The Complete Genome Sequence of a Bile-isolated Stenotrophomonas Maltophilia ZT1

Overview

Journal Gut Pathog

Publisher Biomed Central

Specialty Gastroenterology

Date 2021 Oct 29

PMID 34711270

Citations 1

Authors

Min Zhang

Lixiang Li

Hongwei Pan

Tao Zhou

Affiliations

Soon will be listed here.

Abstract

Background: Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear.

Results: In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC.

Conclusions: This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia.

Citing Articles

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Mikhailovich V, Heydarov R, Zimenkov D, Chebotar I Front Microbiol. 2024; 15:1385631.

PMID: 38741741 PMC: 11089167. DOI: 10.3389/fmicb.2024.1385631.

References

Jackman S, Vandervalk B, Mohamadi H, Chu J, Yeo S, Hammond S . ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res. 2017; 27(5):768-777. PMC: 5411771. DOI: 10.1101/gr.214346.116. View

Kalidasan V, Joseph N, Kumar S, Hamat R, Neela V . Iron and Virulence in : All We Know So Far. Front Cell Infect Microbiol. 2018; 8:401. PMC: 6240677. DOI: 10.3389/fcimb.2018.00401. View

Yu T, Li L, Zhao Q, Wang P, Zuo X . Complete genome sequence of bile-isolated strain 352. Gut Pathog. 2019; 11:16. PMC: 6480912. DOI: 10.1186/s13099-019-0294-9. View

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2013; 1(1):18. PMC: 3626529. DOI: 10.1186/2047-217X-1-18. View

Hu L, Xu X, Li H, Gao L, Chen X, Sun N . Surveillance of antimicrobial susceptibility patterns among Stenotrophomonas maltophilia isolated in China during the 10-year period of 2005-2014. J Chemother. 2017; 30(1):25-30. DOI: 10.1080/1120009X.2017.1378834. View

Kaya M, Bestas R, Bacalan F, Bacaksiz F, Arslan E, Kaplan M . Microbial profile and antibiotic sensitivity pattern in bile cultures from endoscopic retrograde cholangiography patients. World J Gastroenterol. 2012; 18(27):3585-9. PMC: 3400861. DOI: 10.3748/wjg.v18.i27.3585. View

Yero D, Huedo P, Conchillo-Sole O, Martinez-Servat S, Mamat U, Coves X . Genetic Variants of the DSF Quorum Sensing System in Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates. Front Microbiol. 2020; 11:1160. PMC: 7283896. DOI: 10.3389/fmicb.2020.01160. View

Pinski A, Zur J, Hasterok R, Hupert-Kocurek K . Comparative Genomics of and Revealed Characteristic Features of Both Species. Int J Mol Sci. 2020; 21(14). PMC: 7404187. DOI: 10.3390/ijms21144922. View

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

10.

di Gregorio M, Cautela J, Galantini L . Physiology and Physical Chemistry of Bile Acids. Int J Mol Sci. 2021; 22(4). PMC: 7916809. DOI: 10.3390/ijms22041780. View

11.

Alsuhaibani M, Aljarbou A, Althawadi S, AlSweed A, Al-Hajjar S . Stenotrophomonas maltophilia bacteremia in children: risk factors and mortality rate. Antimicrob Resist Infect Control. 2021; 10(1):19. PMC: 7825200. DOI: 10.1186/s13756-021-00888-w. View

12.

Adegoke A, Stenstrom T, Okoh A . as an Emerging Ubiquitous Pathogen: Looking Beyond Contemporary Antibiotic Therapy. Front Microbiol. 2017; 8:2276. PMC: 5714879. DOI: 10.3389/fmicb.2017.02276. View

13.

Nas M, White R, DuMont A, Lopez A, Cianciotto N . Stenotrophomonas maltophilia Encodes a VirB/VirD4 Type IV Secretion System That Modulates Apoptosis in Human Cells and Promotes Competition against Heterologous Bacteria, Including Pseudomonas aeruginosa. Infect Immun. 2019; 87(9). PMC: 6704607. DOI: 10.1128/IAI.00457-19. View

14.

Esposito A, Pompilio A, Bettua C, Crocetta V, Giacobazzi E, Fiscarelli E . Evolution of in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study. Front Microbiol. 2017; 8:1590. PMC: 5581383. DOI: 10.3389/fmicb.2017.01590. View

15.

Grant J, Stothard P . The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 2008; 36(Web Server issue):W181-4. PMC: 2447734. DOI: 10.1093/nar/gkn179. View

16.

Chen L, Zheng D, Liu B, Yang J, Jin Q . VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res. 2015; 44(D1):D694-7. PMC: 4702877. DOI: 10.1093/nar/gkv1239. View

17.

Brooke J . Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev. 2012; 25(1):2-41. PMC: 3255966. DOI: 10.1128/CMR.00019-11. View

18.

Han L, Zhang R, Jia L, Bai S, Liu X, Wei R . Diversity of L1/L2 genes and molecular epidemiology of high-level carbapenem resistance Stenotrophomonas maltophilia isolates from animal production environment in China. Infect Genet Evol. 2020; 86:104531. DOI: 10.1016/j.meegid.2020.104531. View

19.

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

20.

Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O . New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59(3):307-21. DOI: 10.1093/sysbio/syq010. View