Molecular Identification and Phylogenetic Analysis of Fluoroquinolone-Resistant Bacteria Isolated from Poultry Manure-Amended Agricultural Soils in Khorasan Razavi Province, Iran

Document Type : Original Article

Authors

1 Dept. of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran.

2 Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran

10.22111/jep.2026.55880.1112

Abstract

Long-term poultry manure application introduces strong selective pressure and persistent veterinary antibiotic residues into agricultural soils, establishing critical environmental antimicrobial resistance hotspots. This study investigated the molecular taxonomy, phenotypic traits, and phylogenetic diversity of fluoroquinolone-resistant bacteria isolated from manure-amended fields in Khorasan Razavi Province, northeastern Iran. Cultivation on ciprofloxacin-supplemented selective media yielded three resistant bacterial isolates; among these, a distinct Gram-negative coccobacillus exhibited high-level phenotypic resistance with an exceptionally high minimum inhibitory concentration (MIC) of 35 µg/mL. Bidirectional Sanger sequencing successfully recovered a 1,411 bp fragment of its 16S rRNA gene. Although preliminary BLASTn alignment analysis showed a high sequence identity of 98.87% to Acinetobacter baumannii reference strains, a global Maximum Likelihood phylogenetic tree reconstructed using RAxML with 500 bootstrap replicates definitively revealed that the isolate does not cluster within the strict A. baumannii monophyletic clade (97% support). Instead, it occupies a unique, transitional phylogenetic position as a sister lineage to Acinetobacter soli and the core A. baumannii complex, leading to its taxonomic classification as Acinetobacter sp. strain NEY04 (GenBank: PZ542786). Ultimately, given the prominent role of this genus in driving horizontal gene transfer, these findings establish a vital evolutionary baseline for future down-stream sequencing of specific genetic mechanisms within environmental agro-ecosystems.

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Journal of Epigenetics
Volume 7, Issue 1
April 2026
Pages 56-63

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History

  • Receive Date: 18 June 2026
  • Accept Date: 22 June 2026

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