Assessment of genotyping markers in the molecular characterization of a population of clinical isolates of Fusarium in Colombia

Valeria Velásquez-Zapata, Katherine Palacio-Rúa, Luz E. Cano, Adelaida Gaviria-Rivera, .

DOI: https://doi.org/10.7705/biomedica.5869
Keywords: Fusarium, fusariosis, genotyping techniques, bacteriophage M13, elongin, genetics, population, DNA fingerprinting
Abstract Authors Downloads References How to Cite

Abstract

Introduction: Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for humans and animals. Prevalence of clinical fusariosis and lack of effective treatments have increased the interest in the precise diagnosis, which implies a molecular characterization of Fusarium populations.
Objective: We compared different genotyping markers in their assessment of the genetic variability and molecular identification of clinical isolates of Fusarium.
Materials and methods: We evaluated the performance of the fingerprinting produced by two random primers: M13, which amplifies a minisatellite sequence, and (GACA)4, which corresponds to a simple repetitive DNA sequence. Using the Hunter Gaston Discriminatory Index (HGDI), an analysis of molecular variance (AMOVA), and a Mantel test, the resolution of these markers was compared to the reference sequencing-based and PCR genotyping methods.
Results: The highest HGDI value was associated with the M13 marker followed by (GACA)4. AMOVA and the Mantel tests supported a strong correlation between the M13 classification and the reference method given by the partial sequencing of the transcription elongation factor 1-alpha (TEF1-α) and rDNA 28S.
Conclusion: The strong correlation between the M13 classification and the sequencingbased reference together with its higher resolution demonstrates its adequacy for the characterization of Fusarium populations.

Downloads

Download data is not yet available.
  • Valeria Velásquez-Zapata Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA; Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA https://orcid.org/0000-0002-2756-2156
  • Katherine Palacio-Rúa Laboratorio Integrado de Medicina Especializada, Facultad de Medicina, IPS Universitaria, Universidad de Antioquia, Medellín, Colombia https://orcid.org/0000-0002-3714-6359
  • Luz E. Cano Grupo de Micología Médica y Experimental, Corporación para Investigaciones Biológicas, Medellín, Colombia; Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia https://orcid.org/0000-0001-5581-3015
  • Adelaida Gaviria-Rivera Escuela de Biociencias, Facultad de Ciencias, Universidad Nacional de Colombia, Medellín, Colombia https://orcid.org/0000-0002-0701-0127

References

Salas I, Hernández-Chavarría F. Fusarium como agente etiológico de onicomicosis: Informe de tres casos y revisión de la literatura. Rev Costarric Cienc Méd. 2005;26:53-9.

Garnica M, Nucci M. Epidemiology of Fusariosis. Curr Fungal Infect Rep. 2013;7:301-5. https://doi.org/10.1007/s12281-013-0161-y

Nelson PE, Dignani MC, Anaissie EJ. Taxonomy, biology, and clinical aspects of Fusarium species. Clin Microbiol Rev. 1994;7:479-504. https://doi.org/10.1128/CMR.7.4.479

Desjardins AE, Proctor RH. Molecular biology of Fusarium mycotoxins. Int J Food Microbiol. 2007;119:47-50. https://doi.org/10.1016/j.ijfoodmicro.2007.07.024

Dyavaiah M, Ramani R, Chu DS, Ritterband DC, Shah MK, Samsonoff W, et al. Molecular characterization, biofilm analysis and experimental biofouling study of Fusarium isolates from recent cases of fungal keratitis in New York State. BMC Ophthalmol. 2007;7:1. https://doi.org/10.1186/1471-2415-7-1

Raad II, Hachem RY, Herbrecht R, Graybill JR, Hare R, Corcoran G, et al. Posaconazole as salvage treatment for invasive fusariosis in patients with underlying hematologic malignancy and other conditions. Clin Infect Dis. 2006;42:1398-403. https://doi.org/10.1086/503425

Thomas B, Audonneau NC, Machouart M, Debourgogne A. Fusarium infections: Epidemiological aspects over 10 years in a university hospital in France. J Infect Public Health. 2020;13:1089-93. https://doi.org/10.1016/j.jiph.2020.06.007

Al-hatmi AMS, Hagen F, Menken SBJ, Meis JF, De Hoog GS, de Hoog GS. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015. Emerg Microbes Infect. 2016;5:1-11. https://doi.org/10.1038/emi.2016.126

Olivares R, Alfaro J, Díaz MC, Thompson L. Fusariosis diseminada por Fusarium oxysporum en un paciente adulto con leucemia mieloide aguda y neutropenia severa febril. Rev Chil Infec. 2005;22:356-60. https://doi.org/10.4067/S0716-10182005000600009

Krcmery V, Jesenska Z, Spanik S, Gyarfas J, Nogova J, Botek R, et al. Fungaemia due to Fusarium spp. in cancer patients. J Hosp Infect. 1997;36:223-8. https://doi.org/10.1016/s0195-6701(97)90197-3

Ahmed H, Howton TC, Sun Y, Weinberger N, Belkhadir Y, Mukhtar MS. Network biology discovers pathogen contact points in host protein-protein interactomes. Nat Commun. 2018;9:1-13. https://doi.org/10.1038/s41467-018-04632-8

Herkert PF, Al-hatmi AMS, Salvador GLDO, Muro MD, Pinheiro RL, Nucci M, et al. Molecular characterization and antifungal susceptibility of clinical Fusarium species from Brazil. Front Microbiol. 2019;10:1-11. https://doi.org/10.3389/fmicb.2019.00737

Guarro J, Nucci M, Akiti T, Gené J. Mixed infection caused by two species of Fusarium in a human immunodeficiency virus-positive patient. J Clin Microbiol. 2000;38:3460-2. https://doi.org/10.1128/JCM.38.9.3460-3462.2000

Tortorano AM, Prigitano A, Dho G, Esposto MC, Gianni C, Grancini A, et al. Species distribution and in vitro antifungal susceptibility patterns of 75 clinical isolates of Fusarium spp. from northern Italy. Antimicrob Agents Chemother. 2008;52:2683-5. https://doi.org/10.1128/AAC.00272-08

Guarro J. Fusariosis, a complex infection caused by a high diversity of fungal species refractory to treatment. Eur J Clin Microbiol Infect Dis. 2013;32:1491-500. https://doi.org/10.1007/s10096-013-1924-7

O’Donnell K, Al-Hatmi AMS, Aoki T, Brankovics B, Cano-Lira JF, Coleman JJ, et al. No to Neocosmospora: phylogenomic and practical reasons for continued inclusion of the Fusarium solani species complex in the genus Fusarium. mSphere. 2020;5. https://doi.org/10.1128/msphere.00810-20

Sandoval-Denis M, Lombard L, Crous PW. Back to the roots: A reappraisal of Neocosmospora. Persoonia. 2019;43:90-185. https://doi.org/10.3767/persoonia.2019.43.04

Castro-López N, Casas C, Sopó L, Rojas A, Del Portillo P, Cepero-de García MC, et al. Fusarium species detected in onychomycosis in Colombia. Mycoses. 2009;52:350-6. https://doi.org/10.1111/j.1439-0507.2008.01619.x

De Bedout C, Tabares Á, Arango M, Restrepo A. Importancia creciente de los géneros Fusarium y Scytalidium como agentes de onicomicosis. Revista de la Asociación Colombiana de Dermatología y Cirugía Dermatológica. 2001;9:593-9.

Morales CA, Solórzano A, Rojas AP. Características epidemiológicas y clínicas de las onicomicosis causadas por Fusarium spp. en un centro de referencia de Bogotá , Colombia, 2001-2010. Revista de la Asociación Colombiana de Dermatología y Cirugía Dermatológica. 2013;1:21-8.

Guevara-Suárez M, Cano-Lira JF, Cepero de García MC, et al. Genotyping of Fusarium isolates from onychomycoses in Colombia: Detection of two new species within the Fusarium solani species complex and in vitro antifungal susceptibility testing. Mycopathologia. 2016;181:165-74. https://doi.org/10.1007/s11046-016-9983-9

Acevedo-Granados YF, Cano LE, Gaviria-Rivera AM. Identificación de aislamientos clínicos de Fusarium spp. mediante técnicas moleculares en Colombia. Bistua Revista de la Facultad de Ciencias Básicas. 2014;12:143-59.

Gaviria-Rivera A, Giraldo-López A, Santa-Cardona C, Cano-Restrepo L. Molecular identification of clinical isolates of Fusarium in Colombia. Rev Salud Pública. 2018;20:94-102. https://doi.org/10.15446/rsap.v20n1.51923

Batista BG, de Chaves MA, Reginatto P, Saraiva OJ, Fuentefria AM. Human fusariosis: An emerging infection that is difficult to treat. Rev Soc Bras Med Trop. 2020;53:1-7. https://doi.org/10.1590/0037-8682-0013-2020

Gaviria-Rivera A, Giraldo-López A, Cano-Restrepo LE. In vitro antifungal susceptibility of clinical isolates of Fusarium from Colombia. Rev Salud Pública. 2017;19:237-88. https://doi.org/10.15446/rsap.V19n6.54654

Leslie JF, Summerell BA. The Fusarium Laboratory Manual. Ames, Iowa, USA: Blackwell Publishing; 2006. p. 387.

Hue FX, Huerre M, Rouffault MA, De Bievre C. Specific detection of Fusarium species in blood and tissues by a PCR technique. J Clin Microbiol. 1999;37:2434-8. https://doi.org/10.1128/jcm.37.8.2434-2438.1999

Jaeger EEM, Carroll NM, Choudhury S, Dunlop AA, Towler HMA, Matheson MM, et al. Rapid detection and identification of Candida, Aspergillus, and Fusarium species in ocular samples using nested PCR. J Clin Microbiol. 2000;38:2902-8. https://doi.org/10.1128/JCM.38.8.2902-2908.2000

O’Donnell K, Humber RA, Geiser DM, Kang S, Park B, Robert VARG, et al. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST. Mycologia. 2012;104:427-45. https://doi.org/10.3852/11-179

Hennequin C, Abachin E, Symoens F, Lavarde V, Reboux G, Nolard N, et al. Identification of Fusarium species involved in human infections by 28S rRNA gene sequencing. J Clin Microbiol. 1999;37:3586-9. https://doi.org/10.1128/jcm.37.11.3586-3589.1999

Kristensen R, Torp M, Kosiak B, Holst-Jensen A. Phylogeny and toxigenic potential is correlated in Fusarium species as revealed by partial translation elongation factor 1 alpha gene sequences. Mycol Res. 2005;109:173-86. https://doi.org/10.1017/S0953756204002114

Debourgogne A, Gueidan C, Hennequin C, Contet-audonneau N, Hoog S De, Machouart M. Development of a new MLST scheme for differentiation of Fusarium solani Species Complex (FSSC) isolates. J Microbiol Methods. 2010;82:319-23. https://doi.org/10.1016/j.mimet.2010.07.008

Shehata AS, Mukherjee PK, Aboulatta HN, el-Akhras AI, Abbadi SH, Ghannoum MA. Singlestep PCR using (GACA)4 primer: Utility for rapid identification of dermatophyte species and strains. J Clin Microbiol. 2008;46:2641-5. https://doi.org/10.1128/JCM.00697-08

Roque HD, Vieira R, Rato S, Luz-Martins M. Specific primers for rapid detection of Microsporum audouinii by PCR in clinical samples. J Clin Microbiol. 2006;44:4336-41. https://doi.org/10.1128/JCM.00759-06

Ohst T, de Hoog S, Presber W, Stavrakieva V, Graser Y. Origins of microsatellite diversity in the Trichophyton rubrum/T . violaceum clade (Dermatophytes). J Clin Microbiol. 2004;42:4444-8. https://doi.org/10.1128/JCM.42.10.4444-4448.2004

Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: An application of Simpson’s index of diversity. J Clin Microbiol. 1988;26:2465-6. https://doi.org/10.1128/jcm.26.11.2465-2466.1988

Sola C, Filliol I, Legrand E, Lesjean S, Locht C, Supply P, et al. Genotyping of the Mycobacterium tuberculosis complex using MIRUs: Association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol. 2003;3:125-33. https://doi.org/10.1016/S1567-1348(03)00011-X

Excoffier L, Lischer HEL. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10:564-7. https://doi.org/10.1111/j.1755-0998.2010.02847.x

Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289-300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x

Wickham H. ggplot2: Elegant graphics for data analysis. New York: Springer-Verlag; 2016.

Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics. 1992;131:479-91.

Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967;27:209-20.

Burgess LW. Fusarium: An ubiquitous fungus of global significance. Microbiology Australia. 2006;33:22. https://doi.org/10.1071/MA12022

El-Kzzaz MK, El-Fadly GB, Hassan MAA, El-Kot GAN. Identification of some Fusarium spp. using molecular biology techniques. Egypt J Phytopathol. 2008;36:57-69.

Park B, Park J, Cheong K-C, Choi J, Jung K, Kim D, et al. Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing. Nucleic Acids Res. 2011;39(Suppl.1):D640-6. https://doi.org/10.1093/nar/gkq1166

Donnell KO, Sutton DA, Rinaldi MG, Sarver BAJ, Balajee SA, Schroers H, et al. Internetaccessible DNA sequence database for identifying Fusaria from human and animal infections. J Clin Microbiol. 2010;48:3708-18. https://doi.org/10.1128/JCM.00989-10

van Diepeningen AD, Feng P, Ahmed S, Sudhadham M, Bunyaratavej S, de Hoog GS. Spectrum of Fusarium infections in tropical dermatology evidenced by multilocus sequencing typing diagnostics. Mycoses. 2015;58:48-57. https://doi.org/10.1111/myc.12273

Vassart G, Georges M, Monsieur R, Brocas H, Lequarre AS, Christophe D. A sequence in M13 phage detects hypervariable minisatellites in human and animal DNA. Science. 1987;235:683-4. https://doi.org/10.1126/science.2880398

Anderson MJ, Gull K, Al AET. Molecular typing by random amplification of polymorphic DNA and M13 Southern hybridization of related paired isolates of Aspergillus fumigatus. J Clin Microbiol. 1996;34:87-93. https://doi.org/10.1128/jcm.34.1.87-93.1996

Chang DC, Grant GB, O’Donnell K, Wannemuehler KA, Noble-Wang J, Rao CY, et al. Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution. JAMA. 2006;296:953-63. https://doi.org/10.1001/jama.296.8.953

How to Cite
1.
Velásquez-Zapata V, Palacio-Rúa K, Cano LE, Gaviria-Rivera A. Assessment of genotyping markers in the molecular characterization of a population of clinical isolates of Fusarium in Colombia. biomedica [Internet]. 2022 Mar. 1 [cited 2024 May 18];42(1):18-30. Available from: https://revistabiomedica.org/index.php/biomedica/article/view/5869

Some similar items:

Published
2022-03-01
Issue
Vol. 42 No. 1 (2022)
Section
Original articles

Altmetric

Funding data

Article metrics
Abstract views
Galley vies
PDF Views
HTML views
Other views
Crossref Cited-by logo
1 Cites in Crossref to date
QR Code