Metagenomics for Surveillance of Pathogens and/or Antimicrobial Resistance

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: 10 July 2024 | Viewed by 1567

Special Issue Editor


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Guest Editor
Laboratory of Bioinformatics and Genetics of Microorganisms, Institute of Biological Sciences, Federal University of Pará (UFPA), Belem 66075-110, PA, Brazil
Interests: bioinformatics; environmental genomics; environmental surveillance; Internet of Things (IoT); software development

Special Issue Information

Dear Colleagues,

Metagenomics has revolutionized the field of surveillance for pathogens and antimicrobial resistance due to its ability to analyze complex microbial communities directly from environmental or clinical samples. Metagenomics offers a powerful bioprospection tool for understanding and monitoring the spread of pathogens and the emergence of antimicrobial resistance. In this Special Issue, we aim to highlight the latest advancements and applications of metagenomics in surveillance, including new tools or approaches, shedding light on its potential for improving public health outcomes.

In this Special Issue, we invite contributions that showcase the diverse applications of metagenomics in surveillance, including but not limited to the following:

  1. Surveillance of pathogens: highlighting the use of metagenomics for monitoring outbreaks, identifying the sources of infections, and tracking the transmission dynamics of pathogens;
  2. Environmental surveillance: exploring how metagenomics can be utilized to monitor the presence and spread of pathogens and/or antimicrobial resistance in environmental samples, such as water and soil;
  3. Clinical applications: showcasing the use of metagenomics in clinical settings for diagnosing infections, guiding treatment decisions, and monitoring the effectiveness of interventions;
  4. The One Health approach: demonstrating how metagenomics can bridge the gap between human, animal, and environmental health by providing a holistic understanding of the dynamics of pathogens due to anthropogenic impacts and antimicrobial resistance.

We encourage researchers from various disciplines, including microbiology, genomics, bioinformatics, epidemiology, and public health, to contribute their original research, reviews, and other scholarly works to this Special Issue. We hope that this collection of articles will foster collaborations, inspire new research directions, and contribute to the development of innovative approaches for safeguarding public health.

Dr. Rommel Thiago Jucá Ramos
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. 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
  • metagenomics
  • pathogen
  • environmental surveillance
  • clinical
  • one health

Published Papers (1 paper)

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Research

15 pages, 1136 KiB  
Article
Insights into the Microbiome and Antibiotic Resistance Genes from Hospital Environmental Surfaces: A Prime Source of Antimicrobial Resistance
by Alfizah Hanafiah, Asif Sukri, Hamidah Yusoff, Chia Sing Chan, Nur Hazlin Hazrin-Chong, Sharifah Azura Salleh and Hui-min Neoh
Antibiotics 2024, 13(2), 127; https://doi.org/10.3390/antibiotics13020127 - 26 Jan 2024
Viewed by 1331
Abstract
Hospital environmental surfaces are potential reservoirs for transmitting hospital-associated pathogens. This study aimed to profile microbiomes and antibiotic resistance genes (ARGs) from hospital environmental surfaces using 16S rRNA amplicon and metagenomic sequencing at a tertiary teaching hospital in Malaysia. Samples were collected from [...] Read more.
Hospital environmental surfaces are potential reservoirs for transmitting hospital-associated pathogens. This study aimed to profile microbiomes and antibiotic resistance genes (ARGs) from hospital environmental surfaces using 16S rRNA amplicon and metagenomic sequencing at a tertiary teaching hospital in Malaysia. Samples were collected from patient sinks and healthcare staff counters at surgery and orthopaedic wards. The samples’ DNA were subjected to 16S rRNA amplicon and shotgun sequencing to identify bacterial taxonomic profiles, antibiotic resistance genes, and virulence factor pathways. The bacterial richness was more diverse in the samples collected from patient sinks than those collected from staff counters. Proteobacteria and Verrucomicrobia dominated at the phylum level, while Bacillus, Staphylococcus, Pseudomonas, and Acinetobacter dominated at the genus level. Staphylococcus epidermidis and Staphylococcus aureus were prevalent on sinks while Bacillus cereus dominated the counter samples. The highest counts of ARGs to beta-lactam were detected, followed by ARGs against fosfomycin and cephalosporin. We report the detection of mcr-10.1 that confers resistance to colistin at a hospital setting in Malaysia. The virulence gene pathways that aid in antibiotic resistance gene transfer between bacteria were identified. Environmental surfaces serve as potential reservoirs for nosocomial infections and require mitigation strategies to control the spread of antibiotic resistance bacteria. Full article
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