Assessment of Antibiotic Residues and Antibiotic Resistance Genes in Poultry Gut Microbiome

Assessment of Antibiotic Residues and Antibiotic Resistance Genes in Poultry Gut Microbiome

Conference proceedings

Livestock farming is a major contributor to the environmental release of antibiotics. Manure containing antibiotic residues is applied to fields as fertilizer, leading to the contamination of soil. The presence of antibiotics and their metabolites in the environment contributes to the development of antimicrobial resistance of bacteria (AMR), which poses a serious risk to human health. Moreover, the gut microbiome of livestock by itself—especially chickens—serves as a major reservoir enabling the transmission of antibiotic resistance genes (ARGs) between animals and humans. This study analysed fecal samples from chickens at a commercial farm in the Czech Republic, where antibiotic treatment was applied. Antibiotic residues were quantified using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Metagenomic sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) were used to identify genes associated with antibiotic resistance (ARGs). As a consequence of antibiotic treatment, enrofloxacin (ENR) was detected in the samples (up to tens of mg/kg), along with its known metabolite and degradation product, ciprofloxacin (CIP), which was present in all samples (up to units of mg/kg). The concentration of ENR in fecal samples decreased exponentially over time following antibiotic administration, with the trend being statistically significant. A simultaneous decrease in CIP concentration was also observed. DNA from 40-day-old chickens was sequenced using shotgun metagenomics, subsequently ARGs were identified in the fecal samples, revealing that the most abundant resistance genes belonged to aminoglycosides, MLSB (Macrolide–Lincosamide–Streptogramin B) and tetracyclines classes. The obtained results reveal a high presence of ARGs and antibiotic residues in the poultry gut microbiome, highlighting the need for continuous monitoring. This complementary approach provides a solid foundation for tracking the spread of antimicrobial resistance in agricultural environments.

Livestock farming is a major contributor to the environmental release of antibiotics. Manure containing antibiotic residues is applied to fields as fertilizer, leading to the contamination of soil. The presence of antibiotics and their metabolites in the environment contributes to the development of antimicrobial resistance of bacteria (AMR), which poses a serious risk to human health. Moreover, the gut microbiome of livestock by itself—especially chickens—serves as a major reservoir enabling the transmission of antibiotic resistance genes (ARGs) between animals and humans. This study analysed fecal samples from chickens at a commercial farm in the Czech Republic, where antibiotic treatment was applied. Antibiotic residues were quantified using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Metagenomic sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) were used to identify genes associated with antibiotic resistance (ARGs). As a consequence of antibiotic treatment, enrofloxacin (ENR) was detected in the samples (up to tens of mg/kg), along with its known metabolite and degradation product, ciprofloxacin (CIP), which was present in all samples (up to units of mg/kg). The concentration of ENR in fecal samples decreased exponentially over time following antibiotic administration, with the trend being statistically significant. A simultaneous decrease in CIP concentration was also observed. DNA from 40-day-old chickens was sequenced using shotgun metagenomics, subsequently ARGs were identified in the fecal samples, revealing that the most abundant resistance genes belonged to aminoglycosides, MLSB (Macrolide–Lincosamide–Streptogramin B) and tetracyclines classes. The obtained results reveal a high presence of ARGs and antibiotic residues in the poultry gut microbiome, highlighting the need for continuous monitoring. This complementary approach provides a solid foundation for tracking the spread of antimicrobial resistance in agricultural environments.

antibiotics; enrofloxacin; ciprofloxacin; poultry; metagenomics; HT-qPCR; antibiotic resistance genes (ARGs); antimicrobial resistance (AMR); livestock farming; LC-MS/MS

antibiotics; enrofloxacin; ciprofloxacin; poultry; metagenomics; HT-qPCR; antibiotic resistance genes (ARGs); antimicrobial resistance (AMR); livestock farming; LC-MS/MS

HAMPLOVÁ, M.; PARTOVI NASR, M.; ČEJKOVÁ, D.; FARKOVÁ, V.; ZLÁMALOVÁ GARGOŠOVÁ, H.

09.09.2025

Spektroskopická společnost Jana Marka Marci

Brno

978-80-88195-68-9

1

https://skolams2025.spektroskopie.cz/sites/default/files/SkolaMS_2025_Mladi_vpred_a_postery.pdf

Abstrakt Hamplova M_