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. 2025 Apr 22:15:1549523.
doi: 10.3389/fcimb.2025.1549523. eCollection 2025.

The metagenomic and whole-genome metagenomic detection of multidrug-resistant bacteria from subclinical mastitis-affected cow's milk in India

Ayyasamy Manimaran  1 , Perumal Arumugam Desingu  2 , Arumugam Kumaresan  1 , Poonam Singh  1 , Komala Subramanya  1 , Pramod Dodamani  1 , Parmar Ankitkumar Dineshbhai  1
Affiliations

The metagenomic and whole-genome metagenomic detection of multidrug-resistant bacteria from subclinical mastitis-affected cow's milk in India

Ayyasamy Manimaran et al. Front Cell Infect Microbiol. .

Abstract

Multidrug-resistant (MDR) bacteria in farm animal products threaten human health by causing zoonotic infections. The complete genome sequences of MDR bacteria from subclinical mastitis-affected cow's milk have not yet been comprehensively documented in India. In this study, using a bacterial metagenomic sequencing approach, we detected the nearly complete genome sequences of Pseudomonas veronii and Staphylococcus xylosus from subclinical mastitis-affected cow's milk. Furthermore, we sequenced the nearly complete genome sequences of Escherichia coli, Klebsiella pneumoniae, Staphylococcus hominis, and S. xylosus from subclinical mastitis-affected cow's milk using a whole-genome metagenomic sequencing method. Our analysis subsequently revealed that the complete genome sequences of the identified bacteria contained MDR genes and genes for multiple virulence factors. These MDR bacteria may pose a public health risk through exposure to milkers, milk handlers, and farm workers or through the handling and consumption of unpasteurized milk.

Keywords: E. coli; ESKAPE pathogens; mastitis-affected cow’s milk; multidrug-resistant bacteria; pathogenic bacteria.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
(A) Cow with clinical mastitis-affected udder. (B) Formation of gel in the paddle containing an equal amount of milk and CMT solution, indicating the SCM in the left front quarter of the cow. (C) IMViC tests show positive for the indole and methyl red tests and negative for the remaining tests. It is indicative of Escherichia coli-positive. (D) Pink colonies of E coli growth on MacConkey agar. (E) Pink color rod-shaped E coli in Gram staining. (F) Yellow color Staphylococcus spp. colony growth in MSA. (G) Bunch of grape-like purple color Staphylococcus spp. cocci in Gram staining. (H) Colorless Streptococcus spp. colony growth in Edward’s medium. (I) Purple color chains of Streptococcus spp. cocci in Gram staining.
Figure 2
Figure 2
The circular genome map depicting the ORFs, CARDs, rRNAs, ncRNAs, and tRNAs of (A) Escherichia coli, (B) Klebsiella pneumoniae, and (C) Staphylococcus hominis.
Figure 3
Figure 3
The circular genome map depicting the ORFs, CARDs, rRNAs, ncRNAs, and tRNAs of (A) Staphylococcus xylosus, (B) Pseudomonas veronii, and (C) Staphylococcus xylosus (detected using the metagenomic approach).
Figure 4
Figure 4
The table represents the virulence genes detected in Escherichia coli, Klebsiella pneumoniae, Staphylococcus hominis, Staphylococcus xylosus, and Pseudomonas veronii (details are provided in Supplementary Data Sheet 3 ).
See this image and copyright information in PMC

References

    1. Alawneh J. I., Vezina B., Ramay H. R., Al-Harbi H., James A. S., Soust M., et al. . (2020). Survey and sequence characterization of bovine mastitis-associated escherichia coli in dairy herds. Front. Vet. Sci. 7. doi: 10.3389/fvets.2020.582297 - DOI - PMC - PubMed
    1. Alcock B. P., Huynh W., Chalil R., Smith K. W., Raphenya A. R., Wlodarski M. A., et al. . (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 51, D690–D699. doi: 10.1093/nar/gkac920 - DOI - PMC - PubMed
    1. Anika T. T., Noman Z. A., Islam M. S., Sultana N., Ashraf M. N., Pervin M., et al. . (2023). Draft genome sequence of multidrug-resistant Escherichia coli MAHK_SCM_BAU_30A strain isolated from a subclinical mastitis cow in Bangladesh. Microbiol. Resour. Announc. 12, e0071323. doi: 10.1128/MRA.00713-23 - DOI - PMC - PubMed
    1. Ashraf D., Ombarak R. A., Samir A., Abdel-Salam A. B. (2023). Characterization of multidrug-resistant potential pathogens isolated from milk and some dairy products in Egypt. J. Adv. Vet. Anim. Res. 10, 275–283. doi: 10.5455/javar.2023.j679 - DOI - PMC - PubMed
    1. Azimi S., Thomas J., Cleland S. E., Curtis J. E., Goldberg J. B., Diggle S. P. (2021). O-specific antigen-dependent surface hydrophobicity mediates aggregate assembly type in pseudomonas aeruginosa. mBio 12, e0086021. doi: 10.1128/mBio.00860-21 - DOI - PMC - PubMed

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