1
|
George PBL, Hillary LS, Leclerc S, Cooledge EC, Lemieux J, Duchaine C, Jones DL. Needles in haystacks: monitoring the potential escape of bioaerosolised antibacterial resistance genes from wastewater treatment plants with air and phyllosphere sampling. Can J Microbiol 2024. [PMID: 38608289 DOI: 10.1139/cjm-2023-0226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Wastewater treatment plants are well-known point sources of emissions of antibacterial resistance genes (ARGs) into the environment. Although most work to date has focused on ARG dispersal via effluent, aerial dispersal in bioaerosols is a poorly understood, but likely important vector for ARG dispersal. Recent evidence suggests that ARG profiles of the conifer needle phyllosphere could be used to measure bioaerosol dispersal from anthropogenic sources. Here, we assessed airborne dispersal of ARGs from wastewater treatment plants in Wales, UK and Quebec, Canada, using conifer needles as passive bioaerosol monitors. ARG profiles of wastewater were compared to those of conifer phyllosphere using high-throughput qPCR. ARG richness was significantly lower in conifer phyllosphere samples than wastewater samples, though no differences were observed across the dispersal gradients. Mean copy number of ARGs followed a similar trend. ARG profiles showed limited, but consistent patterns with increasing distance from wastewater treatment plants, but these did not align with those of wastewater samples. For example, proportional abundance of aminoglycosides decreased over the dispersal gradient in Wales, whereas mobile genetic elements showed the inverse relationship. In summary, while distinct ARG profiles exist along dispersal gradients, links to those of wastewater were not apparent.
Collapse
Affiliation(s)
- Paul B L George
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Quebec City, QC G1V 4G5, Canada
| | - Luke S Hillary
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Samantha Leclerc
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Quebec City, QC G1V 4G5, Canada
| | - Emily C Cooledge
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Joanie Lemieux
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Quebec City, QC G1V 4G5, Canada
| | - Caroline Duchaine
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Quebec City, QC G1V 4G5, Canada
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| |
Collapse
|
2
|
Edwin NR, Fitzpatrick AH, Brennan F, Abram F, O'Sullivan O. An in-depth evaluation of metagenomic classifiers for soil microbiomes. ENVIRONMENTAL MICROBIOME 2024; 19:19. [PMID: 38549112 PMCID: PMC10979606 DOI: 10.1186/s40793-024-00561-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. RESULTS In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. CONCLUSION This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.
Collapse
Affiliation(s)
- Niranjana Rose Edwin
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Functional Environmental Microbiology, School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | | | - Fiona Brennan
- Teagasc, Soils, Environment and Landuse Department, Johnstown Castle, Wexford, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Orla O'Sullivan
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
- VistaMilk SFI Research Centre, Cork, Ireland.
| |
Collapse
|
3
|
Abdulkadir N, Saraiva JP, Zhang J, Stolte S, Gillor O, Harms H, Rocha U. Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater. Microbiol Spectr 2024; 12:e0291823. [PMID: 38289113 PMCID: PMC10913551 DOI: 10.1128/spectrum.02918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/25/2023] [Indexed: 03/06/2024] Open
Abstract
Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species ( average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities. IMPORTANCE Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.
Collapse
Affiliation(s)
- Nafi’u Abdulkadir
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
- Department of Biochemistry, Faculty of Natural Science, University of Leipzig, Leipzig, Germany
| | - Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
| | - Junya Zhang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Stefan Stolte
- Institute of Water Chemistry, Technical University of Dresden, Dresden, Germany
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, J. Blaustein Institutes for Desert Research, Ben Gurion University, Midreshet Ben Gurion, Israel
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
- Department of Biochemistry, Faculty of Natural Science, University of Leipzig, Leipzig, Germany
| | - Ulisses Rocha
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
| |
Collapse
|
4
|
Kos D, Schreiner B, Thiessen S, McAllister T, Jelinski M, Ruzzini A. Insight into antimicrobial resistance at a new beef cattle feedlot in western Canada. mSphere 2023; 8:e0031723. [PMID: 37855607 PMCID: PMC10732036 DOI: 10.1128/msphere.00317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/07/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE A better understanding of how environmental reservoirs of ARGs in the feedlot relate to those found in animal pathogens will help inform and improve disease management, treatment strategies, and outcomes. Monitoring individual cattle or small groups is invasive, logistically challenging, expensive, and unlikely to gain adoption by the beef cattle industry. Wastewater surveillance has become standard in public health studies and has inspired similar work to better our understanding of AMR in feedlots. We derived our insights from sampling water bowls in a newly established feedlot: a unique opportunity to observe AMR prior to animal arrival and to monitor its development over 2 months. Importantly, the bacterial community of a single water bowl can be influenced by direct contact with hundreds of animals. Our results suggest that water bowl microbiomes are economical and pragmatic sentinels for monitoring relevant AMR mechanisms.
Collapse
Affiliation(s)
- Daniel Kos
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Brittany Schreiner
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Tim McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Murray Jelinski
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Antonio Ruzzini
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
5
|
Abstract
Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.
Collapse
Affiliation(s)
- María Mercedes Zambrano
- Corpogen Research Center, Bogotá, Colombia;
- Dirección de Investigaciones y Transferencia de Conocimiento, Universidad Central, Bogotá, Colombia
| |
Collapse
|
6
|
Williams RBH. Adapt or perish. eLife 2022; 11:83617. [PMID: 36346384 PMCID: PMC9642989 DOI: 10.7554/elife.83617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Microbial communities in wastewater treatment plants provide insights into the development and mechanisms of antimicrobial resistance.
Collapse
Affiliation(s)
- Rohan BH Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore
| |
Collapse
|