Evidence map›Paper›PMID 41535901›Full record

ArticleBMC veterinary research2026

Whole genome sequencing reveals environmental pathogen misidentification and potential for cross-phylum antimicrobial resistance gene transfer in bovine mastitis: a pilot genomic study.

A Muhee, A Pandit, Sobby Jan, Iqra Shafi Khan, Nuzhat Hassan, R A Bhat, M I Yatoo

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Article in BMC veterinary research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

7 authors.

A MuheeDivision of Veterinary Clinical Complex, FVSc & AH, Shuhama, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India.
A PanditMountain Livestock Research Institute, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India. arif.pandit@skuastkashmir.ac.in.
Sobby JanDivision of Veterinary Epidemiology and Preventive Medicine, FVSc & AH, Shuhama, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India.
Iqra Shafi KhanDivision of Veterinary Clinical Complex, FVSc & AH, Shuhama, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India.
Nuzhat HassanDivision of Veterinary Epidemiology and Preventive Medicine, FVSc & AH, Shuhama, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India.
R A BhatDivision of Veterinary Clinical Complex, FVSc & AH, Shuhama, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India.
M I YatooDivision of Veterinary Clinical Complex, FVSc & AH, Shuhama, Sher E Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe diagnosis of bovine mastitis relies predominantly on conventional microbiological methods optimized for common pathogens, potentially ignoring environmental bacteria with complex antimicrobial resistance profiles.

methodsThis pilot study combined conventional identification with whole genome sequencing (WGS) analysis of bovine mastitis isolates. A total of 330 milk samples were analyzed using standard microbiological methods, followed by comprehensive genomic characterization of two representative multidrug-resistant isolates using Illumina NovaSeq 6000 sequencing. The limited sample size reflects the pilot nature of this proof-of-concept study. Analysis of antimicrobial resistance genes was performed using BLAST searches against the Comprehensive Antibiotic Resistance Database.

resultsOf 330 samples, 202 (61.2%) tested positive for mastitis. WGS revealed misidentification of critical species of an environmental pathogen (Stutzerimonas stutzeri) and comparative analysis with E. coli (included as a control for a known mastitis pathogen). An isolate originally characterized as Gram-positive with Staphylococcus-like morphology was definitively identified as Stutzerimonas stutzeri by genomic analysis. Both isolates harbored diverse antimicrobial resistance genes with phylogenetic origins spanning multiple bacterial orders and phyla (Enterobacterales, Bacillales, Pseudomonadales, Enterococcales), suggesting a potential for horizontal gene transfer. Mobile genetic elements such as plasmids, integrons and insertion sequences were identified in both genomes, consistent with the ability for gene mobility. Phylogenetic analysis revealed that resistance genes originated from Proteobacteria (61%) and Firmicutes (39%), indicating cross-phylum gene exchange.

conclusionsThis pilot study provides preliminary evidence that whole genome sequencing can identify bacterial species that may be missed by traditional diagnostic methods. Analysis of two isolates revealed evidence of horizontal gene transfer potential in mastitis-associated bacteria. The environmental pathogen S. stutzeri may represent a poorly recognized opportunistic mastitis pathogen with significant resistance potential. Based on these exploratory findings from two cases, our results suggest the potential utility of genomic surveillance approaches in veterinary diagnostic microbiology, necessitating larger validation studies.

Indexed as

Drug Resistance, BacterialDrug Resistance, Multiple, BacterialMastitis, BovineAnimalsCattleFemaleGene Transfer, HorizontalGenome, BacterialMilkPhylogenyPilot ProjectsWhole Genome SequencingAntimicrobial resistanceBovine mastitisDairy cattleDiagnostic limitationsHorizontal gene transferStutzerimonas stutzeriVeterinary microbiologyWhole genome sequencing

Identifiers

PMID41535901
PMCPMC12933902

What Socratic holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.