A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland

Gomez-Alvarez, Vicente; Siponen, Sallamaari; Kauppinen, Ari; Hokajärvi, Anna-Maria; Tiwari, Ananda; Sarekoski, Anniina; Miettinen, Ilkka T.; Torvinen, Eila; Pitkänen, Tarja

doi:10.1016/j.watres.2022.119495

Cited by 12 publications

(9 citation statements)

References 84 publications

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“…Furthermore, early studies of these DWDSs found a higher diversity of eukaryotic and archaea communities in non-disinfected DWDSs (A-B) compared to disinfected systems (C-E) ( Inkinen et al, 2019 and 2021 ). In contrast, the abundance of functional genes based on metagenomic analysis was higher in disinfected DWDSs samples than in non-disinfected samples ( Gomez-Alvarez et al, 2023 ).…”

Section: Resultsmentioning

confidence: 95%

Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland

Siponen,

Jayaprakash,

Hokajärvi

et al. 2024

Water Research

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Section: Resultsmentioning

confidence: 95%

Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland

Siponen,

Jayaprakash,

Hokajärvi

et al. 2024

Water Research

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“…The metagenomic sequencing showed that the abundance of sulphonamide and fluoroquinolone resistance genes decreased compared with that in measurements by [ 1 , 4 , 27 ]. Compared with [ 2 , 3 , 28 ]’s measurements, the abundance of glycopeptide resistance genes and AdeF and qacG multidrug resistance genes was high, indicating that the Chinese government’s policy of reducing and replacing antibiotics in animal husbandry has played a role in altering the abundances of antibiotic resistance genes.…”

Section: Discussionmentioning

confidence: 99%

“…Metagenomics is emerging as a valuable alternative to DNA sequencing for studying microbial diversity in veterinary clinical and water samples [ 4 , 5 ]. Traditional methods, such as culturing bacterial pathogens or sequencing isolates, can be logistically challenging and impractical in certain situations.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China

Rui,

Qiu

2024

Microorganisms

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This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were vanT_gene, vanY_gene, adeF, qacG, Mtub_rpsL_STR, vanY_gene_, vanW_gene, Mtub_murA_FOF, vanY_gene, vanH_gene, FosG, rsmA, qacJ, RbpA, vanW_gene, aadA6, vanY_gene, sul4, sul1, and InuF. The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are Streptococcus agalactiae and Streptococcus anginosus; Enterococcus faecalis; Enterococcus faecium; Actinomyces viscosus and Bacillus cereus. Enterococcus faecium; Clostridium tetani; Streptococcus agalactiae and Streptococcus anginosus; Streptococcus agalactiae and Streptococcus anginosus; Acinetobacter baumannii, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Corynebacterium jeikeium, Corynebacterium urealyticum, Mycobacterium kansasii, Mycobacterium tuberculosis, Schaalia odontolytica, and Trueperella pyogenes; Mycobacterium avium and Mycobacterium tuberculosis; Aeromonas caviae, Enterobacter hormaechei, Vibrio cholerae, Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus; Pseudomonas aeruginosa and Pseudomonas fluorescens; Staphylococcus aureus and Staphylococcus equorum; M. avium, Achromobacter xylosoxidans, and Acinetobacter baumannii; Sphingobium yanoikuyae, Acinetobacter indicus, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered.

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“…The low representativeness of the DWGC for non-disinfected systems suggests that additional effort is required to populate the DWGC with genomes from these systems. It is important to note that non-disinfected systems are significantly more diverse as compared to disinfected systems 3,4,11,13,14 and thus ensuring a DWGC representative for non-disinfected systems will be challenging.…”

Section: An Uncultured Genus Of High Prevalence Was Observed In Drink...mentioning

confidence: 99%

New drinking water genome catalog identifies a globally distributed bacterial genus adapted to disinfected drinking water systems

Sudarshan,

Dai,

Gabrielli

et al. 2024

Preprint

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Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from non-disinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomevar) within this genus is detected in >82% of drinking water systems included in this study. We propose a provisional name for this uncultured bacterium as Raskinella chlorumaquaticus and describe the genus as Raskinella (pending SeqCode approval). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, able to metabolize halogenated compounds, proliferates in a biofilm-based environment and shows clear indications of disinfection-mediated selection.

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A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland

Cited by 12 publications

References 84 publications

Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland

Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland

Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China

New drinking water genome catalog identifies a globally distributed bacterial genus adapted to disinfected drinking water systems

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