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Microorganisms
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Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic...
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Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading 2.0

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 7311

Special Issue Editor

Dr. Andrew Shelenkov

E-Mail Website
Guest Editor
Central Research Institute of Epidemiology, Moscow, Russia
Interests: bioinformatics; NGS; ESKAPE pathogens; genomic epidemiology; antibiotic resistance; antimicrobial peptides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue “Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading”

Antibiotic resistance acquisition by pathogenic and opportunistic bacteria has become a major problem worldwide, which was already being noticed as a global healthcare threat by the World Health Organization. The spread of multidrug-resistant bacteria, especially the ones producing extended-spectrum β-lactamases (ESBLs), represents a major challenge in clinical settings. However, the mechanisms of antibiotic resistance acquisition and spreading among different bacterial species cannot be easily revealed by the traditional phenotypic analyses. Whole-genome sequencing (short- and long-read) is currently attracting increased attention since it allows for accurately and rapidly obtain data regarding the presence of specific antibiotic resistance genes and their locations in a bacterial genome (chromosomal or plasmid). A plasmid reconstruction using long-read sequencing data can provide essential information regarding the mechanisms of antibiotic resistance acquisition and the methods of its spreading across different species and world regions.

For this Special Issue, we therefore invite you to contribute original research and review papers describing the application of the whole-genome sequencing of bacterial pathogens for revealing antimicrobial resistance genes, comparing phenotypic and genomic resistance profiles, reconstructing plasmids, performing epidemiological surveillance, and elucidating the mechanisms and/or methods of the spreading and acquisition of antimicrobial resistance. Novel computational approaches and pipelines for performing such investigations are particularly welcome.

Dr. Andrew Shelenkov
Guest Editor

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. Microorganisms 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 2700 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

  • whole genome sequencing
  • pathogenic bacteria
  • antibiotic resistance
  • genomic epidemiology
  • bioinformatics
  • antimicrobial resistance prediction
  • plasmid assembly

Published Papers (3 papers)

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Research

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15 pages, 4204 KiB  
Article
Gonococcal Genetic Island in the Global Neisseria gonorrhoeae Population: A Model of Genetic Diversity and Association with Resistance to Antimicrobials
by Dmitry Kravtsov, Dmitry Gryadunov and Boris Shaskolskiy
Microorganisms 2023, 11(6), 1547; https://doi.org/10.3390/microorganisms11061547 - 10 Jun 2023
Viewed by 1116
Abstract
The aim of this work was to study the genetic diversity of the gonococcal genetic island (GGI) responsible for the type IV secretion system (T4SS) and the association of a functionally active GGI with antimicrobial resistance. An analysis of the GGI in a [...] Read more.
The aim of this work was to study the genetic diversity of the gonococcal genetic island (GGI) responsible for the type IV secretion system (T4SS) and the association of a functionally active GGI with antimicrobial resistance. An analysis of the GGI in a sample of 14,763 genomes of N. gonorrhoeae isolates from the Pathogenwatch database collected in 1996–2019 from 68 countries was performed. A model of GGI’s genetic diversity that divides the global gonococcal population into fifty-one GGI clusters and three GGI superclusters based on the allele type of the traG gene and substitutions of the atlA and ych genes for eppA and ych1 has been proposed, reflecting differences among isolates in the T4SS functionality. The NG-MAST and MLST typing schemes (with accuracies of 91% and 83%, respectively) allowed the determination of both the presence of a GGI and the GGI cluster and, correspondingly, the structure of the GGI and the ability to secrete DNA. A statistically significant difference in the proportion of N. gonorrhoeae isolates resistant to ciprofloxacin, cefixime, tetracycline, and penicillin was found when comparing populations with a functional and a non-functional GGI. The presence of a functional GGI did not affect the proportion of azithromycin-resistant isolates. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading 2.0)
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16 pages, 2030 KiB  
Article
Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia
by Anna Egorova, Andrey Shelenkov, Konstantin Kuleshov, Nina Kulikova, Aleksey Chernyshkov, Igor Manzeniuk, Yulia Mikhaylova and Vasiliy Akimkin
Microorganisms 2023, 11(2), 347; https://doi.org/10.3390/microorganisms11020347 - 30 Jan 2023
Cited by 4 | Viewed by 1636
Abstract
Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis [...] Read more.
Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202–280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading 2.0)
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Review

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28 pages, 1973 KiB  
Review
Whole-Genome Sequencing-Based Resistome Analysis of Nosocomial Multidrug-Resistant Non-Fermenting Gram-Negative Pathogens from the Balkans
by Slavil Peykov and Tanya Strateva
Microorganisms 2023, 11(3), 651; https://doi.org/10.3390/microorganisms11030651 - 03 Mar 2023
Cited by 4 | Viewed by 2909
Abstract
Non-fermenting Gram-negative bacilli (NFGNB), such as Pseudomonas aeruginosa and Acinetobacter baumannii, are among the major opportunistic pathogens involved in the global antibiotic resistance epidemic. They are designated as urgent/serious threats by the Centers for Disease Control and Prevention and are part of [...] Read more.
Non-fermenting Gram-negative bacilli (NFGNB), such as Pseudomonas aeruginosa and Acinetobacter baumannii, are among the major opportunistic pathogens involved in the global antibiotic resistance epidemic. They are designated as urgent/serious threats by the Centers for Disease Control and Prevention and are part of the World Health Organization’s list of critical priority pathogens. Also, Stenotrophomonas maltophilia is increasingly recognized as an emerging cause for healthcare-associated infections in intensive care units, life-threatening diseases in immunocompromised patients, and severe pulmonary infections in cystic fibrosis and COVID-19 individuals. The last annual report of the ECDC showed drastic differences in the proportions of NFGNB with resistance towards key antibiotics in different European Union/European Economic Area countries. The data for the Balkans are of particular concern, indicating more than 80% and 30% of invasive Acinetobacter spp. and P. aeruginosa isolates, respectively, to be carbapenem-resistant. Moreover, multidrug-resistant and extensively drug-resistant S. maltophilia from the region have been recently reported. The current situation in the Balkans includes a migrant crisis and reshaping of the Schengen Area border. This results in collision of diverse human populations subjected to different protocols for antimicrobial stewardship and infection control. The present review article summarizes the findings of whole-genome sequencing-based resistome analyses of nosocomial multidrug-resistant NFGNBs in the Balkan countries. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading 2.0)
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