Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication

M Nazmul Hoque; Arif Istiaq; Rebecca A Clement; Keylie M Gibson; Otun Saha; Ovinu Kibria Islam; Ruhshan Ahmed Abir; Munawar Sultana; Amam Zonaed Siddiki; Keith A Crandall; M Anwar Hossain

doi:10.3389/fmicb.2020.00860

Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication

Front Microbiol. 2020 Jun 3:11:860. doi: 10.3389/fmicb.2020.00860. eCollection 2020.

Authors

M Nazmul Hoque^{1

2}, Arif Istiaq^{1

3}, Rebecca A Clement⁴, Keylie M Gibson⁴, Otun Saha¹, Ovinu Kibria Islam^{1

5}, Ruhshan Ahmed Abir⁶, Munawar Sultana¹, Amam Zonaed Siddiki⁷, Keith A Crandall^{4

8}, M Anwar Hossain¹

Affiliations

¹ Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
² Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.
³ Department of Developmental Neurobiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
⁴ Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.
⁵ Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.
⁶ Bio-Bio-1, Bioinformatics Research Foundation, Dhaka, Bangladesh.
⁷ Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh.
⁸ Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.

Abstract

Bovine clinical mastitis (CM) is one of the most prevalent diseases caused by a wide range of resident microbes. The emergence of antimicrobial resistance in CM bacteria is well-known, however, the genomic resistance composition (the resistome) at the microbiome-level is not well characterized. In this study, we applied whole metagenome sequencing (WMS) to characterize the resistome of the CM microbiome, focusing on antibiotics and metals resistance, biofilm formation (BF), and quorum sensing (QS) along with in vitro resistance assays of six selected pathogens isolated from the same CM samples. The WMS generated an average of 21.13 million reads (post-processing) from 25 CM samples that mapped to 519 bacterial strains, of which 30.06% were previously unreported. We found a significant (P = 0.001) association between the resistomes and microbiome composition with no association with cattle breed, despite significant differences in microbiome diversity among breeds. The in vitro investigation determined that 76.2% of six selected pathogens considered "biofilm formers" actually formed biofilms and were also highly resistant to tetracycline, doxycycline, nalidixic acid, ampicillin, and chloramphenicol and remained sensitive to metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found bacterial flagellar movement and chemotaxis, regulation and cell signaling, and oxidative stress to be significantly associated with the pathophysiology of CM. Thus, identifying CM microbiomes, and analyzing their resistomes and genomic potentials will help improve the optimization of therapeutic schemes involving antibiotics and/or metals usage in the prevention and control of bovine CM.

Keywords: clinical mastitis; in vitro resistance assays; microbiome; resistome; whole metagenome sequencing.