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Antibiotic Resistance, Virulence Profile and Genomic Analysis among Multidrug-Resistant Bacteria...
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Antibiotic Resistance, Virulence Profile and Genomic Analysis among Multidrug-Resistant Bacteria Isolated from Humans and Animals

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (15 June 2024) | Viewed by 8938

Special Issue Editors

Dr. Sónia Ramos

E-Mail Website
Guest Editor
Faculty of Veterinary Medicine, Centro Universitário Lisboa, Campo Grande, 376, 1749-024 Lisboa, Portugal
Interests: antibiotic resistance; multidrug-resistant isolates; genomic; food safety; one health
Special Issues, Collections and Topics in MDPI journals
Dr. Alexandra Nunes

E-Mail Website
Guest Editor
Portuguese National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
Interests: microbial genomics; bioinformatics; microbiology; antibiotic resistance; virulence; transcriptomics; infectious diseases; public health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Currently, antimicrobial resistance is one of the greatest threats worldwide, affecting not only humans and animals, but also the environment. Multidrug-resistant (MDR) bacteria, including zoonotic pathogens, can be exchanged between animals and humans mainly via direct contact, but also from the environment or food products. The public health consequences of zoonotic MDR bacteria are invariably difficult to assess as the epidemiology is highly complex, involving the spread of antimicrobial resistance and virulence determinants, consequently leading to the emergence and dissemination of more fitted bacterial clones. Understanding the transmission dynamics of these zoonotic bacteria is therefore of utmost importance, where the One Health approach is essential to manage MDR bacteria and to identify the drivers and determinants for their emergence and persistence. This is mandatory to establish proper control strategies.

This Special Issue seeks manuscript submissions that help to enlighten our understanding of how MDR bacteria in animals and humans are interconnected. Within the One Health framework, manuscripts concerning the following subtopics (though not exclusively) are especially encouraged:

  • Zoonotic bacteria and others;
  • Antimicrobial resistance;
  • Bacterial virulence traits/mechanisms;
  • Microbial genome evolution;
  • Pathogen adaptation;
  • Infectious outbreaks;
  • Sources of infection;
  • Animal–human transmission.

Dr. Sónia Ramos
Dr. Alexandra Nunes
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

  • one health
  • multidrug-resistant bacteria
  • virulence
  • animal–human transmission dynamics
  • microbial evolution
  • genomics
  • epidemiology
  • zoonotic outbreak

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Published Papers (4 papers)

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Research

12 pages, 1942 KiB  
Article
Global Variation in Escherichia coli mcr-1 Genes and Plasmids from Animal and Human Genomes Following Colistin Usage Restrictions in Livestock
by Biel Garcias, Mayra Alejandra Flores, Mercedes Fernández, William Monteith, Ben Pascoe, Samuel K. Sheppard, Marga Martín, Martí Cortey and Laila Darwich
Antibiotics 2024, 13(8), 759; https://doi.org/10.3390/antibiotics13080759 - 12 Aug 2024
Viewed by 1203
Abstract
Antimicrobial resistance (AMR) is a significant global health threat, with multidrug-resistant (MDR) bacterial clones becoming a major concern. Polymyxins, especially colistin, have reemerged as last-resort treatments for MDR Gram-negative infections. However, colistin use in livestock has spread mobile colistin resistance (mcr) [...] Read more.
Antimicrobial resistance (AMR) is a significant global health threat, with multidrug-resistant (MDR) bacterial clones becoming a major concern. Polymyxins, especially colistin, have reemerged as last-resort treatments for MDR Gram-negative infections. However, colistin use in livestock has spread mobile colistin resistance (mcr) genes, notably mcr-1, impacting human health. In consequence, its livestock use was banned in 2017, originating a natural experiment to study bacterial adaptation. The aim of this work was to analyse the changes in the mcr-1 genetic background after colistin restriction across the world. This study analyses 3163 Escherichia coli genomes with the mcr-1 gene from human and livestock hosts, mainly from Asia (n = 2621) and Europe (n = 359). Genetic characterisation identifies IncI2 (40.4%), IncX4 (26.7%), and multidrug-resistant IncHI2 (18.8%) as the most common plasmids carrying mcr-1. There were differences in plasmids between continents, with IncX4 (56.6%) being the most common in Europe, while IncI2 (44.8%) was predominant in Asia. Promoter variants related to reduced fitness costs and ISApl1 showed a distinct pattern of association that appears to be associated with adaptation to colistin restriction, which differed between continents. Thus, after the colistin ban, Europe saw a shift to specialised mcr-1 plasmids as IncX4, while ISApl1 decreased in Asia due to changes in the prevalence of the distinct promoter variants. These analyses illustrate the evolution of mcr-1 adaptation following colistin use restrictions and the need for region-specific strategies against AMR following colistin restrictions. Full article
(This article belongs to the Special Issue Antibiotic Resistance, Virulence Profile and Genomic Analysis among Multidrug-Resistant Bacteria Isolated from Humans and Animals)
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24 pages, 3155 KiB  
Article
Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing
by Menuka Bhandari, Jelmer W. Poelstra, Michael Kauffman, Binta Varghese, Yosra A. Helmy, Joy Scaria and Gireesh Rajashekara
Antibiotics 2023, 12(11), 1637; https://doi.org/10.3390/antibiotics12111637 - 18 Nov 2023
Cited by 7 | Viewed by 2876
Abstract
Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of [...] Read more.
Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans. Full article
(This article belongs to the Special Issue Antibiotic Resistance, Virulence Profile and Genomic Analysis among Multidrug-Resistant Bacteria Isolated from Humans and Animals)
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20 pages, 3588 KiB  
Article
Spread of Pseudomonas aeruginosa ST274 Clone in Different Niches: Resistome, Virulome, and Phylogenetic Relationship
by Gabriela Chichón, María López, María de Toro, Lidia Ruiz-Roldán, Beatriz Rojo-Bezares and Yolanda Sáenz
Antibiotics 2023, 12(11), 1561; https://doi.org/10.3390/antibiotics12111561 - 24 Oct 2023
Cited by 4 | Viewed by 1914
Abstract
Pseudomonas aeruginosa ST274 is an international epidemic high-risk clone, mostly associated with hospital settings and appears to colonize cystic fibrosis (CF) patients worldwide. To understand the relevant mechanisms for its success, the biological and genomic characteristics of 11 ST274-P. aeruginosa strains from clinical [...] Read more.
Pseudomonas aeruginosa ST274 is an international epidemic high-risk clone, mostly associated with hospital settings and appears to colonize cystic fibrosis (CF) patients worldwide. To understand the relevant mechanisms for its success, the biological and genomic characteristics of 11 ST274-P. aeruginosa strains from clinical and non-clinical origins were analyzed. The extensively drug-resistant (XDR/DTR), the non-susceptible to at least one agent (modR), and the lasR-truncated (by ISPsp7) strains showed a chronic infection phenotype characterized by loss of serotype-specific antigenicity and low motility. Furthermore, the XDR/DTR and modR strains presented low pigment production and biofilm formation, which were very high in the lasR-truncated strain. Their whole genome sequences were compared with other 14 ST274-P. aeruginosa genomes available in the NCBI database, and certain associations have been primarily detected: blaOXA-486 and blaPDC-24 genes, serotype O:3, exoS+/exoU− genotype, group V of type IV pili, and pyoverdine locus class II. Other general molecular markers highlight the absence of vqsM and pldA/tleS genes and the presence of the same mutational pattern in genes involving two-component sensor-regulator systems PmrAB and CreBD, exotoxin A, quorum-sensing RhlI, beta-lactamase expression regulator AmpD, PBP1A, or FusA2 elongation factor G. The proportionated ST274-P. aeruginosa results could serve as the basis for more specific studies focused on better antibiotic stewardship and new therapeutic developments. Full article
(This article belongs to the Special Issue Antibiotic Resistance, Virulence Profile and Genomic Analysis among Multidrug-Resistant Bacteria Isolated from Humans and Animals)
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13 pages, 490 KiB  
Article
Evaluation of the Ability to Form Biofilms in KPC-Producing and ESBL-Producing Klebsiella pneumoniae Isolated from Clinical Samples
by Carolina Sabença, Eliana Costa, Sara Sousa, Lillian Barros, Ana Oliveira, Sónia Ramos, Gilberto Igrejas, Carmen Torres and Patrícia Poeta
Antibiotics 2023, 12(7), 1143; https://doi.org/10.3390/antibiotics12071143 - 2 Jul 2023
Cited by 9 | Viewed by 2145
Abstract
The appearance of Klebsiella pneumoniae strains producing extended-spectrum β-lactamase (ESBL), and carbapenemase (KPC) has turned into a significant public health issue. ESBL- and KPC-producing K. pneumoniae’s ability to form biofilms is a significant concern as it can promote the spread of antibiotic [...] Read more.
The appearance of Klebsiella pneumoniae strains producing extended-spectrum β-lactamase (ESBL), and carbapenemase (KPC) has turned into a significant public health issue. ESBL- and KPC-producing K. pneumoniae’s ability to form biofilms is a significant concern as it can promote the spread of antibiotic resistance and prolong infections in healthcare facilities. A total of 45 K. pneumoniae strains were isolated from human infections. Antibiograms were performed for 17 antibiotics, ESBL production was tested by Etest ESBL PM/PML, a rapid test was used to detect KPC carbapenemases, and resistance genes were detected by PCR. Biofilm production was detected by the microtiter plate method. A total of 73% of multidrug resistance was found, with the highest resistance rates to ampicillin, trimethoprim–sulfamethoxazole, cefotaxime, amoxicillin-clavulanic acid, and aztreonam. Simultaneously, the most effective antibiotics were tetracycline and amikacin. blaCTX-M, blaTEM, blaSHV, aac(3)-II, aadA1, tetA, cmlA, catA, gyrA, gyrB, parC, sul1, sul2, sul3, blaKPC, blaOXA, and blaPER genes were detected. Biofilm production showed that 80% of K. pneumoniae strains were biofilm producers. Most ESBL- and KPC-producing isolates were weak biofilm producers (40.0% and 60.0%, respectively). There was no correlation between the ability to form stronger biofilms and the presence of ESBL and KPC enzymes in K. pneumoniae isolates. Full article
(This article belongs to the Special Issue Antibiotic Resistance, Virulence Profile and Genomic Analysis among Multidrug-Resistant Bacteria Isolated from Humans and Animals)
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