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. 2024 Jun 29;14(13):1927.
doi: 10.3390/ani14131927.

Comprehensive Metagenomic Analysis of Veterinary Probiotics in Broiler Chickens

Ádám Kerek  1   2 , István László Román  1 , Ábel Szabó  1 , Márton Papp  2   3 , Krisztián Bányai  1   2   4 , Gábor Kardos  2   5   6   7 , Eszter Kaszab  2   5   8 , Krisztina Bali  2   8 , László Makrai  9 , Ákos Jerzsele  1   2
Affiliations

Comprehensive Metagenomic Analysis of Veterinary Probiotics in Broiler Chickens

Ádám Kerek et al. Animals (Basel). .

Abstract

Probiotics are widely used in broiler chickens to support the gut microbiome, gut health, and to reduce the amount of antibiotics used. Despite their benefits, there is concern over their ability to carry and spread antimicrobial resistance genes (ARGs), posing a significant public health risk. This study utilized next-generation sequencing to investigate ARGs in probiotics approved for poultry, focusing on their potential to be transferred via mobile genetic elements such as plasmids and phages. We examined the gut microbiome and resistome changes in 60 broiler chickens over their rearing period, correlating these changes with different probiotic treatments. Specific resistance mechanisms against critically important antibiotics were identified, including genes related to fluoroquinolone resistance and peptide antibiotic resistance. We also found genes with significant relevance to public health (aadK, AAC(6')-Ii) and multiple drug-resistance genes (vmlR, ykkC, ykkD, msrC, clbA, eatAv). Only one phage-encoded gene (dfrA43) was detected, with no evidence of plasmid or mobile genetic element transmission. Additionally, metagenomic analysis of fecal samples showed no significant changes corresponding to time or diet across groups. Our findings highlight the potential risks associated with the use of probiotics in poultry, particularly regarding the carriage of ARGs. It is crucial to conduct further research into the molecular genetics of probiotics to develop strategies that mitigate the risk of resistance gene transfer in agriculture, ensuring the safe and effective use of probiotics in animal husbandry.

Keywords: NGS; Ross308; antimicrobial resistance; broilers; chickens; probiotics.

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Conflict of interest statement

László Makrai is employed at Autovakcina Kft. company. This organization played no role in sponsoring this research or product advertising. The authors declare no financial interest or relevant conflicts of interest.

Figures

Figure 1
Figure 1
Average weight gain of broilers per week, per group (n = 10 chickens/group). Group I served as the negative control and did not receive probiotics. Group II was treated with BioPlus YC, containing Bacillus licheniformis and Bacillus subtilis. Group III received Agroferm M+C, which includes Enterococcus faecium, Lactobacillus plantarum, and Pediococcus acidilactici. Group IV was given Ecobiol WX, containing Bacillus amyloliquefaciens. Group V received Gastroferm M+C, consisting of Lactobacillus plantarum, Pediococcus acidilactici, and Enterococcus faecium. Finally, Group VI was administered Fecinor Soluble Plus, which contains Enterococcus faecium.
Figure 2
Figure 2
Composition and variation of each sample in response to rearing and different probiotics fed at genus level, expressed as % of total sequence. D—day.
Figure 3
Figure 3
Changes in the microbiome composition at 4 and 42 days of age. D—day.
Figure 4
Figure 4
The enrichment solution containing tiamulin and florfenicol not only eliminated resistant strains in the samples but also led to an enrichment of Gram-negative bacteria. D—day.
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