The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials

Lanza, Val F.; Tedim, Ana P.; Martínez, José Luis; Baquero, Fernando; Coque, Teresa M.

doi:10.1128/microbiolspec.plas-0039-2014

Cited by 90 publications

(87 citation statements)

References 236 publications

(322 reference statements)

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“…However, data on AMR genetics is still limited for public health relevant bacteria that are not as frequently isolated from food such as C. difficile . Furthermore, quantifiable data on AMR gene prevalence as well as the detailed elucidation of genetic linkages between AMR genes and mobile genetic elements such as plasmids, transposons or integrons is rarely reported (Lanza et al, 2015; Martínez et al, 2017). This unfortunately hinders better estimations on AMR gene prevalence and transferability.…”

Section: Discussionmentioning

confidence: 99%

Consumer Exposure to Antimicrobial Resistant Bacteria From Food at Swiss Retail Level

et al. 2018

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Background: Antimicrobial resistance (AMR) in bacteria is an increasing health concern. The spread of AMR bacteria (AMRB) between animals and humans via the food chain and the exchange of AMR genes requires holistic approaches for risk mitigation. The AMRB exposure of humans via food is currently only poorly understood leaving an important gap for intervention design.Method: This study aimed to assess AMRB prevalence in retail food and subsequent exposure of Swiss consumers in a systematic literature review of data published between 1996 and 2016 covering the Swiss agriculture sector and relevant imported food.Results: Data from 313 out of 9,473 collected studies were extracted yielding 122,438 food samples and 38,362 bacteria isolates of which 30,092 samples and 8,799 isolates were AMR positive. A median AMRB prevalence of >50% was observed for meat and seafood harboring Campylobacter, Enterococcus, Salmonella, Escherichia coli, Listeria, and Vibrio spp. and to a lesser prevalence for milk products harboring starter culture bacteria. Gram-negative AMRB featured predominantly AMR against aminoglycosides, cephalosporins, fluoroquinolones, penicillins, sulfonamides, and tetracyclines observed at AMR exposures scores of levels 1 (medium) and 2 (high) for Campylobacter, Salmonella, E. coli in meat as well as Vibrio and E. coli in seafood. Gram-positive AMRB featured AMR against glycoproteins, lincosamides, macrolides and nitrofurans for Staphylococcus and Enterococcus in meat sources, Staphylococcus in seafood as well as Enterococcus and technologically important bacteria (incl. starters) in fermented or processed dairy products. Knowledge gaps were identified for AMR prevalence in dairy, plant, fermented meat and novel food products and for the role of specific indicator bacteria (Staphylococcus, Enterococcus), starter culture bacteria and their mobile genetic elements in AMR gene transfer.Conclusion: Raw meat, milk, seafood, and certain fermented dairy products featured a medium to high potential of AMR exposure for Gram-negative and Gram-positive foodborne pathogens and indicator bacteria. Food at retail, additional food categories including fermented and novel foods as well as technologically important bacteria and AMR genetics are recommended to be better integrated into systematic One Health AMR surveillance and mitigation strategies to close observed knowledge gaps and enable a comprehensive AMR risk assessment for consumers.

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Section: Discussionmentioning

confidence: 99%

Consumer Exposure to Antimicrobial Resistant Bacteria From Food at Swiss Retail Level

et al. 2018

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“…According to Lanza et al (2015), Firmicutes represents a large and diverse phylum that has an outstanding relevance in both the human and animal gut microbiota. The authors reported that 244 of the 1073 fully characterized plasmids from the representatives of Firmicutes carried AR genes and also indicated that lateral transfer between Firmicutes members can occur either by transduction/conjugation mechanisms representing bacterial species specific adaptation or through plasmids or transposons that facilitate complex interactions between different communities.…”

Section: Multidrug Transportersmentioning

confidence: 99%

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

Pitta

Dou

Kumar

et al. 2016

Foodborne Pathogens and Disease

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Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms, but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment through manure, and to this end, we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with 18 antibiotic resistances classes across all samples; however, the most abundant genes were classified under multidrug transporters (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%), and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms. Farm 09 was categorized as a high risk farm, as a greater proportion of AR genes were common to at least three sectors, suggesting possible horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.

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“…Such processes of horizontal gene transfer (HGT) are considered a strong driving force in bacterial evolution and in the ability of bacteria to colonize different niches (2). In addition to permitting the rapid evolution of the bacterial pangenome, HGT is involved in the acquisition of genetic traits that may confer selective advantages to the recipient bacteria, including antibiotic resistance (3). This is particularly important when resistance genes encoded by mobile elements are spread explosively among bacteria in hospitals, posing a serious threat to public health systems (www.cdc.gov/drugresistance/threat-report-2013; www.…”

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confidence: 99%

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

Pluta

Boer

Lorenzo-Díaz

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOB V family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOB V relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. We discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOB V histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.histidine relaxase | antibiotic resistance | horizontal gene transfer | X-ray structure | Staphylococcus aureus A cquisition of exogenous genetic material by bacteria is achieved via conjugative DNA transfer of mobile genetic elements, such as plasmids and especially integrative and conjugative elements and integrative and mobilizable elements (1). Such processes of horizontal gene transfer (HGT) are considered a strong driving force in bacterial evolution and in the ability of bacteria to colonize different niches (2). In addition to permitting the rapid evolution of the bacterial pangenome, HGT is involved in the acquisition of genetic traits that may confer selective advantages to the recipient bacteria, including antibiotic resistance (3). This is particularly important when resistance genes encoded by mobile elements are spread explosively among bacteria in hospitals, posing a serious threat to public health systems (www.cdc.gov/drugresistance/threat-report-2013; www. who.int/drugresistance/documents/surveillancereport/en/). Thus, the so-called mobilome (4) participates in the spread of antibiotic resistance, which is expected to cause 10 million casualties annually by 2050, and the consequent huge economic burden (amr-review.org/sites/default/files/Report-52.15.pdf). This has generated a unanimous call for new approaches to deal with infectious diseases caused by pathogenic bacteria (5).A main performer in HGT is the protein relaxase, a topoisomeraselike enzyme that cleaves supercoiled plasmid DNA in a strandand sequence-specific manner and ligates it after cell-to-cell transfer. Relaxases start DNA transfer by conjugation on recognition of their target DNA, the origin of transfer (oriT), on which they mediate generation of a hairpin-loop structure that leaves the dinucleotide to be cleaved (the nic site) in a singlestranded (ss) DNA configuration (Fig. 1B) (6, 7). On the oriT, the relaxase assembles with other proteins p...

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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials

Cited by 90 publications

References 236 publications

Consumer Exposure to Antimicrobial Resistant Bacteria From Food at Swiss Retail Level

Consumer Exposure to Antimicrobial Resistant Bacteria From Food at Swiss Retail Level

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

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