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Antibiotics
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Antimicrobial Resistance and Food Safety: What Can We Learn from...
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Antimicrobial Resistance and Food Safety: What Can We Learn from Genomics?

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

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 7963

Special Issue Editor

Dr. Saria Otani

E-Mail Website
Guest Editor
DTU Food, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark
Interests: metagenomics; animal and human health; microbiome–host interactions

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is one of the major threats to public health in modern times. Foodborne infections largely contribute to transmitting antimicrobial resistant bacteria, and pose a challenge not only regarding classical foodborne infectious agents such as Campylobacter, but also gut microbiome mutualistic bacteria such as the Bifidobacterium and Escherichia species. The characteristics and dynamics of foodborne diseases and AMR emergence and transmission are becoming increasingly clear with the advancements in next-generation sequencing and third-generation sequencing. This Special Issue seeks research articles that use metagenomics and genomics approaches to elucidate the dynamics and mode of actions between AMR and foodborne infections. It also seeks to investigate how sequencing-based approaches can further explore such topics, beyond simply the diagnosis and description of infectious agents and their AMR profiles.

Dr. Saria Otani
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

  • metagenomics
  • genomics
  • long-read (third-generation) sequencing
  • antimicrobial resistance
  • foodborne diseases

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Published Papers (3 papers)

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Research

11 pages, 1004 KiB  
Article
Foodborne Pathogen Dynamics in Meat and Meat Analogues Analysed Using Traditional Microbiology and Metagenomic Sequencing
by Francesco Bonaldo, Baptiste Jacques Philippe Avot, Alessandra De Cesare, Frank M. Aarestrup and Saria Otani
Antibiotics 2024, 13(1), 16; https://doi.org/10.3390/antibiotics13010016 - 21 Dec 2023
Viewed by 1976
Abstract
Meat analogues play an increasing role in meeting global nutritional needs. However, while it is well known that meat possesses inherent characteristics that create favourable conditions for the growth of various pathogenic bacteria, much less is known about meat analogues. This study aimed [...] Read more.
Meat analogues play an increasing role in meeting global nutritional needs. However, while it is well known that meat possesses inherent characteristics that create favourable conditions for the growth of various pathogenic bacteria, much less is known about meat analogues. This study aimed to compare the growth and survival of Escherichia coli HEHA16, Listeria monocytogenes, Salmonella enterica Typhi, Cronobacter sakazakii, and a cocktail of these bacteria in sterile juices from minced chicken, pig, and beef, as well as pea-based and soy-based minced meat. Traditional microbiology and next-generation sequencing of those metagenomes were employed to analyse the pathogen variability, abundance, and survival after an incubation period. Our findings show that all the meat juices provided favourable conditions for the growth and proliferation of the studied bacteria, with the exception of E. coli HEHA16, which showed lower survival rates in the chicken matrix. Meat analogue juice mainly supported L. monocytogenes survival, with C. sakazakii survival supported to a lesser extent. A correlation was observed between the traditional culturing and metagenomic analysis results, suggesting that further work is needed to compare these technologies in foodborne setups. Our results indicate that plant-based meats could serve as vectors for the transmission of certain, but likely not all, foodborne pathogens, using two accurate detection methods. This warrants the need for additional research to better understand and characterise their safety implications, including their potential association with additional pathogens. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Food Safety: What Can We Learn from Genomics?)
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14 pages, 1410 KiB  
Article
Antimicrobial Resistance Pattern, Clustering Mechanisms and Correlation Matrix of Drug-Resistant Escherichia coli in Black Bengal Goats in West Bengal, India
by Jaydeep Banerjee, Debaraj Bhattacharyya, Md Habib, Siddharth Chaudhary, Suman Biswas, Chinmoy Maji, Pramod Kumar Nanda, Arun K. Das, Premanshu Dandapat, Indranil Samanta, Jose M. Lorenzo, Triveni Dutt and Samiran Bandyopadhyay
Antibiotics 2022, 11(10), 1344; https://doi.org/10.3390/antibiotics11101344 - 1 Oct 2022
Cited by 3 | Viewed by 2415
Abstract
A cross-sectional study covering four agro-climatic zones of West Bengal, India, was carried out to understand the risk-factors, antimicrobial resistance mechanism and clustering of the resistance characteristics of Escherichia coli isolated from healthy (170) and diarrhoeic (74) goats reared under intensive (52) and [...] Read more.
A cross-sectional study covering four agro-climatic zones of West Bengal, India, was carried out to understand the risk-factors, antimicrobial resistance mechanism and clustering of the resistance characteristics of Escherichia coli isolated from healthy (170) and diarrhoeic (74) goats reared under intensive (52) and semi-intensive (192) farming practices. Of the 488 E. coli isolates, the majority, including the extended spectrum (n: 64, 13.11%) and AmpC β-lactamase (ACBL) (n: 86, 17.62%) producers, were resistant to tetracycline (25.2%), followed by enrofloxacin (24.5%), cefotaxime (21.5%) and amikacin (20.5%). Statistical modelling revealed that the isolates from diarrhoeic animals (p < 0.001) are likely to be more ACBL-positive than those from the healthy counterparts. Similarly, cefotaxime (p < 0.05) and enrofloxacin-resistance (p < 0.01) were significantly higher in diarrhoeic goats and in goats reared intensively. The isolates (n = 35) resistant to multiple drugs revealed the presence of β-lactamase [blaCTXM-1-(21), blaSHV-(7), blaTEM-(3), blaCMY-6-(1), blaCITM-(3)]; quinolone [qnrB-(10), qnrS-(7), aac(6’)-Ib-cr-(3)]; tetracycline [tetA-(19), tetB-(4)] and sulphonamide resistance determinants [sul1-(4)]; multiple plasmids, especially those belonging to the IncF and IncI1 replicon types; and active acrAB efflux pumps. Further, two isolates harbored the carbapenem resistance (blaNDM-5) gene and eight were strong biofilm producers. This first ever study conducted to unravel the status of AMR in goat farming reveals that not only the intensive farming practices but also certain clinical ailments such as diarrhoea can increase the shedding of the drug-resistant isolate. The emergence of multi-drug resistant (MDR) E. coli in goats, particularly those that are carbapenem resistant, is a cause for concern that indicates the spread of such pathogens even in the livestock sub-sector generally considered as naive. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Food Safety: What Can We Learn from Genomics?)
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13 pages, 315 KiB  
Article
Antibiotic Resistance Patterns of Listeria Species Isolated from Broiler Abattoirs in Lusaka, Zambia
by Prudence Mpundu, John Bwalya Muma, Andrew Nalishuwa Mukubesa, Henson Kainga, Steward Mudenda, Flavien Nsoni Bumbangi, Walter Muleya, Patrick Katemangwe and Musso Munyeme
Antibiotics 2022, 11(5), 591; https://doi.org/10.3390/antibiotics11050591 - 28 Apr 2022
Cited by 8 | Viewed by 2821
Abstract
L. monocytogenes is a public health threat linked to fast foods such as broiler chickens. This study aimed to verify the occurrence of Listeria species in chickens from abattoirs and evaluate their antimicrobial resistance. In total, 150 broiler carcass swabs distributed as cloacal [...] Read more.
L. monocytogenes is a public health threat linked to fast foods such as broiler chickens. This study aimed to verify the occurrence of Listeria species in chickens from abattoirs and evaluate their antimicrobial resistance. In total, 150 broiler carcass swabs distributed as cloacal (n = 60), exterior surface (n = 60), and environmental (n = 30) were collected. Listeria species were characterized using biochemical tests and PCR. We conducted antibiotic resistance tests using the disc diffusion and Etest (Biomerieux, Durham, NC, USA) methods. Overall isolation of Listeria species was 15% (23/150) 95% CI (10.16–22.33), 2% (3/150) 95% CI (0.52–6.19) and 13% (20/150) 95% CI (8.53–20.08) came from environmental swabs and carcass swabs, respectively. Proportions of positive Listeria isolates were L. monocytogenes 74% (17/23), L. welshimeri 22% (5/23), and L. innocua 4% (1/23). Listeria species from the exterior carcass swabs was 61% (14/23), cloacal swabs 26% (6/23), and environmental swabs 3% (3/23). L. monocytogenes had the greatest resistance percentage to the following antibiotics: clindamycin (61%, 10/23), tetracycline 30% (7/23), and erythromycin 13%, (3/23). Isolation of L. monocytogenes in relatively high numbers, including the antimicrobial profiles, suggests a potential risk of the pathogen remaining viable in the food continuum and a public health risk to would-be consumers. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Food Safety: What Can We Learn from Genomics?)
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