Special Issue "Antibiotic Resistance: Mobility and Microbiomes"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2015).

Special Issue Editors

Guest Editor
Prof. Jonathan Iredell

Centre for Infectious Diseases and Microbiology (CIDM), The University of Sydney and Westmead Millennium Institute, Westmead Hospital, NSW 2145, Australia
Website | E-Mail
Interests: antibiotic resistance; sepsis; critical infection; bacterial ecology; rapid diagnostics
Guest Editor
Dr. Sally Partridge

Centre for Infectious Diseases and Microbiology (CIDM), The University of Sydney and Westmead Millennium Institute, Westmead Hospital, NSW 2145, Australia
Website | E-Mail
Interests: antibiotic resistance; mobile genetic elements; plasmids; bioinformatics

Special Issue Information

Dear Colleagues,

Understanding the rise in antibiotic resistance requires an understanding of the factors that contribute to the mobility of resistance, particularly among Gram-negative bacteria. This includes the small mobile genetic elements that capture and mobilise genes, as well as plasmid and other vehicles, and the relationships between them. The effects of antibiotic selection on polymicrobial populations such as the gut microbiome are also important. In this Special Issue, we aim to deal with the effects of antibiotics at the population level, as well as on individual bacterial cells, and the genetic mobility that determines the ultimate epidemiology and ecology of antibiotic resistance. We welcome submissions (reviews or original articles) that examine genetic ecology and epidemiology of antibiotic resistance, vehicles (resistance plasmids, their antibiotic-susceptible ecological partners and competitors) or antibiotic effects on polymicrobial populations (from wastewater to the gut microbiome). These submissions should be aimed at a biologically literate readership with a general interest in genetics and a desire to better understand the dynamics of antibiotic resistance in highly mobile and recombinant gene pools.

Prof. Jonathan Iredell
Dr. Sally Partridge
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • antibiotic resistance
  • mobile genetic elements
  • plasmids
  • bioinformatics
  • resistance ecology
  • microbiome

Published Papers (4 papers)

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Research

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Open AccessArticle
Daptomycin-Nonsusceptible Staphylococcus aureus: The Role of Combination Therapy with Daptomycin and Gentamicin
Genes 2015, 6(4), 1256-1267; https://doi.org/10.3390/genes6041256
Received: 19 August 2015 / Revised: 5 November 2015 / Accepted: 16 November 2015 / Published: 30 November 2015
Cited by 6 | PDF Full-text (2058 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Reduced susceptibility to daptomycin in Staphylococcus aureus has now been described, leading to clinical failures. Here we determined the impact of daptomycin and gentamicin combination therapy on bactericidal activity and resistance emergence using daptomycin-susceptible and -resistant isolates with mutations linked to previous daptomycin [...] Read more.
Reduced susceptibility to daptomycin in Staphylococcus aureus has now been described, leading to clinical failures. Here we determined the impact of daptomycin and gentamicin combination therapy on bactericidal activity and resistance emergence using daptomycin-susceptible and -resistant isolates with mutations linked to previous daptomycin or vancomycin exposure. Enhanced killing of S. aureus was observed when gentamicin was combined with daptomycin, most commonly with daptomycin concentrations below the peak serum free-drug concentrations achieved with standard dosing. Synergy was seen with daptomycin-susceptible isolates and with isolates resistant to vancomycin and daptomycin. Combination therapy also prevented the emergence of resistance. Daptomycin and gentamicin combination therapy may provide the synergy required to prevent emergence of resistance when daptomycin levels are below peak serum concentrations as would be found in deep-seated, complicated infections. Full article
(This article belongs to the Special Issue Antibiotic Resistance: Mobility and Microbiomes)
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Review

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Open AccessReview
Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance
Genes 2015, 6(4), 1347-1360; https://doi.org/10.3390/genes6041347
Received: 28 August 2015 / Revised: 9 December 2015 / Accepted: 10 December 2015 / Published: 21 December 2015
Cited by 27 | PDF Full-text (102 KB) | HTML Full-text | XML Full-text
Abstract
Clostridium difficile is well recognized as the leading cause of antibiotic-associated diarrhea, having a significant impact in both health-care and community settings. Central to predisposition to C. difficile infection is disruption of the gut microbiome by antibiotics. Being a Gram-positive anaerobe, C. difficile [...] Read more.
Clostridium difficile is well recognized as the leading cause of antibiotic-associated diarrhea, having a significant impact in both health-care and community settings. Central to predisposition to C. difficile infection is disruption of the gut microbiome by antibiotics. Being a Gram-positive anaerobe, C. difficile is intrinsically resistant to a number of antibiotics. Mobile elements encoding antibiotic resistance determinants have also been characterized in this pathogen. While resistance to antibiotics currently used to treat C. difficile infection has not yet been detected, it may be only a matter of time before this occurs, as has been seen with other bacterial pathogens. This review will discuss C. difficile disease pathogenesis, the impact of antibiotic use on inducing disease susceptibility, and the role of antibiotic resistance and mobile elements in C. difficile epidemiology. Full article
(This article belongs to the Special Issue Antibiotic Resistance: Mobility and Microbiomes)
Open AccessReview
Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics
Genes 2015, 6(3), 841-857; https://doi.org/10.3390/genes6030841
Received: 17 July 2015 / Revised: 26 August 2015 / Accepted: 31 August 2015 / Published: 8 September 2015
Cited by 26 | PDF Full-text (791 KB) | HTML Full-text | XML Full-text
Abstract
Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention [...] Read more.
Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century. Full article
(This article belongs to the Special Issue Antibiotic Resistance: Mobility and Microbiomes)
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Other

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Open AccessOpinion
How Porin Heterogeneity and Trade-Offs Affect the Antibiotic Susceptibility of Gram-Negative Bacteria
Genes 2015, 6(4), 1113-1124; https://doi.org/10.3390/genes6041113
Received: 2 July 2015 / Revised: 4 September 2015 / Accepted: 8 October 2015 / Published: 21 October 2015
Cited by 4 | PDF Full-text (1053 KB) | HTML Full-text | XML Full-text
Abstract
Variations in porin proteins are common in Gram-negative pathogens. Altered or absent porins reduce access of polar antibiotics across the outer membrane and can thus contribute to antibiotic resistance. Reduced permeability has a cost however, in lowering access to nutrients. This trade-off between [...] Read more.
Variations in porin proteins are common in Gram-negative pathogens. Altered or absent porins reduce access of polar antibiotics across the outer membrane and can thus contribute to antibiotic resistance. Reduced permeability has a cost however, in lowering access to nutrients. This trade-off between permeability and nutritional competence is the source of considerable natural variation in porin gate-keeping. Mutational changes in this trade-off are frequently selected, so susceptibility to detergents and antibiotics is polymorphic in environmental isolates as well as pathogens. Understanding the mechanism, costs and heterogeneity of antibiotic exclusion by porins will be crucial in combating Gram negative infections. Full article
(This article belongs to the Special Issue Antibiotic Resistance: Mobility and Microbiomes)
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