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Antibiotics
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Molecular Characterization and Antimicrobial Resistance of Pathogens Isolated from Animals
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Molecular Characterization and Antimicrobial Resistance of Pathogens Isolated from Animals

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics in Animal Health".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 3846

Special Issue Editor

Prof. Dr. Isabel Carvalho

E-Mail Website
Guest Editor
1. Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
2. Biochemistry and Molecular Biology, University of La Rioja, Logrono, Spain
3. Laboratory Associated for Green Chemistry (LAQV-REQUIMTE), New University of Lisbon, Monte da Caparica, Portugal
Interests: antibiotic resistance; genetics; Enterobacteriaceae; microbiology; One Health; Maldi-TOF

Special Issue Information

Dear Colleagues,

Antibiotic resistance is considered a significant public health concern, caused by the use, overuse, and misuse of these drugs in clinic prescription and veterinary medicine. According to some estimations, around 700,000 human deaths every year worldwide are due to the failure of antibiotic treatments for bacterial infections. It has been predicted that this will increase to 10 million people/year by 2050, which represents more than the current mortality associated with different cancers. In recent decades, various studies have reported this situation in animals (including wildlife and pets), humans, and the environment, focusing on a One Health approach.

With this Special Issue, we are looking to gather together manuscripts related to antimicrobial resistance among animals, and studies performed in any part of the world are welcome. The isolation of pathogens harboring novel mutations and mobile genetic elements associated with extended-spectrum beta-lactams, carbapenems, methicillin, and vancomycin are strongly encouraged.

Prof. Dr. Isabel Carvalho
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

  • antibiotic resistance
  • molecular biology
  • microbiology
  • genomics
  • multi-drug resistance
  • One Health
  • animals

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Published Papers (3 papers)

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13 pages, 569 KiB  
Article
Serogrouping and Molecular Characterization of ESBL-Producing Avian Pathogenic Escherichia coli from Broilers and Turkeys with Colibacillosis in Algeria
by Nadia Safia Chenouf, Chafik Redha Messaï, Isabel Carvalho, Tamara Álvarez-Gómez, Vanessa Silva, Abdelghani Zitouni, Ahcene Hakem, Patricia Poeta and Carmen Torres
Antibiotics 2025, 14(4), 356; https://doi.org/10.3390/antibiotics14040356 - 31 Mar 2025
Viewed by 413
Abstract
Avian colibacillosis caused by avian pathogenic Escherichia coli (APEC) strains is a bacterial disease responsible for enormous economic losses in the poultry industry, due to high mortality rates in farms, antibiotic therapy costs, and seizures at slaughterhouses. The aim of this study was [...] Read more.
Avian colibacillosis caused by avian pathogenic Escherichia coli (APEC) strains is a bacterial disease responsible for enormous economic losses in the poultry industry, due to high mortality rates in farms, antibiotic therapy costs, and seizures at slaughterhouses. The aim of this study was to characterize the serogroups and molecular features of extended spectrum β-lactamase (ESBL)-producing APEC isolates recovered from 248 liver samples of 215 broilers and 33 turkeys with colibacillosis lesions in northeast Algeria. For this, microbiological tests were carried out, according to the recommended standards: E. coli isolates were recovered using standard microbiological protocols, and identification was carried out by MALDI-TOF MS. Serogrouping was performed using a rapid agglutination slide and the antisera of three O somatic groups (O1, O2, O78). Antimicrobial susceptibility was determined by the disk diffusion method. PCR assays and sequencing were used to detect antimicrobial resistance genes, integrons, phylogrouping, and MLST. Conjugation experiments were also conducted to determine the transferability of the retrieved ESBL-encoding genes. Overall, 211 (85.1%) APEC isolates were collected (one per positive sample), and 164 (77.7%) of them were typable. The O2 and O1 serogroups were the most detected (46.1% in broiler typable isolates and 61.5% in turkey typable isolates). Seventeen APEC isolates were ESBL-producers and harbored the following genes (number of isolates): blaCTX-M-1 (14), blaCTX-M-15 (2), and blaSHV-12 (1). They belonged to phylogroups D (10 isolates), B1 (6 isolates), and B2 (1 isolate). The MLST of 13 ESBL producers revealed seven STs: ST23, ST38, ST48, ST117, ST131, ST1146, and ST5087. The ESBL-encoding genes were transferred by conjugation among 15 ESBL-producing isolates, and transconjugants acquired either the IncK or IncI1 plasmids. Concerted efforts from all poultry actors are needed to establish surveillance monitoring strategies to mitigate the spread of ESBL-producing isolates implicated in avian colibacillosis. Full article
(This article belongs to the Special Issue Molecular Characterization and Antimicrobial Resistance of Pathogens Isolated from Animals)
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20 pages, 5735 KiB  
Article
Antimicrobial Resistance Genes in Clinical Escherichia coli Strains from Livestock and Poultry in Shandong Province, China During 2015–2020
by Miaoli Wang, Shaopeng Wu, Yao Wang, Feng Chen, Zhangqi Shen and Zouran Lan
Antibiotics 2025, 14(1), 95; https://doi.org/10.3390/antibiotics14010095 - 15 Jan 2025
Viewed by 1372
Abstract
Antimicrobial resistant (AMR) Escherichia coli (E. coli) isolated from animals may lead to antibiotic treatment failure and economic losses to farmers. The co-existence of antimicrobial resistant genes (ARGs) in the same isolate presents a major challenge for the prevention and control [...] Read more.
Antimicrobial resistant (AMR) Escherichia coli (E. coli) isolated from animals may lead to antibiotic treatment failure and economic losses to farmers. The co-existence of antimicrobial resistant genes (ARGs) in the same isolate presents a major challenge for the prevention and control of infection in multidrug-resistant (MDR) Gram-negative organisms. There have been a lot of studies on the antibiotic resistance of E. coli in livestock and poultry, but few of them have focused on clinical pathogens. Objective: The aim of this study was to explore the genetic characteristics, co-occurrence, and correlations between ARGs of E. coli isolated from the pathological tissues of livestock and poultry in Shandong Province, East China during 2015–2020. Methods: A total of 158 E. coli strains were collected and subjected to antimicrobial susceptibility testing and sequencing by whole-genome Next Generation Sequencing (NGS). Results: MDR strains accounted for 46.20% of the 158 E. coli strains with the highest resistant rate of ciprofloxacin (71.52%). In addition, strains with blaNDM-5/mcr-1.1 and mcr-1.1/mcr-3.24 were found in chickens, while three strains with Tet(X4) were found in pigs. In addition, the most common serotypes detected were the O serotype (76/158) and H serotype (36/158). Moreover, seventy-one STs were found and the most common STs were ST10 (6.33%), ST155 (6.33%), and ST101 (5.69%). The genetic environment analysis of the phylogroups revealed that E. coli belonging to phylogroup B1, phylogroup A, and phylogroup C constituted 39.87%, 27.85%, and 15.19%, respectively. Through the correlation analysis, mcr genes were observed to have certain relationships with ARGS such as blaTEM, floR, catA/B, and oqx. Conclusions: This study demonstrates the high prevalence and gene diversity of MDR E. coli isolated from a clinic in Shandong Province, East China. We predicted the transmission risk of animal-borne Tet(X4)-bearing and mcr-harboring E. coli to public health and provided insight into the relationship of co-existence or co-transfer between mcr with ARGS. These relationships present a great challenge for the infection control of MDR Gram-negative organisms. Full article
(This article belongs to the Special Issue Molecular Characterization and Antimicrobial Resistance of Pathogens Isolated from Animals)
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19 pages, 7385 KiB  
Article
Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA
by Max Chung, Ethan Dudley, Hatem Kittana, Alexis C. Thompson, Matthew Scott, Keri Norman and Robert Valeris-Chacin
Antibiotics 2024, 13(9), 843; https://doi.org/10.3390/antibiotics13090843 - 4 Sep 2024
Viewed by 1499
Abstract
Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still [...] Read more.
Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements. Full article
(This article belongs to the Special Issue Molecular Characterization and Antimicrobial Resistance of Pathogens Isolated from Animals)
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