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Antibiotics
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Omics of Bacterial Pathogens Applied to Antibiotic Resistance: A One Health and...
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Omics of Bacterial Pathogens Applied to Antibiotic Resistance: A One Health and Host-Pathogen Interaction Approach

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 9771

Special Issue Editors

Prof. Dr. Siomar De Castro Soares

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Guest Editor
Department of Microbiology, Immunology, and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38025-180, Brazil
Interests: bioinformatics; reverse vaccinology; probiotic; immunoinformatics; next generation sequencing data analysis; pan genomics; metagenomics
Prof. Dr. Vasco Ariston De Carvalho Azevedo

E-Mail Website
Guest Editor
Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
Interests: bioinformatics; reverse vaccinology; probiotic; immunoinformatics; next generation sequencing data analysis; pan genomics; metagenomics
Special Issues, Collections and Topics in MDPI journals
Dr. Arun Kumar Jaiswal

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Guest Editor
Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
Interests: pangenomics; reverse vaccinology; drug-discovery; bioinformatics; pathogenomics
Dr. Sandeep Tiwari

E-Mail Website
Guest Editor
Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
Interests: bioinformatics; reverse vaccinology; probiotic; immunoinformatics; next generation sequencing data analysis; pan genomics; metagenomics
Dr. Flávia Figueira Aburjaile

E-Mail Website
Guest Editor
Veterinary School, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
Interests: bioinformatics; reverse vaccinology; probiotic; immunoinformatics; next generation sequencing data analysis; pan genomics; metagenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the advent of next-generation sequencing technologies, the number of genome projects created at genome online databases has increased exponentially, especially bacterial genomes. The high interest in these organisms is mainly due to their ubiquitous nature and their use in industry, agriculture, research, and many other areas. In this scenario, pathogenic bacteria deserve attention due to medical and veterinary importance and are now being highly explored in one health approaches. There are several applications of omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, and others, which may prove very useful in pangenomics, phylogenomics, whole-genome multi-locus sequence typing, reverse vaccinology, subtractive genomics, genome plasticity (focused on pathogenicity and resistance islands), protein–protein interaction, and metabolic pathway prediction. Additionally, those approaches are being constantly explored using several artificial intelligence strategies, such as machine learning. This Special Issue seeks manuscript submissions that further our understanding of host–pathogen interaction, including, but not limited to, the identification of virulence factors and resistance-related genes in pathogenicity and resistance islands in pangenomics approaches, the identification of new vaccine and drug targets using reverse vaccinology and subtractive genomics to circumvent the increasing problem of multi-drug resistance, and protein–protein interaction and metabolic pathway prediction together with analyses of biofilm formation. Submissions on one health, genomic islands, and pangenomics approaches mainly focused on antibiotic resistance are especially encouraged.

Prof. Dr. Siomar De Castro Soares
Prof. Dr. Vasco Ariston De Carvalho Azevedo
Dr. Sandeep Tiwari
Dr. Arun Kumar Jaiswal
Dr. Flávia Figueira Aburjaile
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

  • omics
  • pathogenic bacteria
  • pangenomics
  • one health
  • virulence factors
  • antibiotic resistance
  • reverse vaccinology
  • genomics
  • transcriptomics
  • proteomics

Published Papers (4 papers)

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Research

18 pages, 2359 KiB  
Article
Genomic Characterization of Aeromonas veronii Provides Insights into Taxonomic Assignment and Reveals Widespread Virulence and Resistance Genes throughout the World
by José Cleves da Silva Maia, Gabriel Amorim de Albuquerque Silva, Letícia Stheffany de Barros Cunha, Gisele Veneroni Gouveia, Aristóteles Góes-Neto, Bertram Brenig, Fabrício Almeida Araújo, Flávia Aburjaile, Rommel Thiago Jucá Ramos, Siomar Castro Soares, Vasco Ariston de Carvalho Azevedo, Mateus Matiuzzi da Costa and João José de Simoni Gouveia
Antibiotics 2023, 12(6), 1039; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12061039 - 11 Jun 2023
Cited by 2 | Viewed by 1560
Abstract
Aeromonas veronii is a Gram-negative bacterial species that causes disease in fish and is nowadays increasingly recurrent in enteric infections of humans. This study was performed to characterize newly sequenced isolates by comparing them with complete genomes deposited at the NCBI (National Center [...] Read more.
Aeromonas veronii is a Gram-negative bacterial species that causes disease in fish and is nowadays increasingly recurrent in enteric infections of humans. This study was performed to characterize newly sequenced isolates by comparing them with complete genomes deposited at the NCBI (National Center for Biotechnology Information). Nine isolates from fish, environments, and humans from the São Francisco Valley (Petrolina, Pernambuco, Brazil) were sequenced and compared with complete genomes available in public databases to gain insight into taxonomic assignment and to better understand virulence and resistance profiles of this species within the One Health context. One local genome and four NCBI genomes were misidentified as A. veronii. A total of 239 virulence genes were identified in the local genomes, with most encoding adhesion, motility, and secretion systems. In total, 60 genes involved with resistance to 22 classes of antibiotics were identified in the genomes, including mcr-7 and cphA. The results suggest that the use of methods such as ANI is essential to avoid misclassification of the genomes. The virulence content of A. veronii from local isolates is similar to those complete genomes deposited at the NCBI. Genes encoding colistin resistance are widespread in the species, requiring greater attention for surveillance systems. Full article
(This article belongs to the Special Issue Omics of Bacterial Pathogens Applied to Antibiotic Resistance: A One Health and Host-Pathogen Interaction Approach)
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21 pages, 3738 KiB  
Article
Comparative Genomics of Pseudomonas aeruginosa Strains Isolated from Different Ecological Niches
by Jessica Gómez-Martínez, Rosa del Carmen Rocha-Gracia, Elena Bello-López, Miguel Angel Cevallos, Miguel Castañeda-Lucio, Yolanda Sáenz, Guadalupe Jiménez-Flores, Gerardo Cortés-Cortés, Alma López-García and Patricia Lozano-Zarain
Antibiotics 2023, 12(5), 866; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12050866 - 7 May 2023
Cited by 5 | Viewed by 2509
Abstract
The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, [...] Read more.
The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. blaOXA-488 (a variant of blaOXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches. Full article
(This article belongs to the Special Issue Omics of Bacterial Pathogens Applied to Antibiotic Resistance: A One Health and Host-Pathogen Interaction Approach)
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15 pages, 2066 KiB  
Article
Co-Harboring of Beta-Lactamases and mcr-1 Genes in Escherichia coli and Klebsiella pneumoniae from Healthy Carriers and Backyard Animals in Rural Communities in Ecuador
by Carlos Bastidas-Caldes, Emily Cisneros-Vásquez, Antonella Zambrano, Andrea Mosquera-Maza, William Calero-Cáceres, Joaquín Rey, Yoshimasa Yamamoto, Mayumi Yamamoto, Manuel Calvopiña and Jacobus H. de Waard
Antibiotics 2023, 12(5), 856; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12050856 - 5 May 2023
Cited by 4 | Viewed by 2291
Abstract
Few studies have addressed drug resistance of Enterobacterales in rural communities in developing countries. This study aimed to determine the coexistence of extended-spectrum β-lactamase (ESBL) and carbapenemase genes in Escherichia coli and Klebsiella pneumoniae strains carrying the mcr-1 gene in rural communities in [...] Read more.
Few studies have addressed drug resistance of Enterobacterales in rural communities in developing countries. This study aimed to determine the coexistence of extended-spectrum β-lactamase (ESBL) and carbapenemase genes in Escherichia coli and Klebsiella pneumoniae strains carrying the mcr-1 gene in rural communities in Ecuador from healthy humans and their backyard animals. Sixty-two strains, thirty E. coli and thirty-two K. pneumoniae strains carrying the mcr-1 gene were selected from a previous study. PCR were performed for the presence of ESBLs and carbapenemase genes. The strains were further characterized, and the genetic relationship was studied with multi-locus sequencing typing (MLST) of seven housekeeping genes. Fifty-nine of the sixty-two mcr-1 isolates (95%) harbored at least on β-lactam resistance gene. The most prevalent ESBL genes were the blaTEM genes (present in in 80% of the E. coli strains) and the blaSHV gene (present in 84% of the K. pneumoniae strains). MSLT analysis revealed 28 different sequence types (ST); 15 for E. coli and 12 for K. pneumoniae, with most ST never described in humans and animals. The coexistence of mcr-1 and β-lactams resistant genes in E. coli and K. pneumoniae strains is alarming and threatens the efficacy of last-resort antibiotics. Our findings highlight backyard animals as a reservoir of mcr-1/β-lactams resistant genes. Full article
(This article belongs to the Special Issue Omics of Bacterial Pathogens Applied to Antibiotic Resistance: A One Health and Host-Pathogen Interaction Approach)
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21 pages, 29967 KiB  
Article
Insights into the Vibrio Genus: A One Health Perspective from Host Adaptability and Antibiotic Resistance to In Silico Identification of Drug Targets
by Pedro Henrique Marques, Lígia Carolina da Silva Prado, Andrei Giacchetto Felice, Thaís Cristina Vilela Rodrigues, Ulisses de Padua Pereira, Arun Kumar Jaiswal, Vasco Azevedo, Carlo José Freire Oliveira and Siomar Soares
Antibiotics 2022, 11(10), 1399; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics11101399 - 12 Oct 2022
Cited by 2 | Viewed by 2521
Abstract
The genus Vibrio comprises an important group of ubiquitous bacteria of marine systems with a high infectious capacity for humans and fish, which can lead to death or cause economic losses in aquaculture. However, little is known about the evolutionary process that led [...] Read more.
The genus Vibrio comprises an important group of ubiquitous bacteria of marine systems with a high infectious capacity for humans and fish, which can lead to death or cause economic losses in aquaculture. However, little is known about the evolutionary process that led to the adaptation and colonization of humans and also about the consequences of the uncontrollable use of antibiotics in aquaculture. Here, comparative genomics analysis and functional gene annotation showed that the species more related to humans presented a significantly higher amount of proteins associated with colonization processes, such as transcriptional factors, signal transduction mechanisms, and iron uptake. In comparison, those aquaculture-associated species possess a much higher amount of resistance-associated genes, as with those of the tetracycline class. Finally, through subtractive genomics, we propose seven new drug targets such as: UMP Kinase, required to catalyze the phosphorylation of UMP into UDP, essential for the survival of bacteria of this genus; and, new natural molecules, which have demonstrated high affinity for the active sites of these targets. These data also suggest that the species most adaptable to fish and humans have a distinct natural evolution and probably undergo changes due to anthropogenic action in aquaculture or indiscriminate/irregular use of antibiotics. Full article
(This article belongs to the Special Issue Omics of Bacterial Pathogens Applied to Antibiotic Resistance: A One Health and Host-Pathogen Interaction Approach)
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