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Microorganisms
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Bacterial Antibiotic Resistance, Second Edition
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Bacterial Antibiotic Resistance, Second Edition

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 6203

Special Issue Editor

Dr. Giuseppe Mancuso

E-Mail Website
Guest Editor
Department of Adult and Developmental Human Pathology, University of Messina, 98122 Messina, Italy
Interests: immunology of infectious diseases; innate immunity; macrophage; inflammation; macrophage biology; clinical immunology; epidemiology; sepsis; cytokines; cell culture; immunology; microbiology; monoclonal antibodies; infectious diseases; monocytes; neonatal sepsis; vaccines; antibodiesimmunity; antigen; toll-like receptors; interferon; streptococcus agalactiae; tnf; flow cytometry; il-6; interferon-gamma; phage display
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

This Special Issue is the continuation of our previous Special Issue entitled “Bacterial Antibiotic Resistance”.

Antibiotics have made it possible to treat bacterial infections. Currently, at least 700,000 people worldwide die each year due to antimicrobial resistance (AMR). Without novel and enhanced treatments, the World Health Organization (WHO) predicts that this number could rise to 10 million by 2050, highlighting a primary health concern.

This Special Issue welcomes the submission of articles that provide new insights into bacterial antibiotic resistance and control. We look forward to receiving contributions in the form of reviews, original research, and communications that address the following topics:

  • Mechanisms of bacterial antibiotic resistance.
  • How bacteria acquire resistance.
  • The main antibiotic-resistant pathogens.

Dr. Giuseppe Mancuso
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

  • bacteria
  • antibiotics
  • antibiotic resistance

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Related Special Issue

Published Papers (5 papers)

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Research

18 pages, 1445 KiB  
Article
Antibiotic Resistance and Virulence Determinants of Pseudomonas aeruginosa Isolates Cultured from Hydrocarbon-Contaminated Environmental Samples
by Chioma Lilian Ozoaduche, Balázs Libisch, Daniel Itoro, Iyore Blessing Idemudia, Katalin Posta and Ferenc Olasz
Microorganisms 2025, 13(3), 688; https://doi.org/10.3390/microorganisms13030688 - 19 Mar 2025
Viewed by 263
Abstract
Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a [...] Read more.
Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a P. aeruginosa isolate cultured from a hydrocarbon-contaminated soil sample from Ogoniland, Nigeria, and to compare its characteristics with P. aeruginosa isolates cultured worldwide from hydrocarbon-contaminated environments or from clinical samples. Using the ResFinder reference database, a catB7 chloramphenicol acetyltransferase gene, an ampC-type PDC β-lactamase gene, and an OXA-50 type β-lactamase gene were identified in all P. aeruginosa strains analyzed in this study. In some of these P. aeruginosa strains, loss-of-function mutations were detected in the regulatory genes mexR, nalC, or nalD, predicting an efflux-mediated acquired antibiotic-resistance mechanism. Several P. aeruginosa sequence types that were associated with oil-contaminated environments have also been cultured from human clinical samples worldwide, including sequence types ST532, ST267, ST244, and ST1503. Our findings also indicate that environmental P. aeruginosa may serve as the source of human infections, warranting further studies from a One Health perspective about the application of P. aeruginosa for the in situ bioremediation of hydrocarbon-contaminated sites. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)
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15 pages, 5282 KiB  
Article
Humus Soil Inhibits Antibiotic Resistance Gene Rebound in Swine Manure Composting by Modulating Microecological Niches
by Xiaoxia Hao, Mengting Chen, Weiping Sang, Linyuan Shen, Li Zhu, Dongmei Jiang and Lin Bai
Microorganisms 2025, 13(3), 571; https://doi.org/10.3390/microorganisms13030571 - 3 Mar 2025
Viewed by 533
Abstract
Aerobic composting is widely used for the degradation of organic matter, simultaneously reducing the presence of antibiotic resistance genes (ARGs) in swine manure. However, the phenomenon of abundance rebound or even enrichment of ARGs is still a problem. The effect and mechanism of [...] Read more.
Aerobic composting is widely used for the degradation of organic matter, simultaneously reducing the presence of antibiotic resistance genes (ARGs) in swine manure. However, the phenomenon of abundance rebound or even enrichment of ARGs is still a problem. The effect and mechanism of humus soil (Hs) on ARG reduction by adding it into the piles (0% for the control group (CK); 10% for S1 group; 20% for S2 group; and 30% for S3 group) after the thermophilic phase of composting was investigated. The results indicated that Hs promoted organic matter degradation and nitrogen loss. During days 15–36, the greatest reduction of 69.91% in total ARG abundance was observed in S2, while the abundance rebounded by 222.75% in CK and decreased only 13.71% in S3. With the 20% Hs addition, 85.42% abundance reduction for mobile genetic elements (MGEs) and 100% removal rates for aadA5, aadA9, sul1, sul2, and tetX were achieved. Moreover, the addition of Hs immediately changed the bacterial community structure of the substrate and varied the bacterial community successional direction in the treatments. Additionally, significantly positive correlations (|r| > 0.6; p < 0.05) were found between the top 20 genera and ARGs. The potential host bacteria for ARGs changed from Lactobacillus, Fermentimonas, Pusillimonas, and Ruminofilibacter in CK to Lactobacillus, Romboutsia, and Streptococcus in S2, highlighting the shift and reduction in host bacteria driven by Hs, which, in turn, influenced the abundance variations in ARGs. This study verified the feasibility of inhibiting the rebound of ARG abundance effectively by influencing the microecological niche in the pile, offering an approach for promoting a reduction in ARGs in animal wastes. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)
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16 pages, 2642 KiB  
Article
Determining the Effect of Varied Proportions of Cohort Administered Tulathromycin at Arrival on Nasopharyngeal Microbiota and Performance Characteristics in Yearling Steers in the First 56 Days on Feed
by Blaine T. Johnson, Brad J. White, Raghavendra G. Amachawadi, Michael D. Kleinhenz, Jaymelynn K. Farney, Teresa D. Shippy and Robert L. Larson
Microorganisms 2024, 12(12), 2512; https://doi.org/10.3390/microorganisms12122512 - 5 Dec 2024
Viewed by 1079
Abstract
Metaphylaxis or treating the entire population of cattle at arrival with an antimicrobial has been studied extensively in the cattle industry; however, little information is available on the impacts of treating only a proportion of the population with antimicrobials at arrival. The study [...] Read more.
Metaphylaxis or treating the entire population of cattle at arrival with an antimicrobial has been studied extensively in the cattle industry; however, little information is available on the impacts of treating only a proportion of the population with antimicrobials at arrival. The study objective was to determine potential associations between the proportion of animals in a pen treated with antimicrobial therapy with pen performance and nasopharyngeal microbiome. Yearling steers (n = 160) were randomly allocated to study pens (n = 40) and pens were systematically randomized to one of two antimicrobial treatments (META: all four head received tulathromycin; MIXED: two of four head randomly selected to receive tulathromycin). The study was conducted in conjunction with an essential oil feeding trial. Deep nasal pharyngeal (DNP) swabs were collected from every steer at Days 0, 14, 28, and 56. All DNP swabs were individually cultured for Pasteurella multocida and Mannheimia haemolytica. Samples of DNA were extracted from DNP swabs, pooled by pen, and analyzed by metagenomic shotgun sequencing to compare nasopharyngeal microbiome composition and quantity of resistance genes between test groups. Neither antimicrobial nor essential oil treatment groups had any significant associations with performance or DNP microbiome. Sampling day was significantly associated with alpha and beta diversity at the species level. Shannon’s diversity and Inverse Simpson diversity were significantly lower on Day 14 versus both Day 0 and Day 56. These data indicated a shift in microbial populations across study days; however, the microbiome diversity and relative abundance were not significantly different between antimicrobial treatment groups. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)
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17 pages, 557 KiB  
Article
In-Vitro Antimicrobial Activities of Grape Seed, Green Tea, and Rosemary Phenolic Extracts Against Liver Abscess Causing Bacterial Pathogens in Cattle
by Harith M. Salih, Raghavendra G. Amachawadi, Qing Kang, Yonghui Li and Tiruvoor G. Nagaraja
Microorganisms 2024, 12(11), 2291; https://doi.org/10.3390/microorganisms12112291 - 11 Nov 2024
Viewed by 1526
Abstract
Liver abscesses, which occur in finishing cattle, are of significant economic concern to the feedlot industry. The causative agents include both Fusobacterium necrophorum subspecies (F. necrophorum and F. funduliforme), Trueperella pyogenes (T. pyogenes), and Salmonella enterica serotype Lubbock (S. [...] Read more.
Liver abscesses, which occur in finishing cattle, are of significant economic concern to the feedlot industry. The causative agents include both Fusobacterium necrophorum subspecies (F. necrophorum and F. funduliforme), Trueperella pyogenes (T. pyogenes), and Salmonella enterica serotype Lubbock (S. Lubbock). Tylosin, a macrolide antibiotic, is supplemented in the feed to reduce liver abscesses. However, due to the concern with emergence of antimicrobial resistance, the antimicrobial activities of the plant-based phenolic compounds could be an antibiotic alternative to control liver abscesses. We investigated the inhibitory activities of phenolic compounds extracted from grape seed, green tea, and rosemary on liver-abscess-causing bacterial pathogens. Total phenolic content was determined spectrophotometrically. Anaerobic Brain–Heart Infusion broth (for Fusobacterium) and Muller–Hinton broth (for S. enterica and T. pyogenes) with phenolic extracts at 0, 0.1, 1, and 2 mg/mL were prepared. Growth was measured at 0, 12, 24 and 48 h by determining bacterial concentrations. A micro-broth dilution method was used to quantify the inhibition. Grape seed and green tea phenolics inhibited growth of both Fusobacterium subspecies, T. pyogenes and S. enterica. Green tea at 1 mg/mL concentration was more effective in inhibiting the growth of Fusobacterium when compared to grape seed and rosemary. Green tea at 2 mg/mL was more effective than at 1 mg/mL against Salmonella. The inhibitory effect was dose-dependent, which was consistent across all strains within the same bacterial species. The phenolic extracts were inhibitory against T. pyogenes with minimum inhibitory concentration ranging from 6.25 to 12.5 µg/mL. Among the phenolic extracts tested, green tea showed the most potent activity, suggesting its strong potential as a natural alternative to conventional antibiotics. Plant-based phenolic compounds supplemented in the feed may have the potential to control liver abscesses. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)
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16 pages, 2314 KiB  
Article
How Gut Microbiome Perturbation Caused by Antibiotic Pre-Treatments Affected the Conjugative Transfer of Antimicrobial Resistance Genes
by Gokhan Yilmaz, Maria Chan, Calvin Ho-Fung Lau, Sabrina Capitani, Mingsong Kang, Philippe Charron, Emily Hoover, Edward Topp and Jiewen Guan
Microorganisms 2024, 12(11), 2148; https://doi.org/10.3390/microorganisms12112148 - 25 Oct 2024
Cited by 1 | Viewed by 1620
Abstract
The global spread of antimicrobial resistance genes (ARGs) poses a significant threat to public health. While antibiotics effectively treat bacterial infections, they can also induce gut dysbiosis, the severity of which varies depending on the specific antibiotic treatment used. However, it remains unclear [...] Read more.
The global spread of antimicrobial resistance genes (ARGs) poses a significant threat to public health. While antibiotics effectively treat bacterial infections, they can also induce gut dysbiosis, the severity of which varies depending on the specific antibiotic treatment used. However, it remains unclear how gut dysbiosis affects the mobility and dynamics of ARGs. To address this, mice were pre-treated with streptomycin, ampicillin, or sulfamethazine, and then orally inoculated with Salmonella enterica serovar Typhimurium and S. Heidelberg carrying a multi-drug resistance IncA/C plasmid. The streptomycin pre-treatment caused severe microbiome perturbation, promoting the high-density colonization of S. Heidelberg and S. Typhimurium, and enabling an IncA/C transfer from S. Heidelberg to S. Typhimurium and a commensal Escherichia coli. The ampicillin pre-treatment induced moderate microbiome perturbation, supporting only S. Heidelberg colonization and the IncA/C transfer to commensal E. coli. The sulfamethazine pre-treatment led to mild microbiome perturbation, favoring neither Salmonella spp. colonization nor a conjugative plasmid transfer. The degree of gut dysbiosis also influenced the enrichment or depletion of the ARGs associated with mobile plasmids or core commensal bacteria, respectively. These findings underscore the significance of pre-existing gut dysbiosis induced by various antibiotic treatments on ARG dissemination and may inform prudent antibiotic use practices. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)
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