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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [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: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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Yuan J, Fei S, Gui Z, Wang Z, Chen H, Sun L, Tao J, Han Z, Ju X, Tan R, Gu M, Huang Z. Association of UGT1A Gene Polymorphisms with BKV Infection in Renal Transplantation Recipients. Curr Drug Metab 2024; 25:188-196. [PMID: 38509677 DOI: 10.2174/0113892002282727240307072255] [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: 11/28/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND BK virus (BKV) infection is an opportunistic infectious complication and constitutes a risk factor for premature graft failure in kidney transplantation. Our research aimed to identify associations and assess the impact of single-nucleotide polymorphisms (SNPs) on metabolism-related genes in patients who have undergone kidney transplantation with BKV infection. MATERIAL/METHODS The DNA samples of 200 eligible kidney transplant recipients from our center, meeting the inclusion criteria, have been collected and extracted. Next-generation sequencing was used to genotype SNPs on metabolism-associated genes (CYP3A4/5/7, UGT1A4/7/8/9, UGT2B7). A general linear model (GLM) was used to identify and eliminate confounding factors that may influence the outcome events. Multiple inheritance models and haplotype analyses were utilized to identify variation loci associated with infection caused by BKV and ascertain haplotypes, respectively. RESULTS A total of 141 SNPs located on metabolism-related genes were identified. After Hardy-Weinberg equilibrium (HWE) and minor allele frequency (MAF) analysis, 21 tagger SNPs were selected for further association analysis. Based on GLM results, no confounding factor was significant in predicting the incidence of BK polyomavirus-associated infection. Then, multiple inheritance model analyses revealed that the risk of BKV infection was significantly associated with rs3732218 and rs4556969. Finally, we detect significant associations between haplotype T-A-C of block 2 (rs4556969, rs3732218, rs12468274) and infection caused by BKV (P = 0.0004). CONCLUSION We found that genetic variants in the UGT1A gene confer BKV infection susceptibility after kidney transplantation.
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Affiliation(s)
- Jingwen Yuan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zeping Gui
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Xiaobing Ju
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Min Gu
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
- Department of Urology, The Second Affiliated Hospital with Nanjing Medical University, Nanjing, 210011, China
| | - Zhengkai Huang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
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