Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

ABSTRACTIn the present study, we characterized antimicrobial resistance profile and genetic relatedness of Aeromonas spp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP), and river water. We detected the presence of genes responsible for the resistance to β-lactam, quinolone, and aminoglycoside. Enterobacterial Repetitive Intergenic Consensus PCR and multilocus sequence typing (MLST) were carried out to differentiate the strains and multilocus phylogenetic analysis (MLPA) was used to identify species. A total of 28 Aeromonas spp. cefotaxime-resistant strains were identified that carried a variety of resistance determinants, including uncommon GES-type β-lactamases. Multidrug-resistant Aeromonas spp. were found in hospital wastewater, WWTP, and sanitary effluent. Among these isolates, we detected A. caviae producing GES-1 or GES-5, as well as A. veronii harboring GES-7 or GES-16. We successfully identified Aeromonas spp. by using MLPA and found that A. caviae was the most prevalent species (85.7%). In contrast, it was not possible to determine sequence type of all isolates, suggesting incompleteness of the Aeromonas spp. MLST database. Our findings reinforce the notion about the ability of Aeromonas spp. to acquire determinants of antimicrobial resistance from the environment. Such ability can be enhanced by the release of untreated healthcare effluents, in addition to the presence of antimicrobials, recognized as potential factors for the spread of resistance. Thus, Aeromonas spp. could be included as priority pathogens under the One Health concept.IMPORTANCEAeromonas species are native bacteria in aquatic ecosystems worldwide. However, they have also been isolated from humans and animals. Globally, aquatic environments have been affected by anthropogenic activities. For example, the excessive use of antimicrobials in medical and veterinary practice causes the development of bacterial resistance. In addition, eliminated hospital and sanitary effluents can also serve as potential sources of bacteria carrying antimicrobial resistance genes. Thereby, impacted environments play an important role in the transmission of these pathogens, their evolution, and dissemination of genes conferring resistance to antimicrobials. Aeromonas spp. have been reported as a reservoir of antimicrobial resistance genes in the environment. In this study, we identified a great repertoire of antimicrobial resistance genes in Aeromonas spp. from diverse aquatic ecosystems, including those that encode enzymes degrading broad-spectrum antimicrobials widely used to treat healthcare-associated infections. These are a public health threat as they may spread in the population.

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Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers

10.1101/506394 ◽

2018 ◽

Author(s):

Charles Langelier ◽

Michael Graves ◽

Katrina Kalantar ◽

Saharai Caldera ◽

Robert Durrant ◽

...

Keyword(s):

Next Generation Sequencing ◽

Antimicrobial Resistance ◽

Gut Microbiota ◽

Microbial Communities ◽

Resistance Gene ◽

Resistance Genes ◽

Antimicrobial Resistance Genes ◽

Antimicrobial Resistance Gene ◽

Global Exchange ◽

Generation Sequencing

AbstractWe engaged metagenomic next generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to understand global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.

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Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

Microbiome ◽

10.1186/s40168-018-0585-2 ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 21

Author(s):

Nitin Kumar Singh ◽

Jason M. Wood ◽

Fathi Karouia ◽

Kasthuri Venkateswaran

Keyword(s):

Antimicrobial Resistance ◽

Microbial Communities ◽

International Space Station ◽

Resistance Genes ◽

Space Station ◽

International Space ◽

Environmental Surfaces ◽

Antimicrobial Resistance Genes

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Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis

Antibiotics ◽

10.3390/antibiotics10020221 ◽

2021 ◽

Vol 10 (2) ◽

pp. 221

Author(s):

Ashenafi F. Beyi ◽

Alan Hassall ◽

Gregory J. Phillips ◽

Paul J. Plummer

Keyword(s):

Antimicrobial Resistance ◽

Microbial Communities ◽

Resistance Genes ◽

Bacterial Species ◽

Tetracycline Resistance ◽

Digital Dermatitis ◽

Proximity Ligation ◽

Tetracycline Resistance Genes ◽

Complex Microbial Community ◽

Antimicrobial Resistance Genes

Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.

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Correction to: Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

Microbiome ◽

10.1186/s40168-018-0609-y ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 4

Author(s):

Nitin Kumar Singh ◽

Jason M. Wood ◽

Fathi Karouia ◽

Kasthuri Venkateswaran

Keyword(s):

Antimicrobial Resistance ◽

Microbial Communities ◽

International Space Station ◽

Resistance Genes ◽

Space Station ◽

International Space ◽

Environmental Surfaces ◽

Antimicrobial Resistance Genes

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Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

Microorganisms ◽

10.3390/microorganisms9040707 ◽

2021 ◽

Vol 9 (4) ◽

pp. 707

Author(s):

J. Christopher Noone ◽

Fabienne Antunes Ferreira ◽

Hege Vangstein Aamot

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Virulence Gene ◽

Orthopaedic Implant ◽

Metagenomic Sequencing ◽

Gene Detection ◽

Shotgun Metagenomic Sequencing ◽

Antimicrobial Resistance Genes ◽

Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

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