Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems

Vieira, Tatiana R.; de Oliveira, Esther F. Cavinatto; Cibulski, Samuel P.; Silva, Núbia M.V.; Borba, Mauro R.; Oliveira, Celso J.B.; Cardoso, Marisa

doi:10.1016/j.psj.2023.103002

Cited by 3 publications

(6 citation statements)

References 56 publications

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“…The literature contains numerous studies that demonstrate the circulation of a large diversity of known ARGs in the food chain, including several ARGs of critical importance (Alexa et al., 2024 ; Guron et al., 2019 ; Sequino et al., 2024 ; Vieira et al., 2023 ). According to the existing evidence, the major carriers of ARGs in food and associated environments are members of the ESKAPEE group and other closely related taxa, with notable examples including Pseudomonas , Acinetobacter and Staphylococcus .…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have described Pseudomonas , Acinetobacter and Aeromonas among the most predominant genera associated with AMR found in meat (Bloomfield et al., 2023 ; Li et al., 2020 ; Vieira et al., 2023 ). These findings are in agreement with studies that have identified Pseudomonas and Acinetobacter as highly prevalent on surfaces in slaughterhouses and meat processing facilities (Alvarez‐Molina et al., 2023 ; Cobo‐Díaz et al., 2021 ).…”

Section: The Resistome Of Food Productsmentioning

confidence: 99%

“…The ARGs most frequently identified in chicken and pork meats were associated with resistance to beta‐lactams, aminoglycosides or tetracyclines (Bloomfield et al., 2023 ; Li et al., 2020 ; Vieira et al., 2023 ). Furthermore, Bloomfield et al.…”

Section: The Resistome Of Food Productsmentioning

confidence: 99%

“…Vieira et al. ( 2023 ) found that the microbial composition and the profile of ARGs and mobile genetic elements in retail frozen chicken carcasses from certified organic production systems and certified antimicrobial‐free production were similar to those from conventional production systems. However, chicken carcasses from certified organic systems and antimicrobial‐free production had a lower abundance of ARGs and mobile genetic elements compared to those from conventional production systems.…”

Section: The Resistome Of Food Productsmentioning

confidence: 99%

“…This approach allows an in‐depth analysis of resistomes (the complete set of ARGs in a given niche) without the limitations of other methods, which are based on the analysis of a limited range of antimicrobial resistant strains from selected taxa through culture‐based approaches, or ARGs of concern through qPCR (De Filippis et al., 2017 ; Sabater et al., 2021 ). Recent research studies and perspective articles have highlighted the great potential of NGS for revealing the resistome composition in food products (Bloomfield et al., 2023 ; Vieira et al., 2023 ; Walsh et al., 2020 ) and food processing environments (Cobo‐Díaz et al., 2021 ; De Filippis et al., 2021 ), with important findings regarding the understanding of sources and routes of transmission of AMR throughout the food chain.…”

Section: Introductionmentioning

confidence: 99%

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The resistome of the food chain: A One Health perspective

Fernández‐Trapote,

Oliveira,

Cobo‐Díaz

et al. 2024

Microbial Biotechnology

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Antimicrobial resistance (AMR) represents a significant global health problem which challenges Sustainable Development Goal 3 of the United Nations, with growing concerns about the possibility of AMR transmission through the food chain. The indiscriminate use of antimicrobials for the treatment of food production animals and for agricultural crop improvement, in addition to the direct discharge of livestock farm residues to sewage and the use of animal manure in agriculture, are among the factors that can facilitate the selection and transmission of AMR throughout the food chain. The study of food microbiomes has been boosted by the advent of next‐generation sequencing techniques, which have enabled gaining in‐depth understanding of the diversity of antimicrobial resistance genes present in food and associated environments (the so‐called resistome). The aim of this review is to provide an accurate and comprehensive overview of the knowledge currently available on the resistome of the most frequently consumed foods worldwide, from a One Health perspective. To this end, the different metagenomic studies which have been conducted to characterize the resistome of foods are compiled and critically discussed.

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Section: Discussionmentioning

confidence: 99%

Section: The Resistome Of Food Productsmentioning

confidence: 99%

Section: The Resistome Of Food Productsmentioning

confidence: 99%

Section: The Resistome Of Food Productsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The resistome of the food chain: A One Health perspective

Fernández‐Trapote,

Oliveira,

Cobo‐Díaz

et al. 2024

Microbial Biotechnology

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Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

Pillay,

Calderón-Franco,

Abeel

2024

Preprint

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Purpose: Infectious diseases represent a major global health threat due to the rapid spread of pathogens, leading to widespread outbreaks. Concurrently, antimicrobial resistance (AMR) is increasing, making standard treatments less effective and complicating infection management. Effective surveillance systems are essential to address these challenges. Methods: We conducted a proof-of-concept study to evaluate a portable in-field microbial lab against a traditional molecular lab for DNA isolation, sequencing, microbial detection, antibiotic resistance gene identification, and plasmid classification. Samples from lake water, wastewater treatment plant sludge, and retail meat were selected to reflect relevant surveillance vectors. This approach provides valuable data for environmental monitoring, public health, and food safety, aiding in outbreak preparedness. We compared results using five metrics: DNA yield and purity, read N50, taxonomic classification, antibiotic resistance gene identification (ARGs), and plasmid classification. Results: Our study found that metagenomic bacterial DNA isolation from environmental and food sources is feasible with portable lab technology, producing >800ng of DNA, suitable for Nanopore sequencing. DNA from retail meat, lake, and sludge samples resulted in similar read numbers and read N50 values. Taxonomic classification was achieved at the genus and species levels. A Jaccard similarity of over 50% was observed in the top 20 most abundant species between chicken samples, and lake samples. ESKAPE pathogens were detected in chicken and lake samples. ARGs and plasmids were also identified in both retail meat and lake samples. Conclusion: This study demonstrates that in-field DNA isolation and sequencing are feasible with minimal equipment, yielding results comparable to traditional lab methods.

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Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

Pillay,

Calderón-Franco,

Abeel

2024

Preprint

View full text Add to dashboard Cite

Purpose Infectious diseases represent a major global health threat due to the rapid spread of pathogens, leading to widespread outbreaks. Concurrently, antimicrobial resistance (AMR) is increasing, making standard treatments less effective and complicating infection management. Effective surveillance systems are essential to address these challenges. Methods: We conducted a proof-ofconcept study to evaluate a portable in-field microbial lab against a traditional molecular lab for DNA isolation, sequencing, microbial detection, antibiotic resistance gene identification, and plasmid classification. Samples from lake water, wastewater treatment plant sludge, and retail meat were selected to reflect relevant surveillance vectors. This approach provides valuable data for environmental monitoring, public health, and food safety, aiding in outbreak preparedness. We compared results using five metrics: DNA yield and purity, read N50, taxonomic classification, antibiotic resistance gene identification (ARGs), and plasmid classification. Results: Our study found that metagenomic bacterial DNA isolation from environmental and food sources is feasible with portable lab technology, producing ≥ 800ng of DNA, suitable for Nanopore sequencing. DNA from retail meat, lake, and sludge samples resulted in similar read numbers and read N50 values. Taxonomic classification was achieved at the genus and species levels. A Jaccard similarity of over 50% was observed in the top 20 most abundant species between chicken samples, and lake samples. ESKAPE pathogens were detected in chicken and lake samples. ARGs and plasmids were also identified in both retail meat and lake samples. Conclusion: This study demonstrates that in-field DNA isolation and sequencing are feasible with minimal equipment, yielding results comparable to traditional lab methods.

show abstract

Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems

Cited by 3 publications

References 56 publications

The resistome of the food chain: A One Health perspective

The resistome of the food chain: A One Health perspective

Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

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