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Antibiotics
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Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria
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Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria

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 August 2025 | Viewed by 8883

Special Issue Editors

Dr. Daniel Gyamfi Amoako

E-Mail Website
Guest Editor
1. Department of Pathobiology, University of Guelph, Guelph, ON, Canada
2. Antimicrobial Research Unit, College of Health Sciences, University of KwaZuluNatal, Durban 4000, South Africa
Interests: antimicrobial resistance; molecular genetics; one-health genomics; pathogenomics; applied bioinformatics; machine learning analytics
Special Issues, Collections and Topics in MDPI journals
Dr. Linda Bester

E-Mail Website
Guest Editor
1. College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
2. Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
Interests: bacteria epidemiology; molecular surveillance of bacteria; one-health genomics; zoonotic pathogens; human health risk
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the ever-evolving battle against antimicrobial resistance (AMR), our understanding of the genomic landscape of bacteria and their mechanisms of evolution has become pivotal. In bacteria, resistance to antibiotics is determined by genetic factors such as chromosomes, plasmids or other movable genetic elements. Although antimicrobial resistance genes (ARGs) typically exhibit significant sequence variability, such as the impact of different concentrations of antibiotics on their genomic dynamics, the impact of this diversity on AMR is still unclear. Therefore, understanding the dynamic changes and mobilization of antibiotic resistance genes in humans, animals, plants and environmental microorganisms through genomics and metagenomics methods is crucial.

This Special Issue seeks to foster a comprehensive understanding of the genetic underpinnings of bacterial antimicrobial resistance and the evolutionary dynamics that underlie these adaptations.

Dr. Daniel Gyamfi Amoako
Dr. Linda Bester
Guest Editors

Manuscript Submission Information

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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.

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

  • antimicrobial resistance mechanism
  • mobile genetic element
  • horizontal gene transfer
  • resistome
  • evolution
  • molecular phylogenetics
  • genomics
  • bioinformatics analysis
  • next-generation sequencing

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Published Papers (7 papers)

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Research

24 pages, 4343 KiB  
Article
Genomic Insights of Antibiotic-Resistant Escherichia coli Isolated from Intensive Pig Farming in South Africa Using ‘Farm-to-Fork’ Approach
by Shima E. Abdalla, Linda A. Bester, Akebe L. K. Abia, Mushal Allam, Arshad Ismail, Sabiha Y. Essack and Daniel G. Amoako
Antibiotics 2025, 14(5), 446; https://doi.org/10.3390/antibiotics14050446 - 28 Apr 2025
Viewed by 51
Abstract
Background/Objectives: Intensive pig farming is a critical component of food security and economic activity in South Africa; however, it also presents a risk of amplifying antimicrobial resistance (AMR). This study provides genomic insights into antibiotic-resistant Escherichia coli (E. coli) circulating [...] Read more.
Background/Objectives: Intensive pig farming is a critical component of food security and economic activity in South Africa; however, it also presents a risk of amplifying antimicrobial resistance (AMR). This study provides genomic insights into antibiotic-resistant Escherichia coli (E. coli) circulating across the pork production chain, using a ‘farm-to-fork’ approach. Methods: A total of 417 samples were collected from various points along the production continuum, including the farm (n = 144), transport (n = 60), and abattoir (n = 213). E. coli isolates were identified using the Colilert-18 system, and their phenotypic resistance was tested against 20 antibiotics. Thirty-one isolates were selected for further characterization based on their resistance profiles and sampling sources, utilizing whole-genome sequencing and bioinformatic analysis. Results: The isolates exhibited varying resistance to critical antibiotics used in both human and animal health, including ampicillin (31/31, 100%), tetracycline (31/31, 100%), amoxicillin–clavulanate (29/31, 94%), chloramphenicol (25/31, 81%), and sulfamethoxazole–trimethoprim (10/31, 33%). Genetic analysis revealed the presence of resistance genes for β-lactams (blaEC, blaTEM), trimethoprim/sulfonamides (dfrA1, dfrA5, dfrA12, sul2, sul3), tetracyclines (tetA, tetB, tetR, tet34), aminoglycosides (aadA, strA, aph variants), and phenicols (catB4, floR, cmlA1), most of which were plasmid-borne. Virulome analysis identified 24 genes, including toxins and adhesion factors. Mobile genetic elements included 24 plasmid replicons, 43 prophages, 19 insertion sequence families, and 7 class 1 integrons. The E. coli isolates belonged to a diverse range of sequence types, demonstrating significant genetic variability. Further phylogenomic analysis revealed eight major clades, with isolate clustering by sequence type alongside South African environmental and clinical E. coli strains, regardless of their sampling source. Conclusions: The genetic complexity observed across the pork production continuum threatens food safety and may impact human health. These findings underscore the need for enhanced AMR monitoring in livestock systems and support the integration of AMR surveillance into food safety policy frameworks. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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13 pages, 538 KiB  
Article
Resistance of Pseudomonas aeruginosa to Antibiotics During Long-Term Persistence in Patients with Cystic Fibrosis
by Natalia Belkova, Uliana Nemchenko, Elizaveta Klimenko, Nadezhda Smurova, Raisa Zugeeva, Marina Sukhoreva, Viacheslav Sinkov and Evgenij Savilov
Antibiotics 2025, 14(3), 302; https://doi.org/10.3390/antibiotics14030302 - 14 Mar 2025
Viewed by 633
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial respiratory tract infections, significantly affecting morbidity and mortality. It can persist in the lungs of patients with cystic fibrosis (CF) for extended periods because of its adaptive capacity. The main aim of this [...] Read more.
Pseudomonas aeruginosa is one of the leading causes of nosocomial respiratory tract infections, significantly affecting morbidity and mortality. It can persist in the lungs of patients with cystic fibrosis (CF) for extended periods because of its adaptive capacity. The main aim of this study was to determine the phenotypic and genotypic resistance to antibiotics of clinical isolates of P. aeruginosa that persist in patients with CF receiving long-term antimicrobial therapy. The study included nine strains of P. aeruginosa isolated from the sputum of patients with CF admitted to the hospital. Susceptibility to antibiotics was determined using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Whole-genome sequencing was performed for phylogeny, sequence typing, and to identify antibiotic-resistant genes. The study showed that during long-term persistence in the lungs of patients receiving antibacterial therapy, the restoration of susceptibility to antibiotics occurred in some cases. Multilocus sequence typing and phylogeny revealed six sequence types. Functional annotation identified 72 genes responsible for resistance to antibacterial and chemical substances, with either chromosomal or plasmid localisation. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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17 pages, 1473 KiB  
Article
Determination of Antimicrobial Resistance Megaplasmid-Like pESI Structures Contributing to the Spread of Salmonella Schwarzengrund in Japan
by Kanako Ishihara, Suzuka Someno, Kaoru Matsui, Chisato Nakazawa, Takahiro Abe, Hayato Harima, Tsutomu Omatsu, Manao Ozawa, Eriko Iwabuchi and Tetsuo Asai
Antibiotics 2025, 14(3), 288; https://doi.org/10.3390/antibiotics14030288 - 10 Mar 2025
Viewed by 785
Abstract
Background/Objectives: The acquisition of antimicrobial resistance by foodborne pathogens is a serious human health concern. In Japan, combinations of antimicrobial resistance genes in Salmonella from chicken meat were common among several serovars. Therefore, we hypothesized that different S. enterica serovars share a common [...] Read more.
Background/Objectives: The acquisition of antimicrobial resistance by foodborne pathogens is a serious human health concern. In Japan, combinations of antimicrobial resistance genes in Salmonella from chicken meat were common among several serovars. Therefore, we hypothesized that different S. enterica serovars share a common antimicrobial resistance plasmid. Methods: Antimicrobial resistance transfer was tested in S. Infantis and S. Schwarzengrund, the major serovars used as donors. The plasmid structure was determined by subjecting S. Infantis Sal_238 and S. Schwarzengrund Sal_249 to short- and long-read sequencing. Results: The high homology between pSal_249Sch and pSal_238Inf suggests they have a common ancestor. Because the sequences of pSal_238Inf and pSal_249Sch were highly homologous to pESI (a plasmid for emerging S. Infantis), pSal_238Inf and pSal_249Sch were identified as pESI-like plasmids. S. Schwarzengrund is the third Salmonella serovar to expand its distribution related to pESI-like plasmid acquisition. Core-genome multilocus sequence-type analysis revealed that S. Schwarzengrund isolates with pESI-like plasmids from Japan (core-genome sequence-type [cgST] 167363 and cgST287831), the UK (cgST167363), and the USA (cgST167363, cgST196045, and cgST287831) were closely related; they are also suggested to share a common ancestor. The transfer of antimicrobial resistance was observed in combinations of both serovars. Specifically, the tentative plasmid sequence obtained via short-read sequencing, PCR, and conjugation experiments identified deletions of antimicrobial resistance genes (aadA, sul1, and tetA), class 1 integron, mercury resistance operon, and/or plasmid transfer region in the pESI-like plasmid. Conclusion: These data on the structural diversity of pESI-like plasmids suggest that some time has passed since S. Schwarzengrund acquired them. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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19 pages, 1625 KiB  
Article
Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia
by Deneke Wolde, Tadesse Eguale, Girmay Medhin, Aklilu Feleke Haile, Haile Alemayehu, Adane Mihret, Mateja Pirs, Katja Strašek Smrdel, Jana Avberšek, Darja Kušar, Tjaša Cerar Kišek, Tea Janko, Andrej Steyer and Marjanca Starčič Erjavec
Antibiotics 2024, 13(9), 851; https://doi.org/10.3390/antibiotics13090851 - 5 Sep 2024
Cited by 1 | Viewed by 1345
Abstract
The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of [...] Read more.
The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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20 pages, 1065 KiB  
Article
Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study
by Bakoena A. Hetsa, Jonathan Asante, Joshua Mbanga, Arshad Ismail, Akebe L. K. Abia, Daniel G. Amoako and Sabiha Y. Essack
Antibiotics 2024, 13(9), 796; https://doi.org/10.3390/antibiotics13090796 - 23 Aug 2024
Cited by 1 | Viewed by 1453
Abstract
Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, [...] Read more.
Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, South Africa, to gain insights into their resistance mechanisms, virulence factors, and clonal and phylogenetic relationships. Six multidrug-resistant (MDR) S. aureus isolates, comprising three methicillin-resistant S. aureus (MRSA) and three methicillin-susceptible S. aureus (MSSA), underwent whole genome sequencing and bioinformatics analysis. These isolates carried a range of resistance genes, including blaZ, aac(6′)-aph(2″), ant(9)-Ia, ant(6)-Ia, and fosB. The mecA gene, which confers methicillin resistance, was detected only in MRSA strains. The isolates exhibited six distinct spa types (t9475, t355, t045, t1265, t1257, and t7888) and varied in virulence gene profiles. Panton–Valentine leukocidin (Luk-PV) was found in one MSSA isolate. Two SCCmec types, IVd(2B) and I(1B), were identified, and the isolates were classified into four multilocus sequence types (MLSTs), with ST5 (n = 3) being the most common. These sequence types clustered into two clonal complexes, CC5 and CC8. Notably, two MRSA clones were identified: ST5-CC5-t045-SCCmec_I(1B) and the human-associated endemic clone ST612-CC8-t1257-SCCmec_IVd(2B). Phylogenomic analysis revealed clustering by MLST, indicating strong genetic relationships within clonal complexes. These findings highlight the value of genomic surveillance in guiding targeted interventions to reduce treatment failures and mortality. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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14 pages, 1508 KiB  
Article
Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms
by Thunchanok Yaikhan, Sirikan Suwannasin, Kamonnut Singkhamanan, Sarunyou Chusri, Rattanaruji Pomwised, Monwadee Wonglapsuwan and Komwit Surachat
Antibiotics 2024, 13(6), 531; https://doi.org/10.3390/antibiotics13060531 - 6 Jun 2024
Cited by 1 | Viewed by 2085
Abstract
The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. [...] Read more.
The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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18 pages, 2320 KiB  
Article
Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
by Kinga Tóth, Ivelina Damjanova, Levente Laczkó, Lilla Buzgó, Virág Lesinszki, Erika Ungvári, Laura Jánvári, Adrienn Hanczvikkel, Ákos Tóth and Dóra Szabó
Antibiotics 2024, 13(4), 363; https://doi.org/10.3390/antibiotics13040363 - 16 Apr 2024
Cited by 5 | Viewed by 1817
Abstract
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected [...] Read more.
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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