Exploring the contribution of bacteriophages to antibiotic resistance

Lekunberri, Itziar; Subirats, Jèssica; Borrego, Carles M.; Balcázar, José Luís

doi:10.1016/j.envpol.2016.11.059

Cited by 118 publications

(96 citation statements)

References 19 publications

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“…Regarding the resistome of the effluent's viral fraction, which has been overlooked by recent metagenomic studies (Forsberg et al ., ; Yang et al ., ; Zhu et al ., ; Li et al ., ; Pehrsson et al ., ; Ju et al ., ), our data indicated that in contrast to bacteria, effluent wastewater viruses rarely carry ARGs. Remarkably, when comparing our data to those from untreated sewage viromes from different cities and hospitals (Cantalupo et al ., ; Subirats et al ., ; Lekunberri et al ., ), ARG abundance was significantly higher in raw sewage, indicating that wastewater treatment is effective in reducing numbers of viruses carrying ARGs. At the JGI‐IMG database, there is only one viral wastewater metagenome (IMG‐ID 121188; from sludge, as date of 11/6/2018) and had an enrichment of ARGs Mb −1 of metagenome of 0.5; thus in the same order as our obtained values for the viral metagenomes (0.29–0.30).…”

Section: Discussionmentioning

confidence: 91%

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Maestre‐Carballa

Gomez

Navarro

et al. 2019

Environmental Microbiology

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Summary Wastewater treatment plants effluents are considered as hotspots for the dispersion of antibiotic resistance genes (ARGs) into natural ecosystems. The bacterial resistome (ARG collection in a metagenome) analyses have provided clues on antibacterial resistance dynamics. However, viruses and vesicles are frequently ignored. Here, we addressed the bacterial, viral and vesicle resistomes from a representative wastewater effluent in natural conditions and amended with polymyxin, which is used as a last resort antibiotic. Metagenomics showed that the natural prokaryotic resistome was vast (9000 ARG hits/Gb metagenome) and diverse, while viral resistome was two orders of magnitude lower (50 ARG hits/Gb metagenome) suggesting that viruses rarely encoded ARGs. After polymyxin amendment, data showed no ARG enrichment – including to polymyxin – in the microbiome. Remarkably, microbiomes responded to polymyxin with a vast release of putative vesicles (threefold increase compared with the control), which might be used as 'traps' to decrease the antibiotic concentration. Intriguingly, although polymyxin resistance genes (PRGs) were rare in the microbiome (0.018% of total ARG found), in the viral and vesicle fractions, PRGs were more abundant (0.5%–0.8% of total ARG found). Our data suggest that vesicles could have a more active role in the context of transmission of antibiotic resistances.

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Section: Discussionmentioning

confidence: 91%

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Maestre‐Carballa

Gomez

Navarro

et al. 2019

Environmental Microbiology

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“…Adding to the fact that transfer frequency of Tn 554 via transduction is higher than most plasmids [61], we could expect a tremendously fast dissemination of optrA among different Gram-positive species and across different hosts and settings, as seems to be occurring more expressively in the animal production scenario. It has been recently hypothesized that the virome may play a larger role in ABR transfer in non-clinical environments where phages are abundant and frequently carry ABR genes [67].…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of globaloptrA-carryingEnterococcus faecalisuncovers common genetic features and a chromosomal hotspot foroptrAacquisition

Freitas

Tedim

Novais

et al. 2019

Preprint

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27Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally 28 from multiple sources, but we still lack a comprehensive analysis of human and animal optrA-LREfs 29 strains. We investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), 30 virulence, prophages, plasmidome] and optrA-containing platforms of 28 publicly available optrA-31 positive E. faecalis genomes from different hosts in 7 countries. In the genome-level analysis, in house 32 databases with 57 virulence and 391 plasmid replication genes were tested for the first time. Our 33 analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera, 34 mainly but not exclusive from Firmicutes. The content in AMR and virulence genes was highly 35identical in contrast to the diversity of phages and plasmids observed. Epidemiologically unrelated 36 clones (ST476-like and ST21-like) obtained from human clinical and animal hosts in different 37 continents over 5 years (2012)(2013)(2014)(2015)(2016)(2017) were phylogenetically related (3-122 SNPs difference). They also 38 exhibited identical AMR and virulence profiles, highlighting a global spread of optrA-positive strains 39 with relevant adaptive traits in livestock and that they might originate from an animal reservoir. optrA 40 was located on the chromosome within a Tn6674-like element (n=9) or on medium-size plasmids (30-41 60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the 42 immediate gene vicinity of optrA was identical in chromosomal (Tn6674) and plasmid (impB-fexA-43 optrA) backbones. Tn6674 was always inserted in the same ∆radC integration site and embedded in a 44 32 kb chromosomal platform common to diverse strains from different origins (patients, healthy 45 humans, and animals) in Europe, Africa, and Asia during 2012-2018. This platform is conserved 46 among hundreds of E. faecalis genomes and we here propose a conserved chromosomal hotspot for 47 optrA integration. The finding of optrA in strains sharing identical adaptive features and genetic 48 backgrounds across different hosts and countries suggest the occurrence of common and independent 49 genetic events occurring in distant regions, and might explain the easy de novo generation of optrA-50 positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious 51 impact in the efficacy of linezolid for the treatment of Gram-positive infections. 52 53 Oxazolidinones (linezolid and tedizolid) are increasingly used for the treatment of human 55 infections caused by relevant pathogens such as methicillin-resistant Staphylococcus aureus and 56 vancomycin-resistant enterococci [1, 2]. Linezolid resistance rates remain generally low in enterococci 57 causing infections worldwide (<1%) [1, 3], however acquired linezolid resistance genes (cfr, optrA 58 and/or poxtA) are being increasingly reported in different enterococcal species and across different 59 settings [2-7]. Among t...

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“…; Lekunberri et al . ). Indeed, a recent study concluded that phages could largely contribute to ARGs dissemination among nonhuman sources (Lekunberri et al .…”

Section: Methods Of Phage Detection: Advantages and Disadvantagesmentioning

confidence: 97%

“…Indeed, a recent study concluded that phages could largely contribute to ARGs dissemination among nonhuman sources (Lekunberri et al . ). For obvious reasons, anti‐phage mechanisms developed by bacteria are also detrimental of phage biocontrol.…”

Section: Methods Of Phage Detection: Advantages and Disadvantagesmentioning

confidence: 97%

Bacteriophages on dairy foods

2018

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This review focuses on the impact of bacteriophages on the manufacture of dairy foods. Firstly, the impact of phages of lactic acid bacteria in the dairy industry, where they are considered enemies, is discussed. The sources of phage contamination in dairy plants are detailed, with special emphasis on the rise of phage infections related to the growing use of cheese whey as ingredient. Other topics include traditional and new methods of phage detection, quantification and monitoring, and strategies of phage control in dairy plants, either of physical, chemical or biological nature. Finally, the use of phages or purified phage enzymes as allies to control pathogenic bacteria in the food industry is reviewed.

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Exploring the contribution of bacteriophages to antibiotic resistance

Cited by 118 publications

References 19 publications

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Comparative genomics of globaloptrA-carryingEnterococcus faecalisuncovers common genetic features and a chromosomal hotspot foroptrAacquisition

Bacteriophages on dairy foods

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