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Antibiotics
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Microbial Resistance Surveillance and Management in Food Systems
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Microbial Resistance Surveillance and Management in Food Systems

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics Use and Antimicrobial Stewardship".

Deadline for manuscript submissions: 10 October 2025 | Viewed by 2391

Special Issue Editors

Prof. Dr. Carlos Adam Conte Júnior

E-Mail Website
Guest Editor
Center for Food Analysis (NAL-LADETEC), Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Av. Horácio Macedo, Polo de Química, bloco C, 1281-Cidade Universitária, Rio de Janeiro 21941-598, RJ, Brazil
Interests: animal science; molecular biology; biochemistry; molecular techniques; food science; food microbiology; animal-based food; bovine tuberculosis; antimicrobial resistance; analytical method development
Special Issues, Collections and Topics in MDPI journals
Dr. Bruno Dutra da Silva

E-Mail Website
Guest Editor
Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
Interests: food microbiology; natural compounds; microbiology; meat science

Special Issue Information

Dear Colleagues,

Antimicrobial resistance represents a significant challenge in food systems, impacting food safety, public health, and antimicrobial stewardship efforts worldwide. This Special Issue explores current surveillance strategies, management practices, and novel interventions that address microbial resistance in food environments. By compiling diverse perspectives from microbiology, food science, epidemiology, and public health, this edition aims to advance our understanding and management of microbial resistance in food systems, thus promoting sustainable and public health practices.

The scope of this Special Issue includes, but is not limited to, the following topics:

  1. Origin and dissemination of resistant microorganisms in the food production chain;
  2. Methodologies for monitoring antimicrobial-resistant pathogens in food production and distribution chains;
  3. Mechanisms and dynamics of the transmission of antimicrobial resistance through the food production chain;
  4. Strategies to mitigate antimicrobial resistance in food processing and preservation;
  5. Novel antimicrobial agents and alternative strategies that combat resistance in food-borne pathogens.

Prof. Dr. Carlos Adam Conte Júnior
Dr. Bruno Dutra da Silva
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

  • cross-contamination
  • microbial resistance
  • microbial monitoring
  • public health
  • alternative antimicrobials
  • foodborne illnesses
  • food microbiology

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Research

18 pages, 596 KiB  
Article
Antibiotic Resistance in Lactic Acid Bacteria from Dairy Products in Northern Italy
by Irene Floris, Roberta Battistini, Clara Tramuta, Aitor Garcia-Vozmediano, Noemi Musolino, Giulia Scardino, Chiara Masotti, Beatrice Brusa, Riccardo Orusa, Laura Serracca, Elisabetta Razzuoli, Francesca Martucci and Daniela Manila Bianchi
Antibiotics 2025, 14(4), 375; https://doi.org/10.3390/antibiotics14040375 (registering DOI) - 3 Apr 2025
Abstract
Background: The spread of antibiotic resistance genes (ARGs) from the food chain is a significant public health concern. Dairy products from raw milk containing lactic acid bacteria (LAB) resistant to antimicrobials may serve as vectors for the transfer of resistance to commensal [...] Read more.
Background: The spread of antibiotic resistance genes (ARGs) from the food chain is a significant public health concern. Dairy products from raw milk containing lactic acid bacteria (LAB) resistant to antimicrobials may serve as vectors for the transfer of resistance to commensal or potentially pathogenic bacteria in the human gut. Detecting ARGs in dairy products and milk is, therefore, crucial and could aid in the development of strategies to mitigate resistance dissemination through the food chain. Objectives: This study aimed to determine the presence of ARGs and assess the antibiotic susceptibility of LAB strains isolated from dairy products made from raw milk. Methods: Fifty-four LAB strains were isolated from 41 dairy samples and were tested for antimicrobial susceptibility using broth microdilution to determine Minimal Inhibitory Concentration (MIC). Moreover, the presence of resistance genes related to tetracyclines, beta-lactams, quinolones, and erythromycin was examined using six multiplex PCR assays. Results: Lactobacillus spp. and Leuconostoc spp. strains exhibited a high level of resistance to vancomycin (93–100%). Low-level resistance (4.2–20%) was observed in Lactococcus spp. and Lactobacillus spp. strains against tetracycline. Additionally, Lactococcus spp. strains showed resistance to trimethoprim/sulfamethoxazole, erythromycin, and clindamycin. Twenty-two out of 54 LAB strains (40.7%) carried at least one antibiotic resistance gene, and five of these were multidrug-resistant. Genes associated with acquired resistance to tetracycline were commonly detected, with tetK being the most frequent determinant. Conclusions: This study demonstrated that LABs in dairy products can act as reservoirs for ARGs, potentially contributing to the horizontal transfer of resistance within microbial communities in food and consumers. These findings highlight the need for the ongoing surveillance of antibiotic resistance in LAB and the implementation of control measures to minimize the dissemination of resistance through dairy products. Full article
(This article belongs to the Special Issue Microbial Resistance Surveillance and Management in Food Systems)
35 pages, 3667 KiB  
Article
Distribution of Antimicrobial Resistance and Biofilm Production Genes in the Genomic Sequences of S. aureus: A Global In Silico Analysis
by Ana Carolina Silva-de-Jesus, Rafaela G. Ferrari, Pedro Panzenhagen, Anamaria M. P. dos Santos, Ana Beatriz Portes and Carlos Adam Conte-Junior
Antibiotics 2025, 14(4), 364; https://doi.org/10.3390/antibiotics14040364 - 1 Apr 2025
Viewed by 164
Abstract
Background: Staphylococcus aureus constitutes a significant public health threat due to its exceptional adaptability, antimicrobial resistance (AMR), and capacity to form biofilms, all of which facilitate its persistence in clinical and environmental settings. Methods: This study undertook an extensive in silico analysis [...] Read more.
Background: Staphylococcus aureus constitutes a significant public health threat due to its exceptional adaptability, antimicrobial resistance (AMR), and capacity to form biofilms, all of which facilitate its persistence in clinical and environmental settings. Methods: This study undertook an extensive in silico analysis of 44,069 S. aureus genomic sequences acquired from the NCBI database to assess the global distribution of biofilm-associated and resistance-associated genes. The genomes were categorized into human clinical and environmental groups, with clinical samples representing a predominant 96%. Results: The analysis revealed notable regional discrepancies in sequencing efforts, with Europe and North America contributing 76% of the genomes. Key findings include the high prevalence of the ica locus, which is associated with biofilm formation, and its robust correlation with other genes, such as sasG, which was exclusively linked to SCCmec type IIa. The AMR gene analysis revealed substantial genetic diversity within environmental samples, with genes like vga(E) and erm being identified as particularly prominent. The clonal complex analysis revealed ST8 (USA300) and ST5 as the predominant types in human clinical isolates, while ST398 and ST59 were most frequently observed in environmental isolates. SCCmec type IV was globally prevalent, with subtype Iva being strongly associated with ST8 in North America and subtype IVh with ST239 in Europe. Conclusions: These findings underscore the dynamic evolution of S. aureus via mobile genetic elements and highlight the necessity for standardized metadata in public genomic databases to improve surveillance efforts. Furthermore, they reinforce the critical need for a One Health approach in monitoring S. aureus evolution, particularly concerning the co-dissemination of biofilm and resistance genes across various ecological niches. Full article
(This article belongs to the Special Issue Microbial Resistance Surveillance and Management in Food Systems)
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19 pages, 2631 KiB  
Article
The Trade-Off Between Sanitizer Resistance and Virulence Genes: Genomic Insights into E. coli Adaptation
by Vinicius Silva Castro, Yuri Duarte Porto, Xianqin Yang, Carlos Adam Conte Junior, Eduardo Eustáquio de Souza Figueiredo and Kim Stanford
Antibiotics 2025, 14(3), 291; https://doi.org/10.3390/antibiotics14030291 - 11 Mar 2025
Viewed by 306
Abstract
Background: Escherichia coli is one of the most studied bacteria worldwide due to its genetic plasticity. Recently, in addition to characterizing its pathogenic potential, research has focused on understanding its resistance profile to inhibitory agents, whether these be antibiotics or sanitizers. Objectives: The [...] Read more.
Background: Escherichia coli is one of the most studied bacteria worldwide due to its genetic plasticity. Recently, in addition to characterizing its pathogenic potential, research has focused on understanding its resistance profile to inhibitory agents, whether these be antibiotics or sanitizers. Objectives: The present study aimed to investigate six of the main serogroups of foodborne infection (O26, O45, O103, O111, O121, and O157) and to understand the dynamics of heterogeneity in resistance to sanitizers derived from quaternary ammonium compounds (QACs) and peracetic acid (PAA) using whole-genome sequencing (WGS). Methods: Twenty-four E. coli strains with varied resistance profiles to QACs and PAA were analyzed by WGS using NovaSeq6000 (150 bp Paired End reads). Bioinformatic analyses included genome assembly (Shovill), annotation via Prokka, antimicrobial resistance gene identification using Abricate, and core-genome analysis using Roary. A multifactorial multiple correspondence analysis (MCA) was conducted to explore gene–sanitizer relationships. In addition, a large-scale analysis utilizing the NCBI Pathogen Detection database involved a 2 × 2 chi-square test to examine associations between the presence of qac and stx genes. Results: The isolates exhibited varying antimicrobial resistance profiles, with O45 and O157 being the most resistant serogroups. In addition, the qac gene was identified in only one strain (S22), while four other strains carried the stx gene. Through multifactorial multiple correspondence analysis, the results obtained indicated that strains harboring genes encoding Shiga toxin (stx) presented profiles that were more likely to be sensitive to QACs. To further confirm these results, we analyzed 393,216 E. coli genomes from the NCBI Pathogen Detection database. Our results revealed a significant association (p < 0.001) between the presence of qac genes and the absence of stx1, stx2, or both toxin genes. Conclusion: Our findings highlight the complexity of bacterial resistance mechanisms and suggest that non-pathogenic strains may exhibit greater tolerance to QAC sanitizer than those carrying pathogenicity genes, particularly Shiga toxin genes. Full article
(This article belongs to the Special Issue Microbial Resistance Surveillance and Management in Food Systems)
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14 pages, 3634 KiB  
Article
Escherichia coli in Brazilian Poultry Fecal Samples: Co-Carriage of Fosfomycin and ESBL Resistance
by Felipe Juscele, Andre B. S. Saidenberg, Lars E. B. Christoffersen, Sofie M. Edslev, Søren Hallstrøm, Jessica R. Nacarato, Fernanda B. Barbosa, Marcos P. Cunha, Fernanda Esposito, Nilton H. Lincopan, Marc Stegger and Terezinha Knöbl
Antibiotics 2025, 14(3), 269; https://doi.org/10.3390/antibiotics14030269 - 6 Mar 2025
Viewed by 261
Abstract
Background/Objectives: Fosfomycin, a critically important antibiotic, is widely used to treat urinary tract infections (UTIs) caused by multidrug-resistant (MDR) Escherichia coli, particularly those producing extended-spectrum β-lactamases (ESBLs). However, its increasing use in livestock has raised concerns about resistance development and global [...] Read more.
Background/Objectives: Fosfomycin, a critically important antibiotic, is widely used to treat urinary tract infections (UTIs) caused by multidrug-resistant (MDR) Escherichia coli, particularly those producing extended-spectrum β-lactamases (ESBLs). However, its increasing use in livestock has raised concerns about resistance development and global dissemination. This study investigated fosfomycin resistance in E. coli isolates from 400 fecal samples collected at Brazilian broiler farms. Methods: The samples were tested for their minimum inhibitory concentration (MIC), screened with PCR for specific resistance genes, and selected isolated were whole genome sequenced. Results: Phenotypic resistance to fosfomycin was detected in 19% (75/400) of the isolates, while the fosA3 gene, encoding enzymatic resistance, was identified in 4% (16/400) via PCR screening. Long-read sequencing of seven fosA3-positive isolates revealed the presence of fosA3 on IncFII and IncX plasmids, often co-located with blaCTX-M-55 within a conserved IS26-flanked transposon. Comparative genomic analysis of 133,541 global E. coli genomes from EnteroBase showed that 35% harbored similar transposon structures, with 2% carrying fosA3. These fosA3-positive isolates were significantly associated with South America and exhibited high co-carriage of ESBL genes, particularly in environmental and poultry-associated isolates. Phylogenetic analysis demonstrated no clustering by host or geographic origin, highlighting the global dissemination of these resistance determinants. Conclusions: Our findings emphasize the role of poultry production in the spread of fosfomycin and ESBL resistance, driven by transmissible plasmids and co-selection with third-generation cephalosporins. Improved antimicrobial stewardship, surveillance programs, and alternative management strategies are urgently needed to mitigate the dissemination of resistance and preserve fosfomycin’s efficacy in human medicine. Full article
(This article belongs to the Special Issue Microbial Resistance Surveillance and Management in Food Systems)
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10 pages, 843 KiB  
Article
Gene emrC Associated with Resistance to Quaternary Ammonium Compounds Is Common among Listeria monocytogenes from Meat Products and Meat Processing Plants in Poland
by Iwona Kawacka and Agnieszka Olejnik-Schmidt
Antibiotics 2024, 13(8), 749; https://doi.org/10.3390/antibiotics13080749 - 9 Aug 2024
Cited by 1 | Viewed by 1069
Abstract
(1) Background: L. monocytogenes is a food pathogen of great importance, characterized by a high mortality rate. Quaternary ammonium compounds (QACs), such as benzalkonium chloride (BC), are often used as disinfectants in food processing facilities. The effectiveness of disinfection procedures is crucial to [...] Read more.
(1) Background: L. monocytogenes is a food pathogen of great importance, characterized by a high mortality rate. Quaternary ammonium compounds (QACs), such as benzalkonium chloride (BC), are often used as disinfectants in food processing facilities. The effectiveness of disinfection procedures is crucial to food safety. (2) Methods: A collection of 153 isolates of L. monocytogenes from meat processing industry was analyzed for their sensitivity to BC using the agar diffusion method. Genes of interest were detected with PCR. (3) Results: Genes emrC, bcrABC, and qacH were found in 64 (41.8%), 6 (3.9%), and 1 isolate (0.7%), respectively, and 79 isolates (51.6%) were classified as having reduced sensitivity to BC. A strong correlation between carrying QACs resistance-related genes and phenotype was found (p-value < 0.0001). Among 51 isolates originating from bacon (collected over 13 months), 48 had the emrC gene, which could explain their persistent presence in a processing facility. Isolates with the ilsA gene (from LIPI-3) were significantly (p-value 0.006) less likely to carry QACs resistance-related genes. (4) Conclusions: Reduced sensitivity to QACs is common among L. monocytogenes from the meat processing industry. Persistent presence of these bacteria in a processing facility is presumably caused by emrC-induced QACs resistance. Full article
(This article belongs to the Special Issue Microbial Resistance Surveillance and Management in Food Systems)
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