Multi-Platform Approaches for Comprehensive Resistome Profiling in Poultry

Multi-Platform Approaches for Comprehensive Resistome Profiling in Poultry

Abstrakt

Antimicrobial resistance is an escalating global challenge that threatens human health, food security, and medical advancements (1). Over the past few decades, the overuse and misuse of antibiotics have significantly contributed to the global antimicrobial resistance crisis (2). The resistome, comprising antimicrobial resistance genes, provides crucial insights into the mobilome and antimicrobial resistance mechanisms, with the gut microbiome of livestock—especially chickens—serving as a major reservoir that enables ARG transmission between animals and humans (3). Modern molecular approaches have significantly enhanced our understanding of antimicrobial resistance mechanisms and their distribution. Advanced molecular techniques, including transcriptomics, proteomics, and metabolomics, have improved the detection and analysis of antimicrobial resistance across diverse clinical, environmental, and agricultural samples (4,5). In parallel, analytical methods such as chromatographic and spectrometric techniques are employed for the identification and quantification of antibiotic residues across diverse matrices, offering rapid, reliable, highly selective, and sensitive detection of multiple compounds simultaneously (6). This study analyzed fecal samples from broiler chickens at a commercial farm in the Czech Republic using different molecular and MS-based approaches such as metagenomic sequencing, HT-qPCR and LC-MS/MS. DNA from 40-day-old chickens was sequenced using shotgun metagenomics, generating approximately 10 GB of data per sample for downstream analysis. Genes associated with antibiotic resistance were identified, revealing that the most abundant resistance genes belonged to aminoglycosides, MLSB classes. As a consequence of antibiotic treatment, enrofloxacin (ENR) was detected in the samples, along with its known metabolite and degradation product, ciprofloxacin, which was present in all samples. Furthermore, every sample tested positive for resistance genes related to at least one of the following antibiotic classes: betalactams, multidrug resistance, aminoglycosides, tetracyclines, quinolones, MLSB, or vancomycin. The findings highlight a high prevalence of ARGs and antibiotics residues in poultry gut microbiomes, underscoring the need for continuous surveillance. This complementary approach provides a robust framework for tracking the dissemination of antibiotic resistance in agricultural environments and supports the development of more targeted and effective antimicrobial stewardship strategies.

Antimicrobial resistance is an escalating global challenge that threatens human health, food security, and medical advancements (1). Over the past few decades, the overuse and misuse of antibiotics have significantly contributed to the global antimicrobial resistance crisis (2). The resistome, comprising antimicrobial resistance genes, provides crucial insights into the mobilome and antimicrobial resistance mechanisms, with the gut microbiome of livestock—especially chickens—serving as a major reservoir that enables ARG transmission between animals and humans (3). Modern molecular approaches have significantly enhanced our understanding of antimicrobial resistance mechanisms and their distribution. Advanced molecular techniques, including transcriptomics, proteomics, and metabolomics, have improved the detection and analysis of antimicrobial resistance across diverse clinical, environmental, and agricultural samples (4,5). In parallel, analytical methods such as chromatographic and spectrometric techniques are employed for the identification and quantification of antibiotic residues across diverse matrices, offering rapid, reliable, highly selective, and sensitive detection of multiple compounds simultaneously (6). This study analyzed fecal samples from broiler chickens at a commercial farm in the Czech Republic using different molecular and MS-based approaches such as metagenomic sequencing, HT-qPCR and LC-MS/MS. DNA from 40-day-old chickens was sequenced using shotgun metagenomics, generating approximately 10 GB of data per sample for downstream analysis. Genes associated with antibiotic resistance were identified, revealing that the most abundant resistance genes belonged to aminoglycosides, MLSB classes. As a consequence of antibiotic treatment, enrofloxacin (ENR) was detected in the samples, along with its known metabolite and degradation product, ciprofloxacin, which was present in all samples. Furthermore, every sample tested positive for resistance genes related to at least one of the following antibiotic classes: betalactams, multidrug resistance, aminoglycosides, tetracyclines, quinolones, MLSB, or vancomycin. The findings highlight a high prevalence of ARGs and antibiotics residues in poultry gut microbiomes, underscoring the need for continuous surveillance. This complementary approach provides a robust framework for tracking the dissemination of antibiotic resistance in agricultural environments and supports the development of more targeted and effective antimicrobial stewardship strategies.

Antibacterial Resistance Genes (ARGs), Resistome, Metagenomic sequencing, MS-based approaches.

Antibacterial Resistance Genes (ARGs), Resistome, Metagenomic sequencing, MS-based approaches.

Minoo Partovi Nasr1, Marie Hamplová2, Veronika Farkova2, Helena Zlamalova Gargosova 2, Darina Cejkova1 1Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic 2 Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic

22.09.2025

molecular biology

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https://www.microbiome.at/