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Antimicrobial Resistance Genes: Spread and Evolution

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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: 29 June 2025 | Viewed by 11693

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Special Issue Editors

Dr. Angeliki Mavroidi

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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

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Guest Editor

Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
Interests: microbiology; antibiotic resistance; infectious diseases; antimicrobials; microbial molecular biology
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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

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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.

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Keywords

microbes
antimicrobial resistance
resistance genes
gene flow
evolution

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Published Papers (7 papers)

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21 pages, 3320 KiB

Open AccessArticle

Relationship Between CRISPR–Cas Systems and Acquisition of Tetracycline Resistance in Non-Clinical Enterococcus Populations in Bulgaria

by Maria Pandova, Yoana Kizheva and Petya Hristova

Antibiotics 2025, 14(2), 145; https://doi.org/10.3390/antibiotics14020145 - 2 Feb 2025

Viewed by 1120

Abstract

Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR–Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1–10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause. Full article

(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)

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14 pages, 2557 KiB

Open AccessArticle

Detection of Delafloxacin Resistance Mechanisms in Multidrug-Resistant Klebsiella pneumoniae

by András Kubicskó, János Juhász, Katalin Kamotsay, Dora Szabo and Béla Kocsis

Antibiotics 2025, 14(1), 62; https://doi.org/10.3390/antibiotics14010062 - 9 Jan 2025

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Abstract

Background: In this study, the mechanisms implicated in delafloxacin resistance in Klebsiella pneumoniae strains were investigated. Delafloxacin is a novel, broad-spectrum fluoroquinolone that has been approved for clinical application. Methods: In our study, 43 K. pneumoniae strains were assessed, antimicrobial susceptibility testing was performed via the broth microdilution method, and the minimum inhibitory concentration (MIC) values for ciprofloxacin, delafloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotaxime, and imipenem were determined. Four delafloxacin-resistant K. pneumoniae strains were selected for whole-genome sequencing (WGS). Results: The MIC50 values for the 43 K. pneumoniae strains were as follows: ciprofloxacin 0.5 mg/L, levofloxacin 0.25 mg/L, moxifloxacin 0.5 mg/L, and delafloxacin 0.25 mg/L. All four selected delafloxacin-resistant K. pneumoniae strains showed extended-spectrum beta-lactamase production, and one strain exhibited carbapenem resistance. WGS enabled us to determine the sequence types (STs) of these strains, namely, ST307 (two strains), ST377, and ST147. Multiple mutations in quinolone-resistance-determining regions (QRDRs) were detected in all the delafloxacin-resistant K. pneumoniae strains; specifically, gyrA Ser83Ile and parC Ser80Ile were uniformly present in the strains of ST307 and ST147. However, in the ST377 strain, gyrA Ser83Tyr, Asp87Ala, and parC Ser80Ile, amino acid substitutions were detected. We also identified OqxAB and AcrAB efflux pumps in all delafloxacin-resistant K. pneumoniae strains. The association between beta-lactamase production and delafloxacin resistance was determined; specifically, CTX-M-15 production was detected in the ST147, ST307, and ST377 strains. Moreover, NDM-1 was detected in ST147. Conclusions: We conclude that multiple mutations in QRDRs, in combination with OqxAB and AcrAB efflux pumps, achieved delafloxacin resistance in K. pneumoniae. In our study, we report on NDM-1-producing K. pneumoniae ST147 in Hungary. Full article

(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)

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15 pages, 1852 KiB

Open AccessArticle

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

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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 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

Open AccessArticle

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

Cited by 1 | Viewed by 1217

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” 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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18 pages, 3354 KiB

Open AccessArticle

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 2 | Viewed by 1363

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 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

Open AccessArticle

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 1987

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 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 bla_IMP-70, bla_VIM-35, bla_NDM-5 and bla_OXA-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

Open AccessArticle

Comprehensive Analysis of Virulence Determinants and Genomic Islands of bla_NDM-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 4 | Viewed by 2292

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 bla_NDM-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 bla_TEM-1, bla_OXA-1, bla_NDM-1, and one of them also carried bla_CTXM-14, bla_CTXM-15 and bla_LAP-2 plasmidic alleles. Our comprehensive analysis of the WGS assemblies revealed that bla_NDM-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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