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Antibiotics
Special Issues
Antimicrobial Resistance Genes: Spread and Evolution
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Antimicrobial Resistance Genes: Spread and Evolution

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 6486

Special Issue Editors

Dr. Angeliki Mavroidi

E-Mail Website
Guest Editor
Department of Microbiology, University Hospital of Patras, 26500 Rion, Greece
Interests: microbiology; antimicrobial resistance; infectious diseases; epidemiology; evolution; population genetics of pathogens
Prof. Dr. Georgia Vrioni

E-Mail Website
Guest Editor
Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
Interests: medical microbiology; mycology; antimicrobial resistance; molecular microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbes are ubiquitous in the world in which we live. As microbes must face variable environments, many different adaptive strategies can simultaneously exist. Multi-resistance (i.e., resistance to three or more drug classes) is considered to be a key indicator of microbes, because it reduces the options of treatment that are appropriate, and facilitates the transmission of antimicrobial-resistant strains to the community and vice versa. The burden of resistant strains and the threat posed by their increasing incidence worldwide have both healthcare and economic impacts. Besides being used for human therapy, antimicrobials are extensively used for animal farming and for agricultural purposes. Nevertheless, the effect of the use of antimicrobials on the biosphere is wider than this and can impact the structure and activity of environmental microbiota. The clearest consequence of antimicrobial release in natural environments is the emergence and selection of resistant bacteria.

This Special Issue seeks manuscript submissions that further our understanding of antimicrobial resistance, including: a) the identification of epidemic and persistent strains; b) the identification of reservoirs of resistant strains that could persist in the hospital and natural environment, but also in animal and food sources; c) the elucidation of mechanisms of the acquisition and spread of resistance and virulence factors amongst microbial populations; and d) the investigation of gene flow and the evolutionary pathways of antimicrobial resistance among microbial populations.

Dr. Angeliki Mavroidi
Dr. Georgia Vrioni
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 submissions that pass pre-check are 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. Antibiotics 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 2900 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

  • microbes
  • antimicrobial resistance
  • resistance genes
  • gene flow
  • evolution

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Published Papers (5 papers)

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Research

15 pages, 1852 KiB  
Article
Survival Strategies of Staphylococcus aureus: Adaptive Regulation of the Anti-Restriction Gene ardA-H1 Under Stress Conditions
by Flavia Costa Carvalho de Andrade, Mariana Fernandes Carvalho and Agnes Marie Sá Figueiredo
Antibiotics 2024, 13(12), 1131; https://doi.org/10.3390/antibiotics13121131 - 25 Nov 2024
Viewed by 326
Abstract
Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction–modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression [...] Read more.
Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction–modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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14 pages, 1483 KiB  
Article
Unveiling the Dynamics of Antimicrobial Resistance: A Year-Long Surveillance (2023) at the Largest Infectious Disease Profile Hospital in Western Romania
by Sorina Maria Denisa Laitin, Luminita Mirela Baditoiu, Ruxandra Laza, Irina-Maria Stefan, Razvan Sebastian Besliu, Septimiu Radu Susa, Cristian Oancea, Emil Robert Stoicescu, Diana Manolescu and Corneluta Fira-Mladinescu
Antibiotics 2024, 13(12), 1130; https://doi.org/10.3390/antibiotics13121130 - 25 Nov 2024
Viewed by 342
Abstract
Background/Objectives: Antimicrobial resistance (AMR) is a critical global health threat, leading to increased morbidity, mortality, and healthcare costs. This study aimed to identify the most common bacterial pathogens and their resistance profiles from 2179 positive clinical cultures from inpatients at “Victor Babes” [...] Read more.
Background/Objectives: Antimicrobial resistance (AMR) is a critical global health threat, leading to increased morbidity, mortality, and healthcare costs. This study aimed to identify the most common bacterial pathogens and their resistance profiles from 2179 positive clinical cultures from inpatients at “Victor Babes” Hospital of Infectious Disease and Pneumoftiziology Timisoara in 2023. Methods: Samples were collected from sputum, bronchial aspiration, hemoculture, urine, wound secretions, catheter samples, and other clinical specimens. Results: Key pathogens identified included Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii, with notable resistance patterns, observed K. pneumoniae exhibited high resistance rates, notably 41.41% in Quarter 1, while E. coli showed 35.93% resistance in the same period. S. aureus, particularly MRSA, remained a persistent challenge, with 169 cases recorded over the year. A. baumannii and P. aeruginosa displayed alarming levels of multi-drug resistance, especially in Quarter 3 (88.24% and 22.02%, respectively). Although there was a general decline in resistance rates by Quarter 4, critical pathogens such as S. aureus and K. pneumoniae continued to exhibit significant resistance (81.25% and 21.74%, respectively). Conclusions: The study’s findings align with the broader antimicrobial resistance trends observed in Romania, where high resistance rates in K. pneumoniae, E. coli, S. aureus (MRSA), Acinetobacter, and Pseudomonas species have been widely reported, reflecting the country’s ongoing struggle with multi-drug-resistant infections. Despite some reductions in resistance rates across quarters, the persistent presence of these resistant strains underscores the critical need for strengthened antimicrobial stewardship, infection control measures, and continuous surveillance to combat the growing threat of AMR in Romania and similar healthcare settings. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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19 pages, 3354 KiB  
Article
Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes
by Gábor Kardos, Levente Laczkó, Eszter Kaszab, Bálint Timmer, Krisztina Szarka, Eszter Prépost and Krisztián Bányai
Antibiotics 2024, 13(7), 573; https://doi.org/10.3390/antibiotics13070573 - 21 Jun 2024
Cited by 1 | Viewed by 971
Abstract
The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage [...] Read more.
The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from Paenibacillus spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the Paenibacillus spp. and the separation of proteins of Streptomyces origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with Paenibacillus spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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11 pages, 632 KiB  
Article
Scolopax rusticola Carrying Enterobacterales Harboring Antibiotic Resistance Genes
by Valeria Gargano, Delia Gambino, Adriana Maria Oddo, Mariangela Pizzo, Arianna Sucato, Gaetano Cammilleri, Francesco La Russa, Maria Liliana Di Pasquale, Maria Giovanna Parisi, Giovanni Cassata and Giuseppe Giangrosso
Antibiotics 2024, 13(3), 234; https://doi.org/10.3390/antibiotics13030234 - 2 Mar 2024
Viewed by 1747
Abstract
The Eurasian woodcock (Scolopax rusticola) belongs to those bird species that make systematic migratory flights in spring and autumn in search of favorable breeding and wintering areas. These specimens arrive in the Mediterranean Area from northeastern European countries during the autumn [...] Read more.
The Eurasian woodcock (Scolopax rusticola) belongs to those bird species that make systematic migratory flights in spring and autumn in search of favorable breeding and wintering areas. These specimens arrive in the Mediterranean Area from northeastern European countries during the autumn season. The purpose of this study was to assess whether woodcocks can carry antibiotic resistance genes (ARGs) along their migratory routes. Although the role of migratory birds in the spread of some zoonotic diseases (of viral and bacterial etiology) has been elucidated, the role of these animals in the spread of antibiotic resistance has not yet been clarified. In this study, we analyzed the presence of beta-lactam antibiotic resistance genes. The study was conducted on 69 strains from 60 cloacal swabs belonging to an equal number of animals shot during the 2022–2023 hunting season in Sicily, Italy. An antibiogram was performed on all strains using the microdilution method (MIC) and beta-lactam resistance genes were investigated. The strains tested showed no phenotypic resistance to any of the 13 antibiotics tested; however, four isolates of Enterobacter cloacae and three of Klebsiella oxytoca were found to carry the blaIMP-70, blaVIM-35, blaNDM-5 and blaOXA-1 genes. Our results confirm the importance of monitoring antimicrobial resistance among migratory animals capable of long-distance bacteria spread. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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14 pages, 1205 KiB  
Article
Comprehensive Analysis of Virulence Determinants and Genomic Islands of blaNDM-1-Producing Enterobacter hormaechei Clinical Isolates from Greece
by Angeliki Mavroidi, Konstantina Gartzonika, Nick Spanakis, Elisavet Froukala, Christos Kittas, Georgia Vrioni and Athanasios Tsakris
Antibiotics 2023, 12(10), 1549; https://doi.org/10.3390/antibiotics12101549 - 18 Oct 2023
Cited by 1 | Viewed by 1888
Abstract
Nosocomial outbreaks of multidrug-resistant (MDR) Enterobacter cloacae complex (ECC) are often reported worldwide, mostly associated with a small number of multilocus-sequence types of E. hormaechei and E. cloacae strains. In Europe, the largest clonal outbreak of blaNDM-1-producing ECC has been recently [...] Read more.
Nosocomial outbreaks of multidrug-resistant (MDR) Enterobacter cloacae complex (ECC) are often reported worldwide, mostly associated with a small number of multilocus-sequence types of E. hormaechei and E. cloacae strains. In Europe, the largest clonal outbreak of blaNDM-1-producing ECC has been recently reported, involving an ST182 E. hormaechei strain in a Greek teaching hospital. In the current study, we aimed to further investigate the genetic make-up of two representative outbreak isolates. Comparative genomics of whole genome sequences (WGS) was performed, including whole genome-based taxonomic analysis and in silico prediction of virulence determinants of the bacterial cell surface, plasmids, antibiotic resistance genes and virulence factors present on genomic islands. The enterobacterial common antigen and the colanic antigen of the cell surface were identified in both isolates, being similar to the gene clusters of the E. hormaechei ATCC 49162 and E. cloacae ATCC 13047 type strains, whereas the two strains possessed different gene clusters encoding lipopolysaccharide O-antigens. Other virulence factors of the bacterial cell surface, such as flagella, fimbriae and pili, were also predicted to be encoded by gene clusters similar to those found in Enterobacter spp. and other Enterobacterales. Secretion systems and toxin–antitoxin systems, which also contribute to pathogenicity, were identified. Both isolates harboured resistance genes to multiple antimicrobial classes, including β-lactams, aminoglycosides, quinolones, chloramphenicol, trimethoprim, sulfonamides and fosfomycin; they carried blaTEM-1, blaOXA-1, blaNDM-1, and one of them also carried blaCTXM-14, blaCTXM-15 and blaLAP-2 plasmidic alleles. Our comprehensive analysis of the WGS assemblies revealed that blaNDM-1-producing outbreak isolates possess components of the bacterial cell surface as well as genomic islands, harbouring resistance genes to several antimicrobial classes and various virulence factors. Differences in the plasmids carrying β-lactamase genes between the two strains have also shown diverse modes of acquisition and an ongoing evolution of these mobile elements. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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