Antibiotic Resistance Genes from Mat and Planktonic Microbiomes of Antarctic Lake Fryxell and Lake Bonney, and a Mat-forming Culture of Rhodoferax antarcticus

The Antarctic Taylor Valley Lakes Fryxell and Bonney harbor oligotrophic microbial communities that are separated geographically from other aquatic systems. Their microbiomes include planktonic as well as lift-off mat communities that float to the underside of the perennial ice cover and eventually emerge at the surface. We investigated the antibiotic resistance genes (ARGs) from metagenomes of lift-off mats emerging from ice, from filtered water samples of Lake Fryxell, and from filtered water samples of Lake Bonney. ARG sequence markers were designed by ShortBRED-Identify using the Comprehensive Antibiotic Resistance Database (CARD). The overall proportion of ARG hits in the metagenomes was found to be similar to that found in temperate-zone rural water bodies with moderate human inputs (0.0002-0.0007%). The specific ARGs found showed distinct distributions for the two lakes, and for mat versus planktonic sources. An enrichment culture of Rhodoferax antarcticus from a Lake Fryxell mat sample showed a mat-forming phenotype not previously reported for this species. Its genome showed no ARGs associated with Betaproteobacteria, but had ARGs consistent with a Pseudomonas minor component. The Antarctic lake mats and water showed specific ARGs distinctive to the mat and water sources, but overall ARG levels were similar to those of temperate water bodies.

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Distribution of Antibiotic Resistance Genes in Three Different Natural Water Bodies-A Lake, River and Sea

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17020552 ◽

2020 ◽

Vol 17 (2) ◽

pp. 552 ◽

Cited By ~ 4

Author(s):

Sicong Su ◽

Chenyu Li ◽

Jiping Yang ◽

Qunying Xu ◽

Zhigang Qiu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Natural Water ◽

Poyang Lake ◽

Antibiotic Resistance Genes ◽

Water Bodies ◽

Human Beings ◽

Absolute Abundance ◽

Haihe River ◽

Natural Water Bodies

Currently, due to abuse in the use of human antibiotics and the weak regulatory control that the authorities have over sewage discharge and manure management, antibiotic resistance genes (ARGs) have become a new type of environmental pollutant. Three different natural water bodies (Poyang Lake, Haihe River and Qingdao No.1 Bathing Beach seawater) were sampled during the same periods to conduct a longitudinal comparison of distribution. The distribution and expression of 11 ARGs in 20 species were studied, and the correlations between the expression and the distribution of time and space of the ARGs in different water bodies were also analyzed. With the exception of ermA, blaNDM-1 and vanA, which were not detected in seawater, the other ARGs could be detected in all three water bodies. Tetracycline resistance genes (tetC, tetM and tetQ) in the seawater and Haihe River had even reached 100%, and sulfa ARGs (sul1 and sul2) in the seawater and Poyang Lake, as well as sul2 and sul3 in the Haihe River, had also reached 100%. The ARG pollution in Haihe River was much more serious, since 14 and 17 of 20 ARG species were significantly higher compared with seawater and Poyang Lake, respectively. Some ARGs also had a high absolute abundance. The absolute abundance of macrolide resistance genes (ermB) in seawater was as high as 8.61 × 107 copies/L, and the anti-tuberculosis resistant genes (rpoB and katG) in the Haihe River Basin were highly abundant at 1.32 × 106 copies/L and 1.06 × 107 copies/L, respectively. This indicates that ARGs have gradually become more diverse and extensive in natural water bodies. The results of a redundancy analysis (RDA) of the three water bodies showed that although each water body is affected by different factors in space and time, overall, the presence of AGRs is closely related to the production and life of human beings and the migration of animals.

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Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems

Microorganisms ◽

10.3390/microorganisms8091293 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1293

Author(s):

Pedro Blanco-Picazo ◽

Gabriel Roscales ◽

Daniel Toribio-Avedillo ◽

Clara Gómez-Gómez ◽

Conxita Avila ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Communities ◽

Anthropogenic Activities ◽

Antibiotic Resistance Genes ◽

Mediterranean Area ◽

Mediterranean Coast ◽

Anthropogenic Pressure ◽

The Mediterranean ◽

The Antarctic

Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.

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Taxonomic and Functional Distribution of Bacterial Communities in Domestic and Hospital Wastewater System: Implications for Public and Environmental Health

Antibiotics ◽

10.3390/antibiotics10091059 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1059

Author(s):

Ramganesh Selvarajan ◽

Timothy Sibanda ◽

Jeevan Pandian ◽

Kevin Mearns

Keyword(s):

Antibiotic Resistance ◽

Environmental Health ◽

Resistance Genes ◽

Bacterial Communities ◽

Antibiotic Resistance Genes ◽

Domestic Wastewater ◽

Water Bodies ◽

Resistant Bacteria ◽

Hospital Wastewater ◽

Sequence Coverage

The discharge of untreated hospital and domestic wastewater into receiving water bodies is still a prevalent practice in developing countries. Unfortunately, because of an ever-increasing population of people who are perennially under medication, these wastewaters contain residues of antibiotics and other antimicrobials as well as microbial shedding, the direct and indirect effects of which include the dissemination of antibiotic resistance genes and an increase in the evolution of antibiotic-resistant bacteria that pose a threat to public and environmental health. This study assessed the taxonomic and functional profiles of bacterial communities, as well as the antibiotic concentrations in untreated domestic wastewater (DWW) and hospital wastewater (HWW), using high-throughput sequencing analysis and solid-phase extraction coupled to Ultra-high-performance liquid chromatography Mass Spectrometry (UHPLC–MS/MS) analysis, respectively. The physicochemical qualities of both wastewater systems were also determined. The mean concentration of antibiotics and the concentrations of Cl−, F− and PO43 were higher in HWW samples than in DWW samples. The phylum Firmicutes was dominant in DWW with a sequence coverage of 59.61% while Proteobacteria was dominant in HWW samples with a sequence coverage of 86.32%. At genus level, the genus Exiguobacterium (20.65%) and Roseomonas (67.41%) were predominant in DWW and HWW samples, respectively. Several pathogenic or opportunistic bacterial genera were detected in HWW (Enterococcus, Pseudomonas and Vibrio) and DWW (Clostridium, Klebsiella, Corynebacterium, Bordetella, Staphylocccus and Rhodococcus) samples. Functional prediction analysis indicated the presence of beta-lactam resistance, cationic antimicrobial peptide (CAMP) resistance and vancomycin resistance genes in HWW samples. The presence of these antibiotic resistance genes and cassettes were positively correlated with the presence of pathogens. These findings show the risk posed to public and environmental health by the discharge of untreated domestic and hospital wastewaters into environmental water bodies.

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Detection and drug resistance profile of Escherichia coli from subclinical mastitis cows and water supply in dairy farms in Saraburi Province, Thailand

PeerJ ◽

10.7717/peerj.3431 ◽

2017 ◽

Vol 5 ◽

pp. e3431 ◽

Cited By ~ 10

Author(s):

Woranich Hinthong ◽

Natapol Pumipuntu ◽

Sirijan Santajit ◽

Suphang Kulpeanprasit ◽

Shutipen Buranasinsup ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Water Samples ◽

Antibiotic Resistance Genes ◽

Dairy Farms ◽

Subclinical Mastitis ◽

Persistent Problem ◽

E Coli ◽

Milk Samples

Subclinical mastitis is a persistent problem in dairy farms worldwide. Environmental Escherichia coli is the bacterium predominantly responsible for this condition. In Thailand, subclinical mastitis in dairy cows is usually treated with various antibiotics, which could lead to antibiotic resistance in bacteria. E. coli is also a reservoir of many antibiotic resistance genes, which can be conveyed to other bacteria. In this study, the presence of E. coli in milk and water samples was reported, among which enteropathogenic E. coli was predominant, followed by enteroaggregative E. coli and enterohemorrhagic E. coli, which was found only in milk samples. Twenty-one patterns of antibiotic resistance were identified in this study. Ampicillin- and carbenicillin-resistant E. coli was the most common among the bacterial isolates from water samples. Meanwhile, resistance to ampicillin, carbenicillin, and sulfamethoxazole-trimethoprim was the pattern found most commonly in the E. coli from milk samples. Notably, only the E. coli from water samples possessed ESBL phenotype and carried antibiotic resistance genes, blaTEM and blaCMY-2. This indicates that pathogenic E. coli in dairy farms is also exposed to antibiotics and could potentially transfer these genes to other pathogenic bacteria under certain conditions.

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Impact of liquid hog manure applications on antibiotic resistance genes concentration in soil and drainage water in field crops

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0343 ◽

2020 ◽

Vol 66 (10) ◽

pp. 549-561

Author(s):

Élodie Larouche ◽

Mylène Généreux ◽

Marie-Ève Tremblay ◽

Mohamed Rhouma ◽

Marc-Olivier Gasser ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Water Samples ◽

Antibiotic Resistance Genes ◽

Drainage Water ◽

Manure Application ◽

Tillage Practices ◽

Hog Manure ◽

The Impact ◽

Soil And Water

Agricultural practices such as manure applications could contribute to the spread of antibiotic resistance genes (ARGs) within the environment. Our objective was to assess the impact of certain fertilization methods (mineral or manure) and tillage practices (reduced or conventional) on the presence of ARGs and bacteria in soil and drainage water under wheat and grain corn crops. Targeted ARGs tet(T), sul1, and blaCTX-M-1 in liquid hog manure, soil, and water samples were quantified by qPCR. Conventional PCR was used to detect mcr-1 and mcr-2. ARGs in control plots were detected despite the absence of manure, representing an environmental reservoir of resistant microorganisms. The manure application rate higher than 39 m3/ha increased tet(T) and sul1 gene concentrations in soil for more than 180 days. Tillage practices had no impact on ARG concentrations in soil and water samples. The blaCTX-M-1 gene was only detected in seven water samples in 2016, but no link was established with the treatments. The mcr-1 and mcr-2 genes were not detected in all tested samples. This study demonstrated that tet(T) and sul1 gene concentrations increased in soil after liquid hog manure application as well as in drainage water in the next weeks.

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Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance

10.1101/2021.02.04.429629 ◽

2021 ◽

Author(s):

Ross Stuart McInnes ◽

Md. Hassan uz-Zaman ◽

Imam Taskin Alam ◽

Siu Fung Stanley Ho ◽

Robert A. Moran ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Surface Waters ◽

Water Samples ◽

Antibiotic Resistance Genes ◽

Antibiotic Use ◽

Urban Surface ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant

AbstractIn many low- and middle-income countries antibiotic resistant bacteria spread in the environment due to inadequate treatment of wastewater and the poorly regulated use of antibiotics in agri- and aquaculture. Here we characterised the abundance and diversity of antibiotic-resistant bacteria and antibiotic resistance genes in surface waters and sediments in Bangladesh through quantitative culture of Extended-Spectrum Beta-Lactamase (ESBL)-producing coliforms and shotgun metagenomics. Samples were collected from highly urbanised settings (n = 7), from rural ponds with a history of aquaculture-related antibiotic use (n = 11) and from rural ponds with no history of antibiotic use (n = 6). ESBL-producing coliforms were found to be more prevalent in urban samples than in rural samples. Shotgun sequencing showed that sediment samples were dominated by the phylum Proteobacteria (on average 73.8% of assigned reads), while in the water samples Cyanobacteria (on average 60.9% of assigned reads) were the predominant phylum. Antibiotic resistance genes were detected in all samples, but their abundance varied 1,525-fold between sites, with the highest levels of antibiotic resistance genes being present in urban surface water samples. We identified an IncQ1 sulphonamide resistance plasmid ancestral to the widely studied RSF1010 in one of the urban water samples. The abundance of antibiotic resistance genes was significantly correlated (R2 = 0.73; P = 8.9 × 10−15) with the abundance of bacteria originating from the human gut, which suggests that the release of untreated sewage is a driver for the spread of environmental antibiotic resistance genes in Bangladesh, particularly in highly urbanised settings.ImportanceLow- and middle-income countries (LMICs) have higher burdens of multidrug-resistant infections than high-income countries and there is thus an urgent need to elucidate the drivers of the spread of antibiotic-resistant bacteria in LMICs. Here we study the diversity and abundance of antibiotic resistance genes in surface water and sediments from rural and urban settings in Bangladesh. We found that urban surface waters are particularly rich in antibiotic resistance genes, with a higher number of them associated with plasmids indicating that they are more likely to spread horizontally. The abundance of antibiotic resistance genes was strongly correlated with the abundance of bacteria that originate from the human gut, suggesting that uncontrolled release of human waste is a major driver for the spread of antibiotic resistance in the urban environment. Improvements in sanitation in LMICs may thus be a key intervention to reduce the dissemination of antibiotic resistant bacteria.

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Antibiotic resistance genes in treated wastewater and in the receiving water bodies: A pan-European survey of urban settings

Water Research ◽

10.1016/j.watres.2019.06.039 ◽

2019 ◽

Vol 162 ◽

pp. 320-330 ◽

Cited By ~ 40

Author(s):

Damiano Cacace ◽

Despo Fatta-Kassinos ◽

Celia M. Manaia ◽

Eddie Cytryn ◽

Norbert Kreuzinger ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Water Bodies ◽

Treated Wastewater ◽

Urban Settings ◽

European Survey ◽

Receiving Water

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Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada

Applied and Environmental Microbiology ◽

10.1128/aem.00798-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4767-4775 ◽

Cited By ~ 52

Author(s):

Dinesh M. Fernando ◽

Hein Min Tun ◽

Jenna Poole ◽

Rakesh Patidar ◽

Ru Li ◽

...

Keyword(s):

Drinking Water ◽

Antibiotic Resistance ◽

First Nations ◽

Resistance Genes ◽

Water Samples ◽

Microbiological Quality ◽

Antibiotic Resistance Genes ◽

Coliform Bacteria ◽

Nations Community ◽

Drinking Water Samples

ABSTRACTAccess to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely,ampC,tet(A),mecA, β-lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, includingEscherichia coli, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk.IMPORTANCEIn this study, we highlight the poor microbiological quality of drinking water in a First Nations community in Canada. We examined the coliform load as well as the presence of antibiotic resistance genes in these samples. This study examined the presence of antibiotic-resistant genes in drinking water samples from a First Nations Community in Canada. We believe that our findings are of considerable significance, since the issue of poor water quality in First Nations communities in Canada is often ignored, and our findings will help shed some light on this important issue.

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Occurrence of antibiotic resistance genes in reclaimed water and river water in the Werribee Basin, Australia

Journal of Water and Health ◽

10.2166/wh.2010.102 ◽

2010 ◽

Vol 8 (3) ◽

pp. 521-531 ◽

Cited By ~ 20

Author(s):

Fiona Barker-Reid ◽

Ellen M. Fox ◽

Robert Faggian

Keyword(s):

Antibiotic Resistance ◽

River Water ◽

River Basin ◽

Resistance Genes ◽

Water Samples ◽

Reclaimed Water ◽

Antibiotic Resistance Genes ◽

Water Source ◽

Poor Quality ◽

Quality Parameters

The purpose of this study was to investigate the occurrence of antibiotic resistance genes (ARGs) in water used for irrigation in the Werribee River Basin, Australia, including river water and reclaimed effluent water (reclaimed water). Samples of reclaimed water, collected over a one-year period, were screened for the occurrence of ARGs using PCR detection assays. The presence of ARGs in the reclaimed water samples were contrasted with that of water samples taken from the Werribee River Basin, collected over the same time period, from five points selected for varying levels of urban and agricultural impact. Of the 54 river water samples collected, 2 (4%), 2 (4%), 0 and 0 were positive for methicillin, sulfonamide, gentamicin and vancomycin-resistant genes, respectively, while 6 of 11 reclaimed water samples were positive for methicillin (9%) and sulfonamide (45%). The presence/absence of ARGs did not appear to correlate with other measured water quality parameters. The low detection of ARGs in river water indicates that, regardless of its poor quality, the river has not yet been severely contaminated with ARGs. The greater prevalence of ARGs in reclaimed water indicates that this important agricultural water source will need to be monitored into the future.

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