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Antibiotics
Special Issues
Antibiotics Resistance in Animals and the Environment
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Antibiotics Resistance in Animals and 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: 31 May 2024 | Viewed by 10487

Special Issue Editor

Dr. Anil Poudel

E-Mail Website
Guest Editor
Pikes Peak State College, Colorado Springs, CO 80906, USA
Interests: infectious disease and public health; antimicrobial resistance; infectious disease pathophysiology; immunology and vaccine development

Special Issue Information

Dear Colleagues,

Antimicrobial resistance is one of the greatest challenges facing global health security in the modern era. Prevention of this looming “epidemic” requires a better understanding of the factors contributing to the development and spread of resistance, novel interventions, and strategies to break the transmission cycle. Wildlife, particularly animals that roam urban areas, is an important but mostly overlooked component of epidemiology of antimicrobial resistance. Studies continue to uncover many common intrinsic and horizontal transfer mechanisms of resistance from wild birds, mammals, insects, and their environment. Many of these wildlife animals travel great distances, making them an ideal sentinel and a vehicle for rapid dissemination of resistance. This Special Issue seeks manuscript submissions that further our understanding of antimicrobial resistance in wildlife and their environment. Submissions on targeted surveillance of wildlife, sympatric animals and invertebrates, and isolation of microbes harboring novel mutations and mobile genetic elements associated with extended spectrum beta-lactams, carbapenems, methicillin, and vancomycin are especially encouraged.

Dr. Anil Poudel
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
  • environment
  • epidemiology
  • genomics
  • multi-drug resistance
  • sympatric
  • wildlife

Published Papers (8 papers)

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Research

Jump to: Review, Other

16 pages, 1274 KiB  
Article
The Genetic Landscape of Antimicrobial Resistance Genes in Enterococcus cecorum Broiler Isolates
by Yue Huang, Filip Boyen, Gunther Antonissen, Nick Vereecke and Filip Van Immerseel
Antibiotics 2024, 13(5), 409; https://doi.org/10.3390/antibiotics13050409 - 29 Apr 2024
Viewed by 154
Abstract
Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff [...] Read more.
Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff (ECOFF) values (COWT) for ten antimicrobials were determined in a collection of E. cecorum strains. Whole-genome sequencing data were analyzed for a selection of these E. cecorum strains to identify resistance determinants involved in the observed phenotypes. Wild-type and non-wild-type isolates were observed for the investigated antimicrobial agents. Several antimicrobial resistance genes (ARGs) were detected in the isolates, linking phenotypes with genotypes for the resistance to vancomycin, tetracycline, lincomycin, spectinomycin, and tylosin. These detected resistance genes were located on mobile genetic elements (MGEs). Point mutations were found in isolates with a non-wild-type phenotype for enrofloxacin and ampicillin/ceftiofur. Isolates showing non-wild-type phenotypes for enrofloxacin had point mutations within the GyrA, GyrB, and ParC proteins, while five amino acid changes in penicillin-binding proteins (PBP2x superfamily) were observed in non-wild-type phenotypes for the tested β-lactam antimicrobials. This study is one of the first that describes the genetic landscape of ARGs within MGEs in E. cecorum, in association with phenotypical resistance determination. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
17 pages, 1763 KiB  
Article
The Home Environment Is a Reservoir for Methicillin-Resistant Coagulase-Negative Staphylococci and Mammaliicocci
by Mari Røken, Stanislav Iakhno, Anita Haug Haaland, Ane Mohn Bjelland and Yngvild Wasteson
Antibiotics 2024, 13(3), 279; https://doi.org/10.3390/antibiotics13030279 - 19 Mar 2024
Viewed by 915
Abstract
Coagulase-negative staphylococci (CoNS) and mammaliicocci are opportunistic human and animal pathogens, often resistant to multiple antimicrobials, including methicillin. Methicillin-resistant CoNS (MRCoNS) have traditionally been linked to hospitals and healthcare facilities, where they are significant contributors to nosocomial infections. However, screenings of non-hospital environments [...] Read more.
Coagulase-negative staphylococci (CoNS) and mammaliicocci are opportunistic human and animal pathogens, often resistant to multiple antimicrobials, including methicillin. Methicillin-resistant CoNS (MRCoNS) have traditionally been linked to hospitals and healthcare facilities, where they are significant contributors to nosocomial infections. However, screenings of non-hospital environments have linked MRCoNS and methicillin-resistant mammaliicocci (MRM) to other ecological niches. The aim of this study was to explore the home environment as a reservoir for MRCoNS and MRM. A total of 33 households, including households with a dog with a methicillin-resistant staphylococcal infection, households with healthy dogs or cats and households without pets, were screened for MRCoNS and MRM by sampling one human, one pet (if present) and the environment. Samples were analyzed by a selective culture-based method, and bacterial species were identified by MALDI-TOF MS and tested for antibiotic susceptibility by the agar disk diffusion method. Following whole-genome sequencing, a large diversity of SCCmec elements and sequence types was revealed, which did not indicate any clonal dissemination of specific strains. Virulome and mobilome analyses indicated a high degree of species specificity. Altogether, this study documents that the home environment is a reservoir for a variety of MRCoNS and MRM regardless of the type of household. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
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19 pages, 5193 KiB  
Article
Phylogeny, Virulence, and Antimicrobial Resistance Gene Profiles of Enterococcus faecium Isolated from Australian Feedlot Cattle and Their Significance to Public and Environmental Health
by Yohannes E. Messele, Darren J. Trott, Mauida F. Hasoon, Tania Veltman, Joe P. McMeniman, Stephen P. Kidd, Kiro R. Petrovski and Wai Y. Low
Antibiotics 2023, 12(7), 1122; https://doi.org/10.3390/antibiotics12071122 - 28 Jun 2023
Cited by 1 | Viewed by 1322
Abstract
The extent of similarity between E. faecium strains found in healthy feedlot beef cattle and those causing extraintestinal infections in humans is not yet fully understood. This study used whole-genome sequencing to analyse the antimicrobial resistance profile of E. faecium isolated from beef [...] Read more.
The extent of similarity between E. faecium strains found in healthy feedlot beef cattle and those causing extraintestinal infections in humans is not yet fully understood. This study used whole-genome sequencing to analyse the antimicrobial resistance profile of E. faecium isolated from beef cattle (n = 59) at a single feedlot and compared them to previously reported Australian isolates obtained from pig (n = 60) and meat chicken caecal samples (n = 8), as well as human sepsis cases (n = 302). The E. faecium isolated from beef cattle and other food animal sources neither carried vanA/vanB responsible for vancomycin nor possessed gyrA/parC and liaR/liaS gene mutations associated with high-level fluoroquinolone and daptomycin resistance, respectively. A small proportion (7.6%) of human isolates clustered with beef cattle and pig isolates, including a few isolates belonging to the same sequence types ST22 (one beef cattle, one pig, and two human isolates), ST32 (eight beef cattle and one human isolate), and ST327 (two beef cattle and one human isolate), suggesting common origins. This provides further evidence that these clonal lineages may have broader host range but are unrelated to the typical hospital-adapted human strains belonging to clonal complex 17, significant proportions of which contain vanA/vanB and liaR/liaS. Additionally, none of the human isolates belonging to these STs contained resistance genes to WHO critically important antimicrobials. The results confirm that most E. faecium isolated from beef cattle in this study do not pose a significant risk for resistance to critically important antimicrobials and are not associated with current human septic infections. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
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17 pages, 3702 KiB  
Article
Phylogenetic Analysis of Escherichia coli Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates
by Yohannes E. Messele, Darren J. Trott, Mauida F. Hasoon, Tania Veltman, Joe P. McMeniman, Stephen P. Kidd, Steven P. Djordjevic, Kiro R. Petrovski and Wai Y. Low
Antibiotics 2023, 12(5), 895; https://doi.org/10.3390/antibiotics12050895 - 11 May 2023
Viewed by 2145
Abstract
The similarity of commensal Escherichia coli isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine the genetic characteristics and phylogenetic [...] Read more.
The similarity of commensal Escherichia coli isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine the genetic characteristics and phylogenetic relationships among faecal Escherichia coli isolates from beef cattle (n = 37) from a single feedlot in comparison to previously analysed pig faecal (n = 45), poultry extraintestinal (n = 19), and human extraintestinal E. coli isolates (n = 40) from three previous Australian studies. Most beef cattle and pig isolates belonged to E. coli phylogroups A and B1, whereas most avian and human isolates belonged to B2 and D, although a single human extraintestinal isolate belonged to phylogenetic group A and sequence type (ST) 10. The most common E. coli sequence types (STs) included ST10 for beef cattle, ST361 for pig, ST117 for poultry, and ST73 for human isolates. Extended-spectrum and AmpC β-lactamase genes were identified in seven out of thirty-seven (18.9%) beef cattle isolates. The most common plasmid replicons identified were IncFIB (AP001918), followed by IncFII, Col156, and IncX1. The results confirm that feedlot cattle isolates examined in this study represent a reduced risk to human and environmental health with regard to being a source of antimicrobial-resistant E. coli of clinical importance. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
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13 pages, 3177 KiB  
Article
Comparison of Fecal Antimicrobial Resistance Genes in Captive and Wild Asian Elephants
by Kaixun Cao, Yepeng Wang, Xuewei Bai, Jishan Wang, Liting Zhang, Yongjing Tang, Rebecca Caroline Thuku, Wei Hou, Guoxiang Mo, Fei Chen and Lin Jin
Antibiotics 2023, 12(5), 859; https://doi.org/10.3390/antibiotics12050859 - 06 May 2023
Cited by 2 | Viewed by 1809
Abstract
The Asian elephant (Elephas maximus) is a flagship species of tropical rainforests, and it has generated much concern. In this case, the gut bacterial communities of captive and wild Asian elephants are particularly noteworthy. We aim to compare the differences in [...] Read more.
The Asian elephant (Elephas maximus) is a flagship species of tropical rainforests, and it has generated much concern. In this case, the gut bacterial communities of captive and wild Asian elephants are particularly noteworthy. We aim to compare the differences in bacterial diversity and antibiotic resistance gene (ARG) subtypes in fecal samples of Asian elephants from different habitats, which may affect host health. Analyses reveal that differences in the dominant species of gut bacteria between captive and wild Asian elephants may result in significant differences in ARGs. Network analysis of bacterial communities in captive Asian elephants has identified potentially pathogenic species. Many negative correlations in network analysis suggest that different food sources may lead to differences in bacterial communities and ARGs. Results also indicate that the ARG levels in local captive breeding of Asian elephants are close to those of the wild type. However, we found that local captive elephants carry fewer ARG types than their wild counterparts. This study reveals the profile and relationship between bacterial communities and ARGs in different sources of Asian elephant feces, providing primary data for captive breeding and rescuing wild Asian elephants. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
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15 pages, 379 KiB  
Article
Prevalence Estimation, Antimicrobial Susceptibility, and Serotyping of Salmonella enterica Recovered from New World Non-Human Primates (Platyrrhini), Feed, and Environmental Surfaces from Wildlife Centers in Costa Rica
by Ernesto Rojas-Sánchez, Mauricio Jiménez-Soto, Elias Barquero-Calvo, Francisco Duarte-Martínez, Dixie F. Mollenkopf, Thomas E. Wittum and Lohendy Muñoz-Vargas
Antibiotics 2023, 12(5), 844; https://doi.org/10.3390/antibiotics12050844 - 02 May 2023
Viewed by 1714
Abstract
Concern about zoonoses and wildlife has increased. Few studies described the role of wild mammals and environments in the epidemiology of Salmonella. Antimicrobial resistance is a growing problem associated with Salmonella that threatens global health, food security, the economy, and development in [...] Read more.
Concern about zoonoses and wildlife has increased. Few studies described the role of wild mammals and environments in the epidemiology of Salmonella. Antimicrobial resistance is a growing problem associated with Salmonella that threatens global health, food security, the economy, and development in the 21st century. The aim of this study is to estimate the prevalence and identify antibiotic susceptibility profiles and serotypes of non-typhoidal Salmonella enterica recovered from non-human primate feces, feed offered, and surfaces in wildlife centers in Costa Rica. A total of 180 fecal samples, 133 environmental, and 43 feed samples from 10 wildlife centers were evaluated. We recovered Salmonella from 13.9% of feces samples, 11.3% of environmental, and 2.3% of feed samples. Non-susceptibility profiles included six isolates from feces (14.6%): four non-susceptible isolates (9.8%) to ciprofloxacin, one (2.4%) to nitrofurantoin, and one to both ciprofloxacin and nitrofurantoin (2.4%). Regarding the environmental samples, one profile was non-susceptible to ciprofloxacin (2.4%) and two to nitrofurantoin (4.8%). The serotypes identified included Typhimurium/I4,[5],12:i:-, S. Braenderup/Ohio, S. Newport, S. Anatum/Saintpaul, and S. Westhampton. The epidemiological surveillance of Salmonella and antimicrobial resistance can serve in the creation of strategies for the prevention of the disease and its dissemination throughout the One Health approach. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)

Review

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16 pages, 1538 KiB  
Review
European Wild Carnivores and Antibiotic Resistant Bacteria: A Review
by Andreia Garcês and Isabel Pires
Antibiotics 2023, 12(12), 1725; https://doi.org/10.3390/antibiotics12121725 - 13 Dec 2023
Cited by 1 | Viewed by 967
Abstract
Antibiotic resistance is a global concern that affects not only human health but also the health of wildlife and the environment. Wildlife can serve as reservoirs for antibiotic-resistant bacteria, and antibiotics in veterinary medicine and agriculture can contribute to the development of resistance [...] Read more.
Antibiotic resistance is a global concern that affects not only human health but also the health of wildlife and the environment. Wildlife can serve as reservoirs for antibiotic-resistant bacteria, and antibiotics in veterinary medicine and agriculture can contribute to the development of resistance in these populations. Several European carnivore species, such as wolves, foxes, otters, and bears, can be exposed to antibiotics by consuming contaminated food, water, or other resources in their habitats. These animals can also be indirectly exposed to antibiotics through interactions with domestic animals and human activities in their environment. Antibiotic resistance in wildlife can harm ecosystem health and also impact human health indirectly through various pathways, including zoonotic disease transmission. Moreover, the spread of resistant bacteria in wildlife can complicate conservation efforts, as it can threaten already endangered species. This review aims to describe the presence of antibiotic-resistant bacteria in wild carnivores in Europe. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
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Other

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19 pages, 1691 KiB  
Systematic Review
Meta-Analysis and Systematic Review of Phenotypic and Genotypic Antimicrobial Resistance and Virulence Factors in Vibrio parahaemolyticus Isolated from Shrimp
by Varangkana Thaotumpitak, Justice Opare Odoi, Saran Anuntawirun and Saharuetai Jeamsripong
Antibiotics 2024, 13(4), 370; https://doi.org/10.3390/antibiotics13040370 - 17 Apr 2024
Viewed by 648
Abstract
This systematic review and meta-analysis investigates the prevalence of Vibrio parahaemolyticus, its virulence factors, antimicrobial resistance (AMR), and its resistance determinants in shrimp. This study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, to identify and [...] Read more.
This systematic review and meta-analysis investigates the prevalence of Vibrio parahaemolyticus, its virulence factors, antimicrobial resistance (AMR), and its resistance determinants in shrimp. This study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, to identify and select relevant peer-reviewed articles published between January 2020 and December 2022. The search strategy involved multiple online databases, including Google Scholar, PubMed, ScienceDirect, and Scopus. The inclusion criteria focused on studies that examined V. parahaemolyticus prevalence, virulence factors, and AMR in shrimp from farms to retail outlets. A total of 32 studies were analyzed, revealing a pooled estimate prevalence of V. parahaemolyticus in shrimp at 46.0%, with significant heterogeneity observed. Subgroup analysis highlighted varying prevalence rates across continents, emphasizing the need for further investigation. Virulence factor analysis identified thermostable direct hemolysin (tdh) and tdh-related hemolysin (trh) as the most common. Phenotypic AMR analysis indicated notable resistance to glycopeptides, nitrofurans, and beta-lactams. However, the correlation between antimicrobial usage in shrimp farming and observed resistance patterns was inconclusive. Funnel plots suggested potential publication bias, indicating a need for cautious interpretation of findings. This study underscores the urgency of coordinated efforts to address AMR in V. parahaemolyticus to safeguard public health and to ensure sustainable aquaculture practices. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Antimicrobial resistance elements in coastal water recovered from Llanquihue lake, Chile
Authors: Javier Campanini-Salinas 1,2 Alfredo Rodríguez 3 Catherine Opitz 1 John A. Sagredo-Mella 1,2 Nataly D. Rubio 1,2 Daniel A. Medina 1,3
Affiliation: 1. Laboratorio Institucional, Universidad San Sebastián, Puerto Montt, Chile. 2. Facultad de Medicina y Ciencia, Universidad San Sebastián, Puerto Montt, Chile. 3. Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Puerto Montt, Chile.
Abstract: Antibiotic resistance has been declared a global health problem. In Chile, the use of antibiotics should be declared by medical prescription, however, it is unknown what happens to the drugs once the treatment ends. One possibility is that these end up being disposed of in the trash or down the drain. In both scenarios, antibiotics could accumulate in the environment, stimulating the emergence of antimicrobial resistance mechanisms and their transfer between microorganisms. Unfortunately, wasterwater ends up in bodies of water, due to the dragging of elements by rain, or by the presence of illegal water discharges. In this work, we use shotgun metagenomics to elucidate the functional and microbial composition of biohazard elements in the bay of Puerto Varas City, Chile. As expected, we found a high diversity in microbial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in water samples. The results showed the presence of resistance genes to macrolides, beta-lactams, and tetracyclines, which are consistent with the families of antibiotics most used in Chile. In addition, microorganisms isolated from the same sites showed resistance to antimicrobials from the aforementioned families. This is the first work that shows the presence of genomic elements that could constitute a health problem for the people who live around the Llanquihue Lake of Chile, taking into account the importance of the interconnection between environmental, animal, and human health, a concept known as One Health.

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