Pilot Study on Poultry Meat from Antibiotic Free and Conventional Farms: Can Metagenomics Detect Any Difference?

Cesare, Alessandra De; Oliveri, Chiara; Lucchi, Alex; Savini, Federica; Manfreda, Gerardo; Sala, Claudia

doi:10.3390/foods11030249

Cited by 17 publications

(22 citation statements)

References 47 publications

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“…More recently, a single antibiotic-free broiler farm, located in northern Italy, was investigated to quantify some representative ARGs at different sampling sites [ 15 ]. Finally, a metagenomic approach, with the aim to analyze the cecal resistome of broiler carcasses at the slaughterhouse, was performed by De Cesare et al [ 14 ]. In this respect, our study represents a first attempt to compare the distribution of different ARGs against several classes of antibiotics between conventional and antibiotic-free poultry farming systems in Italy, sampling the fecal specimens at the flock level and applying a rapid, low-cost, and relatively easy-to-perform method.…”

Section: Discussionmentioning

confidence: 99%

“…A pilot study, carried out to investigate the intestinal microbioma and ARGs from conventional and antibiotic-free chickens, highlighted a significantly lower antimicrobial resistance load in antibiotic-free production lines. However, this evidence disappeared when the corresponding carcasses were compared [ 14 ]. Conversely, Salerno et al [ 15 ] demonstrated that the abundance of ARGs harbored by the microbial community coming from broilers raised without antibiotics can be considered comparable to what has been reported in conventional farms.…”

Section: Introductionmentioning

confidence: 99%

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Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy

Farooq

Smoglica

Ruffini³

et al. 2022

Animals

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Antimicrobial resistance is a complex and widespread problem threatening human and animal health. In poultry farms, a wide distribution of resistant bacteria and their relative genes is described worldwide, including in Italy. In this paper, a comparison of resistance gene distribution in litter samples, recovered from four conventional and four antibiotic-free broiler flocks, was performed to highlight any influence of farming systems on the spreading and maintenance of resistance determinants. Conventional PCR tests, targeting the resistance genes related to the most used antibiotics in poultry farming, along with some critically important antibiotics for human medicine, were applied. In conventional farms, n. 10 out of n. 30 investigated genes were present in at least one sample, the most abundant fragments being the tet genes specific for tetracyclines, followed by those for aminoglycosides and chloramphenicol. All conventional samples resulted negative for colistin, carbapenems, and vancomycin resistance genes. A similar trend was observed for antibiotic-free herds, with n. 13 out of n. 30 amplified genes, while a positivity for the mcr-1 gene, specific for colistin, was observed in one antibiotic-free flock. The statistical analysis revealed a significant difference for the tetM gene, which was found more frequently in the antibiotic-free category. The analysis carried out in this study allowed us to obtain new data about the distribution of resistance patterns in the poultry industry in relation to farming types. The PCR test is a quick and non-expensive laboratory tool for the environmental monitoring of resistance determinants identifying potential indicators of AMR dissemination.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy

Farooq

Smoglica

Ruffini³

et al. 2022

Animals

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“…Indeed, the effects of different rearing management programs, including CONV and RWA, on growth performance and meat quality in broiler chickens have been investigated in both research and commercial settings [ 20 ]. Antibiotic effects on the gut microbiome composition and diversity have also been investigated in several research trials; however, whether the results of these studies reflect the changes in microbiome under field conditions remains to be investigated [ 20 , 21 ].…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, a higher evenness and diversity were observed in the cecal microbiome of chickens treated with a cocktail of antibiotics compared to the control group that did not receive any antibiotics or feed additives [ 22 ]. Diverse factors, such as gut health management practices and chicken age and breed, can influence the microbiota diversity and population [ 20 , 21 , 23 ]. The notable increase in the cecal microbiome richness and diversity in the conventionally grown chickens on days 10 and 24 could be due to the elimination of the growth of microorganisms in a broad sense by antibiotics might have resulted in an increased abundance of nutrients and ecological niches for the growth of endogenous and exogenous microbes [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens

Kairmi,

Abdelaziz,

Spahany

et al. 2024

PLoS ONE

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The present study was undertaken to profile and compare the cecal microbial communities in conventionally (CONV) grown and raised without antibiotics (RWA) broiler chickens. Three hundred chickens were collected from five CONV and five RWA chicken farms on days 10, 24, and 35 of age. Microbial genomic DNA was extracted from cecal contents, and the V4-V5 hypervariable regions of the 16S rRNA gene were amplified and sequenced. Analysis of 16S rRNA sequence data indicated significant differences in the cecal microbial diversity and composition between CONV and RWA chickens on days 10, 24, and 35 days of age. On days 10 and 24, CONV chickens had higher richness and diversity of the cecal microbiome relative to RWA chickens. However, on day 35, this pattern reversed such that RWA chickens had higher richness and diversity of the cecal microbiome than the CONV groups. On days 10 and 24, the microbiomes of both CONV and RWA chickens were dominated by members of the phylum Firmicutes. On day 35, while Firmicutes remained dominant in the RWA chickens, the microbiome of CONV chickens exhibited am abundance of Bacteroidetes. The cecal microbiome of CONV chickens was enriched with the genus Faecalibacterium, Pseudoflavonifractor, unclassified Clostridium_IV, Bacteroides, Alistipes, and Butyricimonas, whereas the cecal microbiome of RWA chickens was enriched with genus Anaerofilum, Butyricicoccu, Clostridium_XlVb and unclassified Lachnospiraceae. Overall, the cecal microbiome richness, diversity, and composition were greatly influenced by the management program applied in these farms. These findings provide a foundation for further research on tailoring feed formulation or developing a consortium to modify the gut microbiome composition of RWA chickens.

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“…Shotgun whole-metagenome sequencing (WMS) is a reliable tool that can provide a comprehensive and high-resolution analysis of the microbiome and resistome ( Schmieder and Edwards, 2011 ; Nesme et al, 2014 ; Ghanbari et al, 2019 ; Ma et al, 2021 ), and it has been applied to quantify the abundance of many resistance genes in parallel in poultry ( Wang et al, 2017 ; Kumar et al, 2020 ), cattle ( Thomas et al, 2017 ), pig ( Ghanbari et al, 2019 ; Mencía-Ares et al, 2020 ) and the human gut ( Feng et al, 2018 ). Other metagenomic studies have found multiple ARGs in chicken gut as well ( Tong et al, 2017 ; Xiong et al, 2018 ; Eckstrom and Barlow, 2019 ; Wang Y. et al, 2021 ; De Cesare et al, 2022 ). However, WMS provides only limited information regarding ARG activity or the overall functional profile of the active microbial community.…”

Section: Discussionmentioning

confidence: 93%

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

Koorakula

Schiavinato

Ghanbari³

et al. 2022

Front. Microbiol.

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The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

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Pilot Study on Poultry Meat from Antibiotic Free and Conventional Farms: Can Metagenomics Detect Any Difference?

Cited by 17 publications

References 47 publications

Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy

Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

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