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1. Cast iron drinking water pipe biofilms support diverse microbial communities containing antibiotic resistance genes, metal resistance genes, and class 1 integrons

   https://doi.org/10.1039/D0EW01059F  

   Kimbell, Lee K. ; LaMartina, Emily Lou ; Kappell, Anthony D. ; Huo, Jingwan ; Wang, Yin ; Newton, Ryan J. ; McNamara, Patrick J. ( March 2021 , Environmental Science: Water Research & Technology)

   null (Ed.)

   Antimicrobial resistance is a well-documented public health concern. The role that drinking water distribution pipes have as sources of antibiotic resistance genes (ARGs) is not well known. Metals are a known stressor for antibiotic resistance development, implying that aging metal-pipe infrastructure could be a source of ARGs. The objective of this study was to determine if ARGs, metal resistance genes (MRGs), and intI 1 were pervasive across various pipe biofilm sample types (biomass surfaces, pipe surfaces, corrosion tubercles, and under corrosion tubercles) and if the resistance genes associated with particular microbial taxa. Eight sample types in triplicate ( n = 24) were taken from inside a >100 year-old, six ft. section of a full-scale chloraminated cast iron drinking water main. Droplet digital PCR (ddPCR) was employed as a novel approach to quantify ARGs in pipes from full-scale drinking water distribution systems (DWDS) because it yielded higher detection frequencies than quantitative PCR (qPCR). Illumina sequencing was employed to characterize the microbial community based on 16S rRNA genes. ARGs and MRGs were detected in all 24 pipe samples. Every sample contained targeted genes. Interestingly, the mean absolute abundances of ARGs and MRGs only varied by approximately one log value across sample types, but the mean relative abundances (copy numbers normalized to 16S rRNA genes) varied by over two log values. The ARG and MRGs concentrations were not significantly different between sample types, despite significant changes in dominant microbial taxa. The most abundant genera observed in the biofilm communities were Mycobacterium (0.2–70%), and β-lactam resistance genes bla TEM , bla SHV , and the integrase gene of class 1 integrons ( intI 1) were positively correlated with Mycobacterium . The detection of ARGs, MRGs, and class 1 integrons across all sample types within the pipe indicates that pipes themselves can serve as sources for ARGs in DWDS. Consequently, future work should investigate the role of pipe materials as well as corrosion inhibitors to determine how engineering decisions can mitigate ARGs in drinking water that stem from pipe materials. 

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2. Co-occurrence of antimicrobials and metals as potential drivers of antimicrobial resistance in swine farms

   https://doi.org/10.3389/fenvs.2022.1018739  

   Congilosi, Jena L. ; Wallace, Joshua S. ; Neher, Timothy P. ; Howe, Adina ; Soupir, Michelle L. ; Aga, Diana S. ( December 2022 , Frontiers in Environmental Science)

   The application of animal manures to cropland is an important nutrient recycling strategy in many parts of the world. Commonly, aggregated manure wastes contain chemical stressors including veterinary antimicrobials, heavy metals, and antimicrobial resistance genes (ARGs) that can stimulate the development and proliferation of antimicrobial resistance (AMR). While the presence of antimicrobials in manure is well-documented, the co-occurrence of other potentially impactful chemical stressors in swine manure remains underreported. This study quantifies and analyzes correlations between antimicrobials, metals, and certain ARGs present in manure samples from swine farms in Iowa, United States. Relationships between chemical stressors and different stages of swine production or feed composition are also investigated. Results revealed substantial levels of tetracyclines [up to 1,260 µg g −1 dry weight (d.w.) of manure for oxytetracycline] detected in all samples. Tiamulin, two ionophores (monensin and lasalocid), and one macrolide (tilmicosin) were detected at maximum class concentrations of 9.4, 0.547, and 0.472 µg g −1 d.w., respectively. The median relative abundances of ermB and tetM were 0.13 and 0.17 copies g −1 wet weight (w.w.) manure (normalized to 16S gene), respectively. Additionally, high levels of copper (Cu), iron (Fe), and zinc (Zn) were detected in all samples, with maximum concentrations of 887, 1,900, and 2,100 µg g −1 d.w., respectively. Notably, uranium (U) was detected in 11 samples, at concentrations up to 0.77 µg g −1 . A global analysis of AMR-stressor relationships using Spearman’s rank correlation indicates Cu, and Ba are the most positively and significantly correlated with cytotoxic anhydrotetracycline (ATC) and/or anhydrochlortetracycline (ACTC) concentrations in all tested facilities (Cu-ATC: ρ = 0.67, p = 0.0093; Cu-ACTC: ρ = 0.75, p = 0.0022; Ba-ATC: ρ = 0.84, p = 0.0002). Interestingly, ermB and tetM genes were strongly, positively correlated to each other ( ρ = 0.92, p < 0.0001), suggesting possible co-selection, despite the absence of correlation between ARGs and tetracycline concentrations. This study demonstrates the complexity of interactions between antimicrobials, metals, and ARGs in multiple manure storage pits prior to cropland application. 

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3. Arctic plasmidome analysis reveals distinct relationships among associated antimicrobial resistance genes and virulence genes along anthropogenic gradients

   https://doi.org/10.1111/gcb.17293  

   Makowska‐Zawierucha, Nicoletta ; Trzebny, Artur ; Zawierucha, Krzysztof ; Manthapuri, Vineeth ; Bradley, James A ; Pruden, Amy ( May 2024 , Global Change Biology)

   Polar regions are relatively isolated from human activity and thus could offer insight into anthropogenic and ecological drivers of the spread of antibiotic resistance. Plasmids are of particular interest in this context given the central role that they are thought to play in the dissemination of antibiotic resistance genes (ARGs). However, plasmidomes are challenging to profile in environmental samples. The objective of this study was to compare various aspects of the plasmidome associated with glacial ice and adjacent aquatic environments across the high Arctic archipelago of Svalbard, representing a gradient of anthropogenic inputs and specific treated and untreated wastewater outflows to the sea. We accessed plasmidomes by applying enrichment cultures, plasmid isolation and shotgun Illumina sequencing of environmental samples. We examined the abundance and diversity of ARGs and other stress‐response genes that might be co/cross‐selected or co‐transported in these environments, including biocide resistance genes (BRGs), metal resistance genes (MRGs), virulence genes (VGs) and integrons. We found striking differences between glacial ice and aquatic environments in terms of the ARGs carried by plasmids. We found a strong correlation between MRGs and ARGs in plasmids in the wastewaters and fjords. Alternatively, in glacial ice, VGs and BRGs genes were dominant, suggesting that glacial ice may be a repository of pathogenic strains. Moreover, ARGs were not found within the cassettes of integrons carried by the plasmids, which is suggestive of unique adaptive features of the microbial communities to their extreme environment. This study provides insight into the role of plasmids in facilitating bacterial adaptation to Arctic ecosystems as well as in shaping corresponding resistomes. Increasing human activity, warming of Arctic regions and associated increases in the meltwater run‐off from glaciers could contribute to the release and spread of plasmid‐related genes from Svalbard to the broader pool of ARGs in the Arctic Ocean.

    

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4. Critical review of antibiotic resistance genes in the atmosphere

   https://doi.org/10.1039/d2em00091a  

   Kormos, David ; Lin, Kaisen ; Pruden, Amy ; Marr, Linsey C. ( June 2022 , Environmental Science: Processes & Impacts)

   We conducted a critical review to establish what is known about the sources, characteristics, and dissemination of ARGs in the atmosphere. We identified 52 papers that reported direct measurements of bacterial ARGs in air samples and met other inclusion criteria. The settings of the studies fell into the following categories: urban, rural, hospital, industrial, wastewater treatment plants (WWTPs), composting and landfill sites, and indoor environments. Certain genes were commonly studied and generally abundant: sul1 , intI1 , β-lactam ARGs, and tetracycline ARGs. Abundances of total ARGs varied by season and setting, with air in urban areas having higher ARG abundance than rural areas during the summer and vice versa during the winter. There was greater consistency in the types and abundances of ARGs throughout the seasons in urban areas. Human activity within indoor environments was also linked to increased ARG content (abundance, diversity, and concentration) in the air. Several studies found that human exposure to ARGs through inhalation was comparable to exposure through drinking water or ingesting soil. Detection of ARGs in air is a developing field, and differences in sampling and analysis methods reflect the many possible approaches to studying ARGs in air and make direct comparisons between studies difficult. Methodologies need to be standardized to facilitate identification of the dominant ARGs in the air, determine their major sources, and quantify the role of atmospheric transport in dissemination of ARGs in the environment. With such knowledge we can develop better policies and guidelines to limit the spread of antimicrobial resistance. 

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5. Antibiotic resistance genes and taxa analysis from mat and planktonic microbiomes of Antarctic perennial ice-covered Lake Fryxell and Lake Bonney

   https://doi.org/10.1017/S0954102022000360  

   Tallada, Sheetal ; Hall, Grant ; Barich, Daniel ; Morgan-Kiss, Rachael M. ; Slonczewski, Joan L. ( December 2022 , Antarctic Science)

   Abstract The perennial ice-covered lakes of the Antarctic McMurdo Dry Valleys harbour oligotrophic microbial communities that are separated geographically from other aquatic systems. Their microbiomes include planktonic microbes as well as lift-off mat communities that emerge from the ice. We used the ShortBRED protein family profiler to quantify the antibiotic resistance genes (ARGs) from metagenomes of lift-off mats emerging from ice and from filtered water samples of Lake Fryxell and Lake Bonney. The overall proportion of ARG hits was similar to that found in temperate-zone rural ponds with moderate human inputs. Specific ARGs showed distinct distributions for the two lakes and for mat vs planktonic sources. Metagenomic taxa distributions showed that mat phototrophs consisted mainly of cyanobacteria or Betaproteobacteria, whereas the water column phototrophs were mainly protists. An enrichment culture of the Betaproteobacterium Rhodoferax antarcticus from a Lake Fryxell mat sample showed an unusual mat-forming phenotype not previously reported for this species. Its genome showed no ARGs associated with Betaproteobacteria but had ARGs consistent with a minor Pseudomonas 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 with moderate human inputs. 

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