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Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach

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A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 18716

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Dr. Pierluigi Di Ciccio

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Department of Veterinary Science, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Torino, Italy
Interests: food microbiology; food safety; food hygiene; microbial biofilm; food borne pathogens; antimicrobial-resistance
Special Issues, Collections and Topics in MDPI journals

Dr. Selene Rubiola

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Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy
Interests: foodborne parasites; foodborne pathogens; antimicrobial resistance; game meat
Special Issues, Collections and Topics in MDPI journals

Dr. Felice Panebianco

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Department of Veterinary Science, University of Turin Largo Paolo Braccini 2, 10095 Grugliasco, Torino, Italy
Interests: food microbiology; food safety; predictive microbiology; foodborne pathogens; foodborne parasites; seafood

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR), which is defined as the ability of bacteria, viruses, parasites, and fungi to neutralize the effects of antimicrobial agents, has been referred to as the next pandemic. Addressing this global threat requires a One Health approach: on one hand, to monitor the usage of antimicrobial products and to invest in alternatives for animal and human medicine and agriculture, and on the other hand, to track AMR through the different environments and microorganisms, both pathogenic and non-pathogenic. Additionally, there is growing concern about the possible transmission of AMR genes via the food chain and toward the relevance of food-processing environments as reservoirs of AMR. In this context, next-generation sequencing (NGS) technologies, culturomics, and computational approaches may be valuable tools in order to generate AMR related data and combat AMR. Therefore, the purpose of this Special Issue is to collect and publish original research papers or reviews to contribute to the available data and update knowledge on antimicrobials use and antimicrobial resistance in humans, animals, and the environment.

Manuscripts related to the following areas are welcome:

NGS technologies to track AMR;
Epidemiology and surveillance of AMR in humans, animals, and plants;
Antimicrobial use and alternatives in human and animal medicine and agriculture, including antibiotics, antivirals, antifungals, and antiparasitic drugs;
Biocides and antimicrobial resistance;
Microbial biofilm and antimicrobial resistance

We invite you to share your recent findings in this Special Issue.

Dr. Pierluigi Di Ciccio
Dr. Selene Rubiola
Dr. Felice Panebianco
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
antimicrobials
antimicrobial products
antibiotics
biocides
One Health
food safety
next-generation sequencing
AMR surveillance
omics
computational approaches

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Published Papers (7 papers)

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Research

21 pages, 3381 KiB

Open AccessArticle

Chemical Composition and Comprehensive Antimicrobial Activity of an Ethanolic Extract of Propolis from Tunisia

by Nermine Nefzi, Stefania Pagliari, Luca Campone, Wided Megdiche-Ksouri, Filippo Giarratana, Nicola Cicero, Graziella Ziino and Luca Nalbone

Antibiotics 2023, 12(5), 802; https://doi.org/10.3390/antibiotics12050802 - 23 Apr 2023

Cited by 6 | Viewed by 2011

Abstract

In the present study, the chemical composition and the in vitro antimicrobial and antibiofilm activity of an ethanolic extract of propolis (EEP) from Tunisia against different ATCC and wild bacterial strains were evaluated. In situ antimicrobial activity and sensory influence of different EEP concentrations (0.5% and 1%), also in combination with 1% vinegar, were evaluated in chilled vacuum-packed salmon tartare. Furthermore, a challenge test was performed on salmon tartare experimentally contaminated with Listeria monocytogenes and treated with the different EEP formulations. The in vitro antimicrobial and antibiofilm activity was observed only against Gram-positive bacteria, such as L. monocytogenes and S. aureus, both ATCC and wild. Results of the in situ analyses revealed significant antimicrobial activity against aerobic colonies, lactic acid bacteria, Enterobacteriaceae and Pseudomonas spp. only when the EEP was used at 1% and in combination with 1% vinegar. The 1% EEP in combination with 1% vinegar was the most effective treatment also against L. monocytogenes, although 0.5% and 1% EEP used alone also showed antilisterial effects. After 7 days of storage, the sensory influence on odor, taste and color of salmon tartare was negligible for all EEP formulations. In this background, results obtained confirmed the antimicrobial efficacy of propolis which could be proposed as a suitable biopreservative to ensure safety and improve the quality of food. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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19 pages, 499 KiB

Open AccessArticle

Whole Genome Sequencing (WGS) Analysis of Virulence and AMR Genes in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli from Animal and Environmental Samples in Four Italian Swine Farms

by Miryam Bonvegna, Laura Tomassone, Henrik Christensen and John Elmerdahl Olsen

Antibiotics 2022, 11(12), 1774; https://doi.org/10.3390/antibiotics11121774 - 8 Dec 2022

Cited by 5 | Viewed by 3077

Abstract

Whole genome sequencing (WGS) is a powerful tool to analyze bacterial genomes rapidly, and can be useful to study and detect AMR genes. We carried out WGS on a group of Escherichia coli (n = 30), sampled from healthy animals and farm environment in four pigsties in northern Italy. Two × 250bp paired end sequencing strategy on Illumina MiSeq™ was used. We performed in silico characterization of E. coli isolates through the web tools provided by the Center for Genomic Epidemiology (cge.cbs.dtu.dk/services/) to study AMR and virulence genes. Bacterial strains were further analyzed to detect phenotypic antimicrobial susceptibility against several antimicrobials. Data obtained from WGS were compared to phenotypic results. All 30 strains were MDR, and they were positive for the genes bla_CTX-M and bla_TEM as verified by PCR. We observed a good concordance between phenotypic and genomic results. Different AMR determinants were identified (e.g., qnrS, sul, tet). Potential pathogenicity of these strains was also assessed, and virulence genes were detected (e.g., etsC, gad, hlyF, iroN, iss), mostly related to extraintestinal E. coli pathotypes (UPEC/APEC). However, enterotoxin genes, such as astA, ltcA and stb were also identified, indicating a possible hybrid pathogenic nature. Various replicons associated to plasmids, previously recovered in pathogenic bacteria, were identified (e.g., IncN and IncR plasmid), supporting the hypothesis that our strains were pathogenic. Eventually, through WGS it was possible to confirm the phenotypic antibiotic resistance results and to appreciate the virulence side of our ESBL-producing E. coli. These findings highlight the need to monitor commensal E. coli sampled from healthy pigs considering a One Health perspective. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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12 pages, 1729 KiB

Open AccessArticle

Clonal Complexes 23, 10, 131 and 38 as Genetic Markers of the Environmental Spread of Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli

by Lara Pérez-Etayo, David González and Ana Isabel Vitas

Antibiotics 2022, 11(11), 1465; https://doi.org/10.3390/antibiotics11111465 - 24 Oct 2022

Cited by 2 | Viewed by 1752

Abstract

In accordance with the global action plan on antimicrobial resistance adopted by the World Health Assembly in 2015, there is a need to develop surveillance programs for antimicrobial resistant bacteria. In this context, we have analyzed the clonal diversity of Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from aquatic environments and human and food samples in Spain, with the aim of determining possible clonal complexes (CCs) that act as markers of the potential risk of transmission of these resistant bacteria. The phylogenetic groups, sequence types (STs) and CCs were determined by different Polymerase Chain Reaction (PCR) and Multilocus Sequence Typing (MLST) techniques. Phylogroup A was prevalent and was mainly present in food and water strains, while human strains were mostly associated with phylogroup B2. According to the observed prevalence in the different niches, CC23 and CC10 are proposed as markers of phylogroups A and C, related with the spread of bla_CTX-M1 and bla_CTX-M15 genes. Similarly, CC131 and CC38 could be associated to the dissemination of pathogenic strains (phylogroups B2 and D) carrying mainly bla_CTX-M14 and bla_CTX-M15 genes. Some strains isolated from wastewater treatment plants (WWTPs) showed identical profiles to those isolated from other environments, highlighting the importance that water acquires in the dissemination of bacterial resistance. In conclusion, the detection of these genetic markers in different environments could be considered as an alert in the spread of ESBL. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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20 pages, 1862 KiB

Open AccessArticle

Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary

by Balázs Libisch, Sahabi Abdulkadir, Tibor Keresztény, Péter P. Papp, Ferenc Olasz, Hedvig Fébel, Zsuzsanna J. Sándor, Geertrui Rasschaert, Ellen Lambrecht, Marc Heyndrickx, András Szabó, Melinda Kovács and Katalin Posta

Antibiotics 2022, 11(10), 1441; https://doi.org/10.3390/antibiotics11101441 - 20 Oct 2022

Cited by 5 | Viewed by 3160

Abstract

The aim of this study was metagenomics analyses of acquired antibiotic-resistance genes (ARGs) in the intestinal microbiome of two important food-animal species in Hungary from a One Health perspective. Intestinal content samples were collected from 12 domestic pigs (Sus scrofa) and from a common carp (Cyprinus carpio). Shotgun metagenomic sequencing of DNA purified from the intestinal samples was performed on the Illumina platform. The ResFinder database was applied for detecting acquired ARGs in the assembled metagenomic contigs. Altogether, 59 acquired ARG types were identified, 51 genes from domestic pig and 12 genes from the carp intestinal microbiome. ARG types belonged to the antibiotic classes aminoglycosides (27.1%), tetracyclines (25.4%), β-lactams (16.9%), and others. Of the identified ARGs, tet(E), a bla_OXA-_48-like β-lactamase gene, as well as cphA4, ampS, aadA2, qnrS2, and sul1, were identified only in carp but not in swine samples. Several of the detected acquired ARGs have not yet been described from food animals in Hungary. The tet(Q), tet(W), tet(O), and mef(A) genes detected in the intestinal microbiome of domestic pigs had also been identified from free-living wild boars in Hungary, suggesting a possible relationship between the occurrence of acquired ARGs in domestic and wild animal populations. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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9 pages, 509 KiB

Open AccessArticle

Comparison of Antimicrobial Resistances in Escherichia coli from Conventionally and Organic Farmed Poultry from Germany

by Mirjam Grobbel, Jens A. Hammerl, Katja Alt, Alexandra Irrgang, Annemarie Kaesbohrer and Bernd-Alois Tenhagen

Antibiotics 2022, 11(10), 1282; https://doi.org/10.3390/antibiotics11101282 - 21 Sep 2022

Cited by 5 | Viewed by 1891

Abstract

In this study, resistance rates in Escherichia coli from organic and conventional poultry in Germany were compared. Isolates were randomly collected from organic and conventional broiler and turkey flocks at the farm and from turkey meat at retail. Resistance testing was performed as prescribed by Commission implementing decision 2013/652/EU. Logistic regression analyses were performed for the resistance to the different antimicrobials. Overall, resistance rates for the antimicrobials tested were lower in E. coli from organic than from conventionally raised animals. In turkeys, the percentage of isolates susceptible to all antimicrobials tested from animals and meat was twice as high from organic than from conventional origin (~50% vs. <25%). In broilers, the percentage of susceptible isolates from organic farms was five times higher than from conventional farms (70.1% vs. 13.3%) and resistance to three or more classes of antimicrobials was 1.7- to 5.0-fold more common in isolates from conventional farms. The differences between organic and conventional farming were more pronounced in broilers than in turkeys. More studies on turkeys are needed to determine whether this difference is confirmed. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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14 pages, 689 KiB

Open AccessArticle

Antimicrobial Susceptibility Profiles and Molecular Characterisation of Staphylococcus aureus from Pigs and Workers at Farms and Abattoirs in Zambia

by Mulemba Tillika Samutela, Bruno Stephen July Phiri, Edgar Simulundu, Geoffrey Kwenda, Ladslav Moonga, Eugene C. Bwalya, Walter Muleya, Therese Nyirahabimana, Kaunda Yamba, Henson Kainga, Simegnew Adugna Kallu, Innocent Mwape, Andrew Frey, Matthew Bates, Hideaki Higashi and Bernard Mudenda Hang'ombe

Antibiotics 2022, 11(7), 844; https://doi.org/10.3390/antibiotics11070844 - 24 Jun 2022

Cited by 1 | Viewed by 2656

Abstract

Pigs have been shown to be a reservoir for recently emerging livestock-associated Staphylococcus aureus (LA-SA), including methicillin resistant strains in many countries worldwide. However, there is sparse information about LA-SA strains circulating in Zambia. This study investigated the prevalence, phenotypic and genotypic characteristics of S. aureus from pigs and workers at farms and abattoirs handling pigs in Lusaka Province of Zambia. A total of 492 nasal pig swabs, 53 hand and 53 nasal human swabs were collected from farms and abattoirs in selected districts. Standard microbiological methods were used to isolate and determine antimicrobial susceptibility patterns of S. aureus. Polymerase Chain Reaction was used to confirm the species identity and detect antimicrobial resistance and virulence genes of isolates, whereas genetic diversity was evaluated using spa typing. Overall prevalence of S. aureus was 33.1%, 37.8% for pigs and 11.8% for humans. The isolates were resistant to several antibiotics with resistance ranging from 18% to 98% but were all susceptible to vancomycin. Typical LA-SA spa types were detected. The presence of plasmid mediated resistance genes such as tetM (12.8%), other resistance determinants and immune evasion cluster genes among the isolates is of great public health concern. Thus, continuous surveillance of S. aureus using a “One health” approach is warranted to monitor S.aureus infections and spread of antimicrobial resistance. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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9 pages, 651 KiB

Open AccessArticle

mcr-1-Mediated Colistin Resistance and Genomic Characterization of Antimicrobial Resistance in ESBL-Producing Salmonella Infantis Strains from a Broiler Meat Production Chain in Italy

by Patrizia Casagrande Proietti, Laura Musa, Valentina Stefanetti, Massimiliano Orsini, Valeria Toppi, Raffaella Branciari, Francesca Blasi, Chiara Francesca Magistrali, Stefano Capomaccio, Tana Shtylla Kika and Maria Pia Franciosini

Antibiotics 2022, 11(6), 728; https://doi.org/10.3390/antibiotics11060728 - 28 May 2022

Cited by 5 | Viewed by 2844

Abstract

This work aimed to evaluate phenotypically and genotypically the colistin susceptibility of 85 Salmonella Infantis strains isolated in Italy from the broiler production chain, and to apply a whole-genome approach for the determination of genes conferring antimicrobial resistance (AMR). All isolates were tested by the broth microdilution method to evaluate the colistin minimum inhibitory concentrations (MICs). A multiplex PCR was performed in all isolates for the screening of mcr-1, mcr-2, mcr-3 mcr-4, mcr-5 genes and whole-genome sequencing (WGS) of six S. Infantis was applied. Three out of 85 (3.5%) S. Infantis strains were colistin resistant (MIC values ranged from 4 to 8 mg/L) and mcr-1 positive. The mcr-1.1 and mcr-1.2 variants located on the IncX4 plasmid were detected in three different colistin-resistant isolates. The two allelic variants showed identical sequences. All six isolates harbored blaCTXM-1, aac(6′)-Iaa and gyrA/parC genes, mediating, respectively, beta-lactam, aminoglycoside and quinolone resistance. The pESI-megaplasmid carrying tet(A) (tetracycline resistance), dfrA1, (trimethoprim resistance) sul1, (sulfonamide resistance) and qacE (quaternary ammonium resistance) genes was found in all isolates. To our knowledge, this is the first report of the mcr-1.2 variant described in S. Infantis isolated from broilers chickens. Our results also showed a low prevalence of colistin- resistance, probably due to a reduction in colistin use in poultry. This might suggest an optimization of biosecurity control both on farms and in slaughterhouses. Full article

(This article belongs to the Special Issue Antimicrobial Compounds and Antimicrobial Resistance: The Big Challenge of the One Health Approach)

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