Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment

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: 15 October 2024 | Viewed by 2744

Special Issue Editors


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Associate Professor, Department of Microbiology/Zoonoses, School of Medicine, University of Crete, Heraklion, Crete, Greece
Interests: microbial pathogenesis; antibiotics; antimicrobial resistance; epidemiology of infectious diseases; microbiology and eco-epidemiology of zoonotic pathogens; food/water-borne pathogens; public health
Special Issues, Collections and Topics in MDPI journals

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Central Public Health Laboratory, National Public Health Organization, 16672 Vari, Greece
Interests: molecular epidemiology; HAI outbreak investigation; carbapenem and colistin resistance; COVID-19 molecular diagnostics; SARS-CoV-2 genomic surveillance; public health microbiology and epidemiology

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Guest Editor
Unit of Food, Water and Environment, Laboratory of Clinical Microbiology and Microbial Pathogenesis, University of Crete, Heraklion, 71110 Stavrakia, Crete, Greece
Interests: microbiology; public health; water-borne diseases; epidemiology; neural networks; infection; diagnosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is a serious threat to human and animal health, and its investigation needs a One Health approach from an integrated perspective in which human, animal, and environmental compartments are interconnected. There is a growing interest in the role of the environment in the selection, spread and transmission of AMR to humans. Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been suggested as emerging environmental contaminants and potential health threats. Several ARB and ARG sources have been recognized, which includes sewage water discharged from homes, hospitals, pharmaceutical manufacturing facilities, and animal feedlots. However, there are still gaps in reliable and efficient assessments of risks to human health from exposure to ARB and ARGs in the environment, as well as on programs and tools to systematically measure and record antimicrobial contamination and ARB in the environment. Filling these critical research gaps is a prerequisite for the development of mitigation strategies and public health measures to limit environmental contamination from antimicrobial residues and AMR organisms.

Therefore, this Special Issue welcomes collaborative submissions from different research fields that further study and clarify the risks for AMR associated with the environmental compartment, with special reference to distribution dynamics, sources and transmission risks of bacteria, and their antimicrobial resistance genes in the environment.

Dr. Anna Psaroulaki
Dr. Kyriaki Tryfinopoulou
Dr. Dimosthenis Chochlakis
Guest Editors

Manuscript Submission Information

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Keywords

  • antimicrobial resistance (AMR) and one health
  • AMR dissemination in the environment
  • risk assessment of AMR in environmental reservoirs (agroecosystems)
  • antibiotic resistant pathogenic and resident bacteria
  • antibiotic resistance gene (ARG) transfer
  • ARG quantification
  • AMR and food/feed chain
  • antibiotics in animals
  • agrochemicals
  • antibiotic residues

Published Papers (3 papers)

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Research

16 pages, 1031 KiB  
Article
Evolution of Resistance against Ciprofloxacin, Tobramycin, and Trimethoprim/Sulfamethoxazole in the Environmental Opportunistic Pathogen Stenotrophomonas maltophilia
by Luz Edith Ochoa-Sánchez, José Luis Martínez and Teresa Gil-Gil
Antibiotics 2024, 13(4), 330; https://doi.org/10.3390/antibiotics13040330 - 05 Apr 2024
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Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen that produces respiratory infections in immunosuppressed and cystic fibrosis patients. The therapeutic options to treat S. maltophilia infections are limited since it exhibits resistance to a wide variety of antibiotics such as β-lactams, aminoglycosides, tetracyclines, cephalosporins, macrolides, [...] Read more.
Stenotrophomonas maltophilia is an opportunistic pathogen that produces respiratory infections in immunosuppressed and cystic fibrosis patients. The therapeutic options to treat S. maltophilia infections are limited since it exhibits resistance to a wide variety of antibiotics such as β-lactams, aminoglycosides, tetracyclines, cephalosporins, macrolides, fluoroquinolones, or carbapenems. The antibiotic combination trimethoprim/sulfamethoxazole (SXT) is the treatment of choice to combat infections caused by S. maltophilia, while ceftazidime, ciprofloxacin, or tobramycin are used in most SXT-resistant infections. In the current study, experimental evolution and whole-genome sequencing (WGS) were used to examine the evolutionary trajectories of S. maltophilia towards resistance against tobramycin, ciprofloxacin, and SXT. The genetic changes underlying antibiotic resistance, as well as the evolutionary trajectories toward that resistance, were determined. Our results determine that genomic changes in the efflux pump regulatory genes smeT and soxR are essential to confer resistance to ciprofloxacin, and the mutation in the rplA gene is significant in the resistance to tobramycin. We identified mutations in folP and the efflux pump regulator smeRV as the basis of SXT resistance. Detailed and reliable knowledge of ciprofloxacin, tobramycin, and SXT resistance is essential for safe and effective use in clinical settings. Herein, we were able to prove once again the extraordinary ability that S. maltophilia has to acquire resistance and the importance of looking for alternatives to combat this resistance. Full article
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20 pages, 3575 KiB  
Article
Heterogeneous Antibiotic Resistance Gene Removal Impedes Evaluation of Constructed Wetlands for Effective Greywater Treatment
by Daniella Itzhari, Weitao Shuai, Erica M. Hartmann and Zeev Ronen
Antibiotics 2024, 13(4), 315; https://doi.org/10.3390/antibiotics13040315 - 29 Mar 2024
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Abstract
Microorganisms carrying antimicrobial resistance genes are often found in greywater. As the reuse of greywater becomes increasingly needed, it is imperative to determine how greywater treatment impacts antimicrobial resistance genes (ARGs). Using qPCR and SmartChip™ qPCR, we characterized ARG patterns in greywater microbial [...] Read more.
Microorganisms carrying antimicrobial resistance genes are often found in greywater. As the reuse of greywater becomes increasingly needed, it is imperative to determine how greywater treatment impacts antimicrobial resistance genes (ARGs). Using qPCR and SmartChip™ qPCR, we characterized ARG patterns in greywater microbial communities before, during, and after treatment by a recirculating vertical flow constructed wetland. In parallel, we examined the impact of greywater-treated irrigation on soil, including the occurrence of emerging micropollutants and the taxonomic and ARG compositions of microbial communities. Most ARGs in raw greywater are removed efficiently during the winter season, while some ARGs in the effluents increase in summer. SmartChip™ qPCR revealed the presence of ARGs, such as tetracycline and beta-lactam resistance genes, in both raw and treated greywater, but most abundantly in the filter bed. It also showed that aminoglycoside and vancomycin gene abundances significantly increased after treatment. In the irrigated soil, the type of water (potable or treated greywater) had no specific impact on the total bacterial abundance (16S rRNA gene). No overlapping ARGs were found between treated greywater and greywater-irrigated soil. This study indicates ARG abundance and richness increased after treatment, possibly due to the concentration effects of the filter beds. Full article
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11 pages, 507 KiB  
Article
Molecular Characterization of Escherichia coli Producing Extended-Spectrum ß-Lactamase and MCR-1 from Sick Pigs in a Greek Slaughterhouse
by Ermioni Avgere, Christos Zafeiridis, Kassandra A. Procter, Apostolos Beloukas and Panagiota Giakkoupi
Antibiotics 2023, 12(11), 1625; https://doi.org/10.3390/antibiotics12111625 - 14 Nov 2023
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Abstract
The first prospective surveillance of ESBL and colistin-resistant Escherichia coli recovered from sick pigs from a slaughterhouse in Central Greece aimed to investigate the spread of relevant genetic elements. In February 2021, 25 E. coli isolates were subjected to antimicrobial susceptibility testing using disk diffusion [...] Read more.
The first prospective surveillance of ESBL and colistin-resistant Escherichia coli recovered from sick pigs from a slaughterhouse in Central Greece aimed to investigate the spread of relevant genetic elements. In February 2021, 25 E. coli isolates were subjected to antimicrobial susceptibility testing using disk diffusion and broth microdilution techniques. PCR screening was conducted to identify ESBLs and mcr genes. Additional assays, encompassing mating-out procedures, molecular typing utilizing Pulsed-Field Gel Electrophoresis, multilocus sequence typing analysis, and plasmid typing, were also conducted. A 40% prevalence of ESBLs and an 80% prevalence of MCR-1 were identified, with a co-occurrence rate of 32%. The predominant ESBL identified was CTX-M-3, followed by SHV-12. Resistance to colistin, chloramphenicol, cotrimoxazol, and ciprofloxacin was detected in twenty (80%), fifteen (60%), twelve (48%), and four (16%) isolates, respectively. All blaCTX-M-3 harboring plasmids were conjugative, belonging to the incompatibility group IncI1, and approximately 50 kb in size. Those carrying blaSHV-12 were also conjugative, classified into incompatibility group IncI2, and approximately 70 kb in size. The mcr-1 genes were predominantly located on conjugative plasmids associated with the IncX4 incompatibility group. Molecular typing of the ten concurrent ESBL and MCR-1 producers revealed seven multilocus sequence types. The heterogeneous population of E. coli isolates carrying resistant genes on constant plasmids implies that the dissemination of resistance genes is likely facilitated by horizontal plasmid transfer. Full article
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