illness severe long-term consequences, including environmental enteric dysfunction (EED) stunting. In 2018, our cross-sectional study Ethiopia detected 88% of stools from children aged 12–15 months, with an average 11 species per stool using meta-total RNA sequencing. Building on these findings, we conducted longitudinal (December 2020–June 2022) investigate colonization infants identify reservoirs risk factors rural eastern Ethiopia. Results After preliminary screening 15 species-specific quantitative PCR, analyzed four target 2,045 samples (first month just one year life) biannual mothers, siblings, livestock (goats, cattle, sheep, chickens). Candidatus C. infans (41%), C. jejuni (26%), upsaliensis (13%) were identified as the predominant infant gut. Colonization infans C.jejuni increased (C. infans: 0.85%, jejuni-0.98% increase/ day odds colonization) abundance (P = 0.027, 0.024) age. Enteric symptoms strongly associated (diarrhea: OR 2.02 [95%CI: 35%,100%]; fever: 1.62 14%, 83%]) 2.29 46%,100%], 2.53 56%,100%]). Based linear mixed models, found elevated cumulative loads load (especially females 1.5 10%, 67%]), consuming raw milk (OR 2.3 24%,100%]) or those exposed areas contaminated animal droppings 1.6 7%,93%]), while higher ingesting soil feces 2.2 23%,100%]). was also prevalent siblings (56%) mothers (45%), whereas common chickens (38%) small ruminants (goats 27%, sheep 21%). Conclusions highly Ethiopian infants. primarily human hosts, mainly zoonotic sources. Our findings emphasize need for targeted interventions addressing environmental, dietary, behavioral reduce transmission resource-limited settings.

Language: Английский

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Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review

Environmental Research, Journal Year: 2023, Volume and Issue: 246, P. 118052 - 118052

Published: Dec. 30, 2023

The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five encountered a rise ARB cases challenges treating infections due to the growing prevalence of pathogens. Wastewater-based surveillance (WBS) is valuable supplement clinical methods for surveillance, but there lack comprehensive understanding WBS application This review aims compile latest state-of-the-art developments monitoring compare them with practices. After reviewing 1480 papers from primary search, 54 were found relevant, 15 additional WBS-related included. Among 69 studies analyzed, 42 dedicated epidemiology, while 27 focused on wastewater monitoring. PRISMA literature revealed that focus four major objectives ARB: assessing human population, identifying evading treatment, quantifying removal rates, evaluating potential evolution during treatment process. In both contexts, most studied targets pathogens producing carbapenemase extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli Klebsiella spp. vancomycin-resistant Enterococcus (VRE) methicillin-resistant Staphylococcus aureus (MRSA) received more attention epidemiology studies, probably their detection wastewater. Clinical has mostly used culturing, antibiotic susceptibility testing, genotyping, employed PCR-based metagenomics alongside culture-based techniques. Imported resulting international travel hospitalization abroad appear frequently contributed similarities between (e.g., knowledge exchange practices, usage patterns, current landscape) could facilitate collaborative efforts developing implementing population-level screening.

Language: Английский

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Fresh produce as a reservoir of antimicrobial resistance genes: A case study of Switzerland

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 907, P. 167671 - 167671

Published: Oct. 7, 2023

Antimicrobial resistance (AMR) can be transferred to humans through food and fresh produce an ideal vector, as it is often consumed raw or minimally processed. The production environment of the agricultural practices regulations vary substantially worldwide, consequently, contamination sources AMR. In this study, 75 imported non-imported samples purchased from Swiss retailers were tested for presence antimicrobial resistant bacteria (ARB) genes (ARGs). Moreover, plasmidome 4 selected was sequenced have insight on diversity mobile resistome. total, 91 ARB isolated produce, mainly cephalosporin-resistant Enterobacterales (n = 64) carbapenem-resistant P. aeruginosa 13). All aeruginosa, well 16 Enterobacterales' isolates multidrug-resistant. No differences between found regarding number ARB. 95 % at least one ARG detected, being most frequent sul1, blaTEM, ermB. Abundance sul1 intI1 correlated strongly with total amount ARGs, suggesting they could good indicators AMR in produce. Furthermore, fecal marker yccT, indicating that gene sulI significantly higher samples, anthropogenic chain analyses coriander carrot revealed several ARGs conferring antiseptics disinfectants genetic elements. Overall, study demonstrated contributes dissemination

Language: Английский

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Biocontrol in built environments to reduce pathogen exposure and infection risk

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most these microbes are benign, antibiotic-resistant pathogens can colonize emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued microbial composition ecology in different types. These informed vitro that seek to replicate physicochemical features promote pathogenic survival transmission, ultimately facilitating development validation intervention techniques used reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces integrating bacilli into printable materials. Though this work is its infancy, early research suggests potential use biocontrol hospital- home-acquired multidrug-resistant infections. Although hold promise, there an urgent need better understand environments determine how solutions alter species interactions. This review covers our current understanding proposes strategies translate knowledge effective pathogens.

Language: Английский

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City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: March 15, 2024

Anthropogenic activities significantly contribute to the dissemination of antibiotic resistance genes (ARGs), posing a substantial threat humankind. The development methods that allow robust ARG surveillance is long-standing challenge. Here, we use city-scale monitoring ARGs by using two most promising cutting-edge technologies, digital PCR (dPCR) and metagenomics.

Language: Английский

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Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study

BMC Research Notes, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 7, 2025

The World Health Organization (WHO) has declared antimicrobial resistance (AMR) as one of the top threats to global public health. While AMR surveillance human clinical isolates is well-established in many countries, increasing threat intensified efforts detect antibiotic genes (ARGs) accurately and sensitively environmental samples, wastewater, animals, food. Using five ARGs 16S rRNA gene, we compared quantitative PCR (qPCR) metagenomic sequencing (MGS), two commonly used methods uncover wastewater resistome. We both by evaluating ARG detection through a municipal treatment chain. Our results demonstrate that qPCR was more sensitive than MGS, particularly diluted samples with low concentrations such oxidation pond water. However, MGS potentially specific less risk off-target binding concentrated raw sewage. analysis revealed multiple subtypes each gene which could not be distinguished qPCR; these varied across different sample types. findings affect conclusions can drawn when comparing types, terms inferring removal rates or origins genes. conclude appear suitable profile resistome other depending on research question type sample.

Language: Английский

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Use of Wastewater and Electrogenic Bacteria to Generate Eco-Friendly Electricity through Microbial Fuel Cells

Sustainability, Journal Year: 2023, Volume and Issue: 15(13), P. 10640 - 10640

Published: July 6, 2023

Power generation and wastewater treatment are two great challenges for sustainable development. Microbial fuel cells (MFCs) a alternative that can generate bioelectricity in the bioremediation process of wastewater. For this reason, objective research was to through double-chamber microbial-combustion cell systems from Covicorti Wastewater Treatment Plant (PTARC) anodic chamber electrogenic bacteria such as Stenotrophomonas maltophilia, Acinetobacter bereziniae, Achromobacteria xylosoxidans cathode chamber, respectively. Measurements voltage, current, power density, current optical density biochemical oxygen demand (BOD) were made. In addition, metagenomic analysis sample performed. It shown MFC with A. generated highest voltage peak (1.01 ± 0.06 V) on day 24, while S. maltophilia value (0.71 0.02 mA). The pH levels slightly alkaline, maximum conductivity presented by cerevisiae, 81 2 mS/cm 24. On other hand, 195,493 4717 mW/m2 4987 A/cm2, respectively, obtained xylosoxidans. Finally, identified predominant phyla Proteobacteria present samples capable generating electrical energy Bacillota, Pseudomonadota, Bacteroidota, Actinomyketone, Campylobacterota.

Language: Английский

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Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 4, 2023

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few diagnostics are available the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing 593 samples from febrile Nigerian patients collected three settings: i) population-level individuals presenting with symptoms consistent Lassa Fever (LF); ii) real-time investigations outbreaks suspected etiologies; iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including second third documented cases blood-associated dicistrovirus, a highly divergent, unclassified dicistrovirus that name 2. show pegivirus C common co-infection LF associated lower viral loads favorable outcomes. help uncover causes as yellow fever virus, monkeypox noninfectious cause, latter ultimately determined to be pesticide poisoning. demonstrate local, Nigerian-driven metagenomics response complex public health scenarios generates accurate, differential diagnoses, yielding insights inform policy.

Language: Английский

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