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Comparative study on 16s rRNA gene Sequences for clinical and environmental isolates of legionella pneumophila. | ||
| Journal of University of Anbar for Pure Science | ||
| Volume 18, Issue 1, June 2024, Pages 13-25 PDF (550.44 K) | ||
| Document Type: Research Paper | ||
| DOI: 10.37652/juaps.2023.142996.1121 | ||
| Authors | ||
| Mohammed Ibrahim Alani* 1; Ibrahim A. A. Rahman Alani2 | ||
| 1Department of Biology ,College of Science, University of Anbar , Anbar,Iraq | ||
| 2University of Fallujah / Headquarter; Fallujah , Iraq; | ||
| Abstract | ||
| This study aimed to identify and describe the identity and phylogenetic position of two Legionella pneumophila isolates from Falluja, Iraq: one clinical (M1) was isolated from a patient with pneumonia symptoms, and one environmental (H1) was isolated from the surface of a potable water pipe close-ended by the same researchers as this study. This study examined the genetic patterns of 16S rRNA gene sequences at one genetic locus. Direct sequencing of amplified segments was used to determine the genetic variability of bacterial samples. Afterward, a thorough and precise tree was built to test the reported variants' phylogenetic positions and discrimination. It was determined by aligning the M1 sample's nucleic acid sequences with Legionella pneumophila's reference sequences (GenBank acc. no. KF537568.1), which had the highest homology. identified two nucleic acid variations (141A>G and 247T>C) not seen in this reference sequence. The tree analysis showed that the M1 sample was in a distinct evolutionary position and matched numerous European strains. The M1 sample was likewise assumed to have come from the same tree as the other strains, including H1. The nucleic acid variations in the M1 sample changed its phylogenetic position within Legionella pneumophila's clades. The presence of H1 samples near many non-clinical strains showed that the ribosomal RNA used could identify the isolation source. The current study demonstrated that 16S rRNA sequences may identify Legionella pneumophila sequences in samples. This genetic locus can be used to detect additional bacterial phylogenetic distributions. | ||
| Keywords | ||
| Legionella pneumophila,,; ,،16s rRNA gene sequence,,; ,،phylogenetic tree | ||
| References | ||
|
[1] Okunaga M, Kushiro K, Horie R, Kondo A, Abe T. Identification of microbes coexisting with Legionella spp. in bathwaters. NPJ Clean Water. 2022 Dec 1;5(1).
[2] Salinas MB, Fenoy S, Magnet A, Vaccaro L, Gomes TD, Hurtado C, et al. Are pathogenic Legionella non-pneumophila a common bacteria in Water Distribution Networks? Water Res. 2021 May 15;196.
[3] Walker JT, McDermott PJ. Confirming the presence of Legionella pneumophila in your water system: a review of current Legionella testing methods. Journal of AOAC International. 2021 Jul 1;104(4):1135-47.
[4] Tan LT, Tee WY, Khan TM, Ming LC, Letchumanan V. Legionella pneumophila—The causative agent of Legionnaires’ disease. Progress In Microbes & Molecular Biology. 2021 Apr 8;4(1).
[5] Moffa MA, Rock C, Galiatsatos P, Gamage SD, Schwab KJ, Exum NG. Legionellosis on the rise: A scoping review of sporadic, community-acquired incidence in the United States. Epidemiology & Infection. 2023 Jul 28:1-5.
[6] Mentula S, Kääriäinen S, Jaakola S, Niittynen M, Airaksinen P, Koivula I, et al. Tap water as the source of a Legionnaires’ disease outbreak spread to several residential buildings and one hospital, Finland, 2020 to 2021. Euro Surveill. 2023 Mar 1;28(11).
[7] Hiergeist A, Reischl U, Gessner A, Garzetti D, Stecher B, Gálvez EJC, et al. Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. International Journal of Medical Microbiology. 2016 Aug 1;306(5):334–42.
[8] Melaine F, Saad M, Faucher S, Tabrizian M. Selective and High Dynamic Range Assay Format for Multiplex Detection of Pathogenic Pseudomonas aeruginosa, Salmonella typhimurium, and Legionella pneumophila RNAs Using Surface Plasmon Resonance Imaging. Anal Chem. 2017 Jul 18;89(14):7802–7.
[9] Petti CA, Polage CR, Schreckenberger P. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J Clin Microbiol.2005Dec;43(12):6123–5.
[10] Gomez-Valero L, Rusniok C, Buchrieser C. Legionella pneumophila: Population genetics, phylogeny and genomics. Vol. 9, Infection, Genetics and Evolution. 2009. p. 727–39.
[11] Jay ZJ, Inskeep WP. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. Biol Direct. 2015 Jul 9;10(1).
[12] Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019 Dec 1;10(1).
[13] Garcia-Mazcorro JF, Barcenas-Walls JR. Thinking beside the box: Should we care about the non-coding strand of the 16S rRNA gene? Vol. 363, FEMS Microbiology Letters. Oxford University Press; 2016.
[14] Hilbi H, Jarraud S, Hartland E, Buchrieser C. Update on Legionnaires’ disease: Pathogenesis, epidemiology, detection and control: MicroMeeting. In: Molecular Microbiology. Blackwell Publishing Ltd; 2010. p. 1–11.
[15] Lapierre P, Nazarian E, Zhu Y, Wroblewski D, Saylors A, Passaretti T, et al. Legionnaires’ disease outbreak caused by endemic strain of Legionella pneumophila, New York, New York, USA, 2015. Emerg Infect Dis. 2017 Nov 1;23(11):1784–91.
[16] Pascale MR, Mazzotta M, Salaris S, Girolamini L, Grottola A, Simone ML, et al. Evaluation of MALDI–TOF Mass Spectrometry in Diagnostic and Environmental Surveillance of Legionella Species: A Comparison With Culture and Mip-Gene Sequencing Technique. Front Microbiol. 2020 Dec 15;11.
[17] Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res. 2017 Jan 1;45(D1):D37–42.
[18] Zhang Z, Schwartz S, Wagner L, Miller W. A Greedy Algorithm for Aligning DNA Sequences. Vol. 7, JOURNAL OF COMPUTATIONAL BIOLOGY. Mary Ann Liebert, Inc. Pp; 2000.
[19] Letunic I, Bork P. Interactive Tree of Life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res. 2019 Jul 1;47(W1).
[20] Wilson DA, Reischl U, Hall GS, Procop GW. Use of partial 16S rRNA gene sequencing for identification of Legionella pneumophila and non-pneumophila Legionella spp. J Clin Microbiol. 2007 Jan;45(1):257–8.
[21] Stølhaug A, Bergh K. Identification and differentiation of Legionella pneumophila and Legionella spp. with real-time PCR targeting the 16S rRNA gene and species identification by mip sequencing. Appl Environ Microbiol. 2006 Sep;72(9):6394–8.
[22] Foudeh AM, Daoud JT, Faucher SP, Veres T, Tabrizian M. Sub-femtomole detection of 16s rRNA from Legionella pneumophila using surface plasmon resonance imaging. Biosens Bioelectron. 2014 Feb 15;52:129–35.
[23] Baldan R, Cliff PR, Burns S, Medina A, Smith GC, Batra R, et al. Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit. Journal of Infection. 2021 Aug 1;83(2):167–74.
[24] Janczarek M, Palusińska-Szysz M. PCR method for the rapid detection and discrimination of Legionella spp. based on the amplification of pcs, pmtA, and 16S rRNA genes. J Appl Genet. 2016 May 1;57(2):251–61.
[25] Borthong J, Omori R, Sugimoto C, Suthienkul O, Nakao R, Ito K. Comparison of database search methods for the detection of Legionella pneumophila in water samples using metagenomic analysis. Front Microbiol. 2018 Jun 19;9(JUN).
[26] Reuter S, Harrison TG, Köser CU, Ellington MJ, Smith GP, Parkhill J, Peacock SJ, Bentley SD, Török ME. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ open. 2013 Jan 1;3(1):e002175.
[27] Church DL, Cerutti L, Gürtler A, Griener T, Zelazny A, Emler S. Performance and application of 16S rRNA gene cycle sequencing for routine identification of bacteria in the clinical microbiology laboratory. Vol. 33, Clinical Microbiology Reviews. American Society for Microbiology; 2020. p. 1–74.
[28] Wullings BA, Van Der Kooij D. Occurrence and genetic diversity of uncultured Legionella spp. in drinking water treated at temperatures below 15 C. Applied and Environmental Microbiology. 2006 Jan;72(1):157-66.
[29] Coscollá M, Gosalbes MJ, Catalán V, González-Candelas F. Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain). Environ Microbiol. 2006 Jun;8(6):1056–63.
[30] Gomez-Valero L, Rusniok C, Buchrieser C. Legionella pneumophila: Population genetics, phylogeny and genomics. Vol. 9, Infection, Genetics and Evolution. 2009. p. 727–39.
[31] David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, et al. Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genet. 2017;13(6).
[32] Wee BA, Alves J, Lindsay DSJ, Klatt AB, Sargison FA, Cameron RL, et al. Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing. Nat Commun. 2021 Dec 1;12(1).
[33] Levin TC, Goldspiel BP, Malik HS. Density-dependent resistance protects Legionella pneumophila from its own antimicrobial metabolite, HGA. Elife. 2019 May 28;8:e46086.
[34] Sánchez-Busó L, Coscollá M, Pinto-Carbó M, Catalán V, González-Candelas F. Genetic Characterization of Legionella pneumophila Isolated from a Common Watershed in Comunidad Valenciana, Spain. PLoS One. 2013 Apr 25;8(4).
[35] McAdam PR, Vander Broek CW, Lindsay DSJ, Ward MJ, Hanson MF, Gillies M, et al. Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak. Genome Biol. 2014;15(11):504.
[36] Bakour S, Sankar SA, Rathored J, Biagini P, Raoult D, Fournier PE. Identification of virulence factors and antibiotic resistance markers using bacterial genomics. Vol. 11, Future Microbiology. Future Medicine Ltd.; 2016. p. 455–66.
[37] Samrakandi MM, Cirillo SLG, Ridenour DA, Bermudez LE, Cirillo JD. Genetic and phenotypic differences between Legionella pneumophila strains. J Clin Microbiol. 2002;40(4):1352–62.
[38] Sreenath K, Chaudhry R, Vinayaraj E V., Dey AB, Kabra SK, Thakur B, et al. Distribution of Virulence Genes and Sequence-Based Types Among Legionella pneumophila Isolated From the Water Systems of a Tertiary Care Hospital in India. Front Public Health. 2020 Nov 23;8.
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