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Guo X, Zhang Z, Chen Q, Wang L, Xu X, Wei Z, Zhang Y, Chen K, Wang Z, Lu X, Liang Q. Whole Genome Sequencing Highlights the Pathogenic Profile in Nocardia Keratitis. Invest Ophthalmol Vis Sci 2024; 65:26. [PMID: 38502137 PMCID: PMC10959193 DOI: 10.1167/iovs.65.3.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Purpose Nocardia keratitis is a serious and sight-threatening condition. This study aims to reveal the virulence and antimicrobial resistance gene profile of Nocardia strains using whole genome sequencing. Methods Whole-genome sequencing was performed on 23 cornea-derived Nocardia strains. Together with genomic data from the respiratory tract and the environment, 141 genomes were then utilized for phylogenetic and pan-genome analyses, followed by virulence and antibiotic resistance analysis. The correlations between virulence genes and pathogenicity were experimentally validated, including the characteristics of Nocardia colonies and clinical and histopathological evaluations of Nocardia keratitis mice models. Results Whole-genome sequencing of 141 Nocardia strains revealed a mean of 220 virulence genes contributed to bacterial pathogenesis. The mce gene family analysis led to the categorization of strains from the cornea into groups A, B, and C. The colonies of group C had the largest diameter, height, and fastest growth rate. The size of corneal ulcers and the clinical scores showed a significant increase in mouse models induced by group C. The relative expression levels of pro-inflammatory cytokines (CD4, IFN-γ, IL-6Rα, and TNF-α) in the lesion area exhibited an increasing trend from group A to group C. Antibiotic resistance genes (ARGs) spanned nine distinct drug classes, four resistance mechanisms, and seven primary antimicrobial resistance gene families. Conclusions Whole genome sequencing highlights the pathogenic role of mce gene family in Nocardia keratitis. Its distribution pattern may contribute to the distinct characteristics of the growth of Nocardia colonies and the clinical severity of the mice models.
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Affiliation(s)
- Xiaoyan Guo
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zijun Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qiankun Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Leying Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xizhan Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhenyu Wei
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Kexin Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhiqun Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xinxin Lu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qingfeng Liang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Nathar S, Rajmichael R, Jeyaraj Pandian C, Nagarajan H, Mathimaran A, Kingsley JD, Jeyaraman J. Exploring Nocardia's ecological spectrum and novel therapeutic frontiers through whole-genome sequencing: unraveling drug resistance and virulence factors. Arch Microbiol 2024; 206:76. [PMID: 38267747 DOI: 10.1007/s00203-023-03799-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024]
Abstract
Nocardia farcinica is the leading pathogen responsible for nocardiosis, a life-threatening infection primarily affecting immunocompromised patients. In this study, the genomic sequence of a clinically isolated N. farcinica sample was sequenced. Subsequently, the assembled genome was annotated to identify antimicrobial resistance and virulence genes, as well as plasmid and prophages. The analysis of the entire genome size was 6,021,225 bp, with a GC content of 70.78% and consists of 103 contigs and N50 values of 292,531 bp. The genome analysis revealed the presence of several antimicrobial resistance genes, including RbpA, mtrA, FAR-1, blaFAR-1, blaFAR-1_1, and rox. In addition, virulence genes such as relA, icl, and mbtH were also detected. The present study signifies that N. farcinica genome is pivotal for the understanding of antimicrobial resistance and virulence genes is crucial for comprehending resistance mechanism, and developing effective strategies to combat bacterial infections effectively, especially adhesins and toxins. This study aids in identifying crucial drug targets for combating multidrug-resistant N. farcinica in the future.
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Affiliation(s)
- Shaslinah Nathar
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Chitra Jeyaraj Pandian
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, 630 003, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Ahila Mathimaran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India
| | - Jemima D Kingsley
- Orbito Asia Diagnostics Private Limited Coimbatore, Coimbatore, 641 045, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, 630 003, Tamil Nadu, India.
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