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Research Article

Tracing histoplasmosis genomic epidemiology and species occurrence across the USA

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Article: 2315960 | Received 08 Nov 2023, Accepted 04 Feb 2024, Published online: 11 Mar 2024

References

  • Moreira LM, Meyer W, Chame M, et al. Molecular detection of Histoplasma capsulatum in Antarctica. Emerg Infect Dis. 2022 Oct;28(10):2100–2104. doi:10.3201/eid2810.220046
  • Linder KA, Kauffman CA. Histoplasmosis: epidemiology, diagnosis, and clinical manifestations. Curr Fungal Infect Rep. 2019/09/01;13(3):120–128. doi:10.1007/s12281-019-00341-x
  • Emmons CW. Association of bats with histoplasmosis. Public Health Rep (1896). 1958 Jul;73(7):590–595. doi:10.2307/4590196
  • Ajello L. Relationship of Histoplasma Capsulatum to Avian habitats. Public Health Rep (1896). 1964 Mar;79(3):266–270. doi:10.2307/4592099
  • Hoff GL, Bigler WJ. The role of bats in the propagation and spread of histoplasmosis: a review. J Wildl Dis. 1981 Apr;17(2):191–196. doi:10.7589/0090-3558-17.2.191
  • Sil A. Molecular regulation of Histoplasma dimorphism. Curr Opin Microbiol. 2019 Dec;52:151–157. doi:10.1016/j.mib.2019.10.011
  • Benedict K, Mody RK. Epidemiology of Histoplasmosis outbreaks, United States, 1938-2013. Emerg Infect Dis. 2016 Mar;22(3):370–378. doi:10.3201/eid2203.151117
  • Myint T, Leedy N, Villacorta Cari E, et al. HIV-associated Histoplasmosis: current perspectives. HIV AIDS (Auckl). 2020;12:113–125. doi:10.2147/HIV.S185631
  • Wheat LJ, Azar MM, Bahr NC, et al. Histoplasmosis. Infect Dis Clin North Am. 2016 Mar;30(1):207–227. doi:10.1016/j.idc.2015.10.009
  • Mazi PB, Sahrmann JM, Olsen MA, et al. The geographic distribution of Dimorphic Mycoses in the United States for the modern era. Clin Infect Dis. 2023 Apr 3;76(7):1295–1301. doi:10.1093/cid/ciac882
  • Smith DJ, Williams SL. Endemic Mycoses State Partners G, et al. Surveillance for Coccidioidomycosis, Histoplasmosis, and Blastomycosis - United States, 2019. MMWR Surveill Summ. 2022 Aug 19;71(7):1–14. doi:10.15585/mmwr.ss7107a1
  • Maiga AW, Deppen S, Scaffidi BK, et al. Mapping Histoplasma capsulatum exposure, United States. Emerg Infect Dis. 2018 Oct;24(10):1835–1839. doi:10.3201/eid2410.180032
  • McKinsey DS, Pappas PG. Histoplasmosis: time to redraw the map and up our game. Clin Infect Dis. 2020 Mar 3;70(6):1011–1013. doi:10.1093/cid/ciz327
  • Armstrong PA, Jackson BR, Haselow D, et al. Multistate epidemiology of Histoplasmosis, United States, 2011-2014. Emerg Infect Dis. 2018 Mar;24(3):425–431. doi:10.3201/eid2403.171258
  • Teixeira Mde M, Patane JS, Taylor ML, et al. Worldwide phylogenetic distributions and population dynamics of the genus Histoplasma. PLoS Negl Trop Dis. 2016 Jun;10(6):e0004732. doi:10.1371/journal.pntd.0004732
  • Sepulveda VE, Marquez R, Turissini DA, et al. Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum. MBio. 2017 Dec 5;8(6):1–23. doi:10.1128/mBio.01339-17
  • Dingle TC, Croxen MA, Fathima S, et al. Histoplasmosis acquired in Alberta, Canada: an epidemiological and genomic study. Lancet Microbe. 2021 May;2(5):e191–e197. doi:10.1016/S2666-5247(20)30229-9
  • Taylor JW, Jacobson DJ, Kroken S, et al. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol. 2000 Oct;31(1):21–32. doi:10.1006/fgbi.2000.1228
  • Kasuga T, White TJ, Koenig G, et al. Phylogeography of the fungal pathogen Histoplasma capsulatum. Mol Ecol. 2003 Dec;12(12):3383–3401. doi:10.1046/j.1365-294X.2003.01995.x
  • Matute DR, Sepulveda VE. Fungal species boundaries in the genomics era. Fungal Genet Biol. 2019 Jul 4;131:103249. doi:10.1016/j.fgb.2019.103249
  • Victoria ES, Jonathan R, Jingbaoyi L, et al. Phenotypic characterization of cryptic species in the fungal pathogen Histoplasma. bioRxiv. 2024:1–37. 2024.01.08.574719. doi:10.1101/2024.01.08.574719
  • Canteros CE, Zuiani MF, Ritacco V, et al. Electrophoresis karyotype and chromosome-length polymorphism of Histoplasma capsulatum clinical isolates from Latin America. FEMS Immunol Med Microbiol. 2005 Sep 1;45(3):423–428. doi:10.1016/j.femsim.2005.05.015
  • Voorhies M, Cohen S, Shea TP, et al. Chromosome-level genome assembly of a human fungal pathogen reveals synteny among geographically distinct species. mBio. 2022 Feb 22;13(1):e0257421. doi:10.1128/mbio.02574-21
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114–2120. doi:10.1093/bioinformatics/btu170
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754–1760. doi:10.1093/bioinformatics/btp324
  • McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297–1303. doi:10.1101/gr.107524.110
  • Delcher AL, Phillippy A, Carlton J, et al. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 2002 Jun 1;30(11):2478–2483. doi:10.1093/nar/30.11.2478
  • Minh BQ, Schmidt HA, Chernomor O, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020 May 1;37(5):1530–1534. doi:10.1093/molbev/msaa015
  • Minh BQ, Nguyen MA, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 2013 May;30(5):1188–1195. doi:10.1093/molbev/mst024
  • Guindon S, Dufayard JF, Lefort V, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010 May;59(3):307–321. doi:10.1093/sysbio/syq010
  • Raj A, Stephens M, Pritchard JK. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics. 2014 Jun;197(2):573–589. doi:10.1534/genetics.114.164350
  • Jombart T, Ahmed I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011 Nov 1;27(21):3070–3071. doi:10.1093/bioinformatics/btr521
  • Arunmozhi Balajee S, Hurst SF, Chang LS, et al. Multilocus sequence typing of Histoplasma capsulatum in formalin-fixed paraffin-embedded tissues from cats living in non-endemic regions reveals a new phylogenetic clade. Med Mycol. 2013 May;51(4):345–351. doi:10.3109/13693786.2012.733430
  • Theodoro RC, Scheel CM, Brandt ME, et al. PRP8 intein in cryptic species of Histoplasma capsulatum: evolution and phylogeny. Infect Genet Evol. 2013 Aug;18:174–182. doi:10.1016/j.meegid.2013.05.001
  • Gorelick N, Hancher M, Dixon M, et al. Google Earth Engine: planetary-scale geospatial analysis for everyone. Remote Sens Environ. 2017/12/01/;202:18–27. doi:10.1016/j.rse.2017.06.031.
  • Fick SE, Hijmans RJ. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int J Climatol. 2017/10/01;37(12):4302–4315. doi:10.1002/joc.5086.
  • Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic distributions. Ecol Modell. 2006/01/25/;190(3):231–259. doi:10.1016/j.ecolmodel.2005.03.026.
  • Hijmans RJ, Phillips S, Leathwick J, et al. Package ‘dismo’ version 1.3-14 2017. Available from: https://rdrr.io/cran/dismo/.
  • Deepe Jr GS. Outbreaks of histoplasmosis: the spores set sail. PLoS Pathog. 2018 Sep;14(9):e1007213. doi:10.1371/journal.ppat.1007213
  • Canakis A, Kolachana S, Holden VK, et al. Opportunistic knocks: a gardener with ulcerative colitis and new pulmonary nodules. Dig Dis Sci. 2023 Feb;68(2):380–384. doi:10.1007/s10620-022-07785-1
  • Valdez AF, Miranda DZ, Guimaraes AJ, et al. Pathogenicity & virulence of Histoplasma capsulatum - a multifaceted organism adapted to intracellular environments. Virulence. 2022 Dec;13(1):1900–1919. doi:10.1080/21505594.2022.2137987
  • Maxwell CS, Sepulveda VE, Turissini DA, et al. Recent admixture between species of the fungal pathogen Histoplasma. Evolution Letters. 2018/06/01;2(3):210–220. doi:10.1002/evl3.59
  • Kwon-Chung KJ, Bartlett MS, Wheat LJ. Distribution of the two mating types among Histoplasma capsulatum isolates obtained from an urban histoplasmosis outbreak. Sabouraudia. 1984;22(2):155–157. doi:10.1080/00362178485380231
  • Stukenbrock EH. The role of hybridization in the evolution and emergence of new fungal plant pathogens. Phytopathology. 2016 Feb;106(2):104–112. doi:10.1094/PHYTO-08-15-0184-RVW
  • Steensels J, Gallone B, Verstrepen KJ. Interspecific hybridization as a driver of fungal evolution and adaptation. Nat Rev Microbiol. 2021/08/01;19(8):485–500. doi:10.1038/s41579-021-00537-4
  • Samarasinghe H, You M, Jenkinson TS, et al. hybridization facilitates adaptive evolution in two major fungal pathogens. Genes (Basel). 2020 Jan 16;11(1):1–21. doi:10.3390/genes11010101
  • Gabaldon T. Hybridization and the origin of new yeast lineages. FEMS Yeast Res. 2020 Aug 1;20(5):1–8. doi:10.1093/femsyr/foaa040
  • Gonzalez-Gonzalez AE, Aliouat-Denis CM, Carreto-Binaghi LE, et al. An Hcp100 gene fragment reveals Histoplasma capsulatum presence in lungs of Tadarida brasiliensis migratory bats. Epidemiol Infect. 2012 Nov;140(11):1955–1963. doi:10.1017/S0950268811002585
  • Taylor ML, Reyes-Montes MDR, Estrada-Barcenas DA, et al. Considerations about the geographic distribution of Histoplasma species. Appl Environ Microbiol. 2022 Apr 12;88(7):e0201021. doi:10.1128/aem.02010-21
  • Taylor ML, Chávez-Tapia CB, MR R-M. Molecular typing of Histoplasma capsulatum isolated from infected bats, captured in Mexico. Fungal Genet Biol. 2000/08/01/;30(3):207–212. doi:10.1006/fgbi.2000.1219.
  • Vite-Garin T, Estrada-Barcenas DA, Gernandt DS, et al. Histoplasma capsulatum isolated from Tadarida brasiliensis bats captured in Mexico form a sister group to North American Class 2 Clade. J Fungi (Basel). 2021 Jun 30;7(7):1–17. doi:10.3390/jof7070529
  • McMurray DN, Russel LH. Contribution of bats to the maintenance of Histoplasma capsulatum in a cave microfocus. Am J Trop Med Hyg. 1982 May;31(3 Pt 1):527–531. doi:10.4269/ajtmh.1982.31.527
  • Mulec J, Simčič S, Kotar T, et al. Survey of Histoplasma capsulatum in bat guano and status of histoplasmosis in Slovenia, Central Europe. Int J Speleol. 2020;49:10. doi:10.5038/1827-806X.49.1.2297
  • Gugnani HC, Muotoe-Okafor FA, Kaufman L, et al. A natural focus of Histoplasma capsulatum var. duboisii is a bat cave. Mycopathologia. 1994 Sep;127(3):151–157. doi:10.1007/BF01102915
  • Gugnani HC, Denning DW. Infection of bats with Histoplasma species. Med Mycol. 2023 Aug 2;61(8):1–8. doi:10.1093/mmy/myad080
  • Teeling EC, Vernes SC, Davalos LM, et al. Bat biology, genomes, and the Bat1 K Project: to generate chromosome-level genomes for all living bat species. Annu Rev Anim Biosci. 2018 Feb 15;6:23–46. doi:10.1146/annurev-animal-022516-022811
  • Ocampo-Chavira P, Eaton-Gonzalez R, Riquelme M. Of mice and fungi: Coccidioides spp. distribution models. J Fungi (Basel). 2020 Nov 27;6(4):1–14. doi:10.3390/jof6040320
  • Hepler SA, Kaufeld KA, Benedict K, et al. Integrating public health surveillance and environmental data to model presence of Histoplasma in the United States. Epidemiology. 2022;33(5):654–659. doi:10.1097/EDE.0000000000001499