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Antibiotics
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Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance...
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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: closed (31 December 2024) | Viewed by 10801

Special Issue Editors

Dr. Anna Psaroulaki

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Guest Editor
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
Dr. Kyriaki Tryfinopoulou

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Guest Editor
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
Dr. Dimosthenis Chochlakis

E-Mail Website
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

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 (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

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Published Papers (7 papers)

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Research

14 pages, 2941 KiB  
Article
High Antimicrobial Susceptibility of Cloacal Enterococci and Escherichia coli from Free-Living Dalmatian and Great White Pelicans with Detection of Cefotaximase CTX-M-15 Producing Escherichia coli ST69
by Teresa Cardona-Cabrera, Sandra Martínez-Álvarez, Carmen González-Azcona, Carlos Javier Gijón-García, Olga Alexandrou, Giorgos Catsadorakis, Panagiotis Azmanis, Carmen Torres and Ursula Höfle
Antibiotics 2025, 14(1), 83; https://doi.org/10.3390/antibiotics14010083 - 14 Jan 2025
Viewed by 629
Abstract
Background/Objectives: In 2022, an outbreak of H5N1 highly pathogenic avian influenza (HPAI) killed 60% of the largest breeding colony of Dalmatian pelicans (DPs) in the world at Mikri Prespa Lake (Greece), prompting a multidisciplinary study on HPAI and other pathogens. This study determines [...] Read more.
Background/Objectives: In 2022, an outbreak of H5N1 highly pathogenic avian influenza (HPAI) killed 60% of the largest breeding colony of Dalmatian pelicans (DPs) in the world at Mikri Prespa Lake (Greece), prompting a multidisciplinary study on HPAI and other pathogens. This study determines the antimicrobial resistance rates of cloacal enterococci and Escherichia coli in DPs. Methods: Fifty-two blood and cloacal swab samples were collected from 31 nestlings (20 DP/11 great white pelicans) hatched after the H5N1 outbreak at the Prespa colony and 21 subadult/adult DPs captured at a spring migration stopover. The swabs were inoculated in non-selective and chromogenic-selective media. Identification was performed using MALDI-TOF, and antimicrobial susceptibility was tested. The genetic content was characterized using PCR and sequencing, and the clonality of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates was characterized using Multilocus Sequence Typing. Results: Twenty-eight non-repetitive E. coli and 45 enterococci isolates were recovered in non-selective media; most of them were susceptible to all antibiotics tested (85.7% E. coli/91.1% enterococci). Three of the fifty-two samples (6%, all adults) contained ESBL-E. coli isolates (detected in chromogenic ESBL plates), all carrying the blaCTX-M-15 gene and belonging to the lineage ST69. Conclusions: Despite the susceptibility of most fecal E. coli and enterococci isolates to all antibiotics tested, the finding that E. coli of lineage ST69 carry blaCTX-M-15 is of concern. This high-risk clone needs further investigation to elucidate its primary sources and address the growing threat of antimicrobial resistance from an integrated “One Health” perspective. Furthermore, it is imperative to study the potential impacts of ESBL-E. coli on the endangered DP further. Full article
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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14 pages, 4490 KiB  
Article
Local Electric Field-Incorporated In-Situ Copper Ions Eliminating Pathogens and Antibiotic Resistance Genes in Drinking Water
by Ruiqing Li, Haojie Dai, Wei Wang, Rulin Peng, Shenbo Yu, Xueying Zhang, Zheng-Yang Huo, Qingbin Yuan and Yi Luo
Antibiotics 2024, 13(12), 1161; https://doi.org/10.3390/antibiotics13121161 - 2 Dec 2024
Viewed by 1003
Abstract
Background/Objectives: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous [...] Read more.
Background/Objectives: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous chemical dosing, the spread of antibiotic resistance genes (ARGs), and intensive energy consumption. Methods: Here, we perform a simultaneous elimination of pathogens and ARGs in drinking water using local electric fields and in-situ generated trace copper ions (LEF-Cu) without external chemical dosing. A 100-μm thin copper wire placed in the center of a household water pipe can generate local electric fields and trace copper ions near its surface after an external low voltage is applied. Results: The local electric field rapidly damages the outer structure of microorganisms through electroporation, and the trace copper ions can effectively permeate the electroporated microorganisms, successfully damaging their nucleic acids. The LEF-Cu disinfection system achieved complete inactivation (>6 log removal) of Escherichia coli O157:H7, Pseudomonas aeruginosa PAO1, and bacteriophage MS2 in drinking water at 2 V for 2 min, with low energy consumption (10−2 kWh/m3). Meanwhile, the system effectively damages both intracellular (0.54~0.64 log) and extracellular (0.5~1.09 log) ARGs and blocks horizontal gene transfer. Conclusions: LEF-Cu disinfection holds promise for preventing horizontal gene transfer and providing safe drinking water for household applications. Full article
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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9 pages, 810 KiB  
Article
Antimicrobial Resistance Genes in Legionella from Artificial Water Systems: Findings from a Two-Year Study
by Bernardo Beirão Pereira, Mário Marrafa, Carolina Cruz, Lúcia Rodrigues, Filipa Nunes, Silvia Monteiro, Ricardo Santos, Rui Neves Carneiro, Célia Neto, Joana Aguilar, Nuno Rafael Ferreiro, Margarida Passanha, Gonçalo Candeias, Aida Fernandes, Paulo Paixão and Maria Jesus Chasqueira
Antibiotics 2024, 13(12), 1121; https://doi.org/10.3390/antibiotics13121121 - 23 Nov 2024
Viewed by 927
Abstract
Background: Legionella species are the causative agent of Legionnaires’ disease and, as ubiquitous waterborne bacteria, are prone to antimicrobial resistance gene (ARG) acquisition and dissemination due to the antimicrobial contamination of natural environments. Given the potential health risks associated with ARGs, it is [...] Read more.
Background: Legionella species are the causative agent of Legionnaires’ disease and, as ubiquitous waterborne bacteria, are prone to antimicrobial resistance gene (ARG) acquisition and dissemination due to the antimicrobial contamination of natural environments. Given the potential health risks associated with ARGs, it is crucial to assess their presence in the Legionella population. Methods: The ARGs lpeAB and tet56 were detected in 348 samples, isolates, and DNA extracts using conventional PCR. In a subset of lpeAB-positive isolates, azithromycin (AZT) MIC values were obtained using the EUCAST protocol and LpeAB activity was evaluated through an efflux pump inhibition assay. Results: The lpeAB gene was found in 19% (66/348) of samples, with higher detection rates in the L. pneumophila and L. pneumophila sg1 subgroups, at 30% and 41%, respectively. A positive association between lpeAB and L. pneumophila sg1 was found. The MIC values of the lpeAB-positive isolates ranged from 0.064 to 2 mg/L. LpeAB inhibition resulted in 2- and 4-fold MIC reductions in 10 of the 13 isolates analyzed. One sample each of L. longbeacheae and L. bozemanae was found to possess the tet56 gene. Conclusions: The lpeAB gene is predominant in L. pneumophila sg1. A few isolates with the lpeAB gene exhibited MIC values below the EUCAST tentative highest MIC values for wild-type isolates. Expanding ARG monitoring in Legionella is essential to assess the public health risk of Legionnaires’ disease. Full article
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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21 pages, 1520 KiB  
Article
On-Site Inactivation for Disinfection of Antibiotic-Resistant Bacteria in Hospital Effluent by UV and UV-LED
by Takashi Azuma, Masaru Usui, Tomohiro Hasei and Tetsuya Hayashi
Antibiotics 2024, 13(8), 711; https://doi.org/10.3390/antibiotics13080711 - 29 Jul 2024
Viewed by 1482
Abstract
The problem of antimicrobial resistance (AMR) is not limited to the medical field but is also becoming prevalent on a global scale in the environmental field. Environmental water pollution caused by the discharge of wastewater into aquatic environments has caused concern in the [...] Read more.
The problem of antimicrobial resistance (AMR) is not limited to the medical field but is also becoming prevalent on a global scale in the environmental field. Environmental water pollution caused by the discharge of wastewater into aquatic environments has caused concern in the context of the sustainable development of modern society. However, there have been few studies focused on the treatment of hospital wastewater, and the potential consequences of this remain unknown. This study evaluated the efficacy of the inactivation of antimicrobial-resistant bacteria (AMRB) and antimicrobial resistance genes (AMRGs) in model wastewater treatment plant (WWTP) wastewater and hospital effluent based on direct ultraviolet (UV) light irradiation provided by a conventional mercury lamp with a peak wavelength of 254 nm and an ultraviolet light-emitting diode (UV-LED) with a peak emission of 280 nm under test conditions in which the irradiance of both was adjusted to the same intensity. The overall results indicated that both UV- and UV-LED-mediated disinfection effectively inactivated the AMRB in both wastewater types (>99.9% after 1–3 min of UV and 3 min of UV-LED treatment). Additionally, AMRGs were also removed (0.2–1.4 log10 for UV 254 nm and 0.1–1.3 log10 for UV 280 nm), and notably, there was no statistically significant decrease (p < 0.05) in the AMRGs between the UV and UV-LED treatments. The results of this study highlight the importance of utilizing a local inactivation treatment directly for wastewater generated by a hospital prior to its flow into a WWTP as sewage. Although additional disinfection treatment at the WWTP is likely necessary to remove the entire quantity of AMRB and AMRGs, the present study contributes to a significant reduction in the loads of WWTP and urgent prevention of the spread of infectious diseases, thus alleviating the potential threat to the environment and human health risks associated with AMR problems. Full article
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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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 - 5 Apr 2024
Cited by 2 | Viewed by 2206
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
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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18 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
Viewed by 1724
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
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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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
Viewed by 1976
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
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment)
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