Prague Med. Rep. 2021, 122, 96-105

https://doi.org/10.14712/23362936.2021.10

Salmonella Paratyphi Infection: Use of Nanopore Sequencing as a Vivid Alternative for the Identification of Invading Bacteria

Martin Chmel1,2, Oldřich Bartoš2,3, Ondřej Beran1, Petr Pajer2, Jiří Dresler2, Martina Čurdová4, Michal Holub1

1Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic
2Military Health Institute, Military Medical Agency, Prague, Czech Republic
3Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
4Department of Clinical Microbiology, Military University Hospital Prague, Prague, Czech Republic

Received July 23, 2020
Accepted April 30, 2021

References

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410. <https://doi.org/10.1016/S0022-2836(05)80360-2>
2. Bochkareva, O. O., Moroz, E. V., Davydov, I. I., Gelfand, M. S. (2018) Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics 19(1), 1–17. <https://doi.org/10.1186/s12864-018-5245-1>
3. Chamberlain, S. A., Szöcs, E. (2013) Taxize: Taxonomic search and retrieval in R. F1000Res. 2, 191. <https://doi.org/10.12688/f1000research.2-191.v1>
4. Dowle, M., Srinivasan A. (2019) Extension of “data.frame” (R package data.table version 1.12.8). Available at: https://CRAN.R-project.org/package=data.table
5. Fuselli, S., Baptista, R. P., Panziera, A., Magi, A., Guglielmi, S., Tonin, R., Benazzo, A., Bauzer, L. G., Mazzoni, C. J., Bertorelle, G. (2018) A new hybrid approach for MHC genotyping: High-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra). Heredity 121(4), 293–303. <https://doi.org/10.1038/s41437-018-0070-5>
6. Götz, S., García-Gómez, J. M., Terol, J., Williams, T. D., Nagaraj, S. H., Nueda, M. J., Robles, M., Talón, M., Dopazo, J., Conesa, A. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 36(10), 3420–3435. <https://doi.org/10.1093/nar/gkn176>
7. Hassold, T., Abruzzo, M., Adkins, K., Griffin, D., Merrill, M., Millie, E., Saker, D., Shen, J., Zaragoza, M. (1996) Human aneuploidy: Incidence, origin, and etiology. Environ. Mol. Mutagen. 28(3), 167–175. <https://doi.org/10.1002/(SICI)1098-2280(1996)28:3<167::AID-EM2>3.0.CO;2-B>
8. Kim, D., Song, L., Breitwieser, F. P., Salzberg, S. L. (2016) Centrifuge: Rapid and sensitive classification of metagenomic sequences. Genome Res. 26(12), 1721–1729. <https://doi.org/10.1101/gr.210641.116>
9. Kolmogorov, M., Yuan, J., Lin, Y., Pevzner, P. A. (2019) Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37(5), 540–546. <https://doi.org/10.1038/s41587-019-0072-8>
10. Li, H. (2018) Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34(18), 3094–3100. <https://doi.org/10.1093/bioinformatics/bty191>
11. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R.; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16), 2078–2079. <https://doi.org/10.1093/bioinformatics/btp352>
12. Magi, A., Semeraro, R., Mingrino, A., Giusti, B., D’Aurizio, R. (2018) Nanopore sequencing data analysis: State of the art, applications and challenges. Brief. Bioinform. 19(6), 1256–1272.
13. Maskey, A. P., Day, J. N., Phung, Q. T., Thwaites, G. E., Campbell, J. I., Zimmerman, M., Farrar, J. J., Basnyat, B. (2006) Salmonella enterica serovar Paratyphi A and S. enterica serovar Typhi cause indistinguishable clinical syndromes in Kathmandu, Nepal. Clin. Infect. Dis. 42(9), 1247–1253. <https://doi.org/10.1086/503033>
14. Matono, T., Kutsuna, S., Kato, Y., Katanami, Y., Yamamoto, K., Takeshita, N., Hayakawa, K., Kanagawa, S., Kaku, M., Ohmagari, N. (2017) Role of classic signs as diagnostic predictors for enteric fever among returned travellers: Relative bradycardia and eosinopenia. PloS One 12(6), e0179814. <https://doi.org/10.1371/journal.pone.0179814>
15. Norris, A. L., Workman, R. E., Fan, Y., Eshleman, J. R., Timp, W. (2016) Nanopore sequencing detects structural variants in cancer. Cancer Biol. Ther. 17(3), 246–253. <https://doi.org/10.1080/15384047.2016.1139236>
16. Olopoenia, L. A. (2000) Classic methods revisited: Widal agglutination test – 100 years later: Still plagued by controversy. Postgrad. Med. J. 76(892), 80–84. <https://doi.org/10.1136/pmj.76.892.80>
17. Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12, 385. <https://doi.org/10.1186/1471-2105-12-385>
18. R Core Team (2019) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Auatria. Available at: https://www.R-project.org/
19. Schadt, E. E., Turner, S., Kasarskis, A. (2010) A window into third-generation sequencing. Hum. Mol. Genet. 19(R2), R227–R240. <https://doi.org/10.1093/hmg/ddq416>
20. Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M. C. (2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods 15(6), 461–468. <https://doi.org/10.1038/s41592-018-0001-7>
21. Simpson, G. G. (1951) The species concept. Evolution 5, 285–298. <https://doi.org/10.1111/j.1558-5646.1951.tb02788.x>
22. Song, J. H., Cho, H., Park, M. Y., Na, D. S., Moon, H. B., Pai, C. H. (1993) Detection of Salmonella typhi in the blood of patients with typhoid fever by polymerase chain reaction. J. Clin. Microbiol. 31(6), 1439–1443. <https://doi.org/10.1128/jcm.31.6.1439-1443.1993>
23. Tennant, S. M., Toema, D., Qamar, F., Iqbal, N., Boyd, M. A., Marshall, J. M., Blackwelder, W. C., Wu, Y., Quadri, F., Khan, A., Aziz, F., Ahmad, K., Kalam, A., Asif, E., Qureshi, S., Khan, E., Zaidi, A. K., Levine, M. M. (2015) Detection of typhoidal and paratyphoidal Salmonella in blood by real-time polymerase chain reaction. Clin. Infect. Dis. 61, S241–S250 (Suppl. 4). <https://doi.org/10.1093/cid/civ726>
24. Ton, K. N. T., Cree, S. L., Gronert-Sum, S. J., Merriman, T. R., Stamp, L. K., Kennedy, M. A. (2018) Multiplexed nanopore sequencing of HLA-B locus in Māori and Pacific Island samples. Front. Genet. 9, 152. <https://doi.org/10.3389/fgene.2018.00152>
25. Váradi, L., Luo, J. L., Hibbs, D. E., Perry, J. D., Anderson, R. J., Orenga, S., Groundwater, P. W. (2017) Methods for the detection and identification of pathogenic bacteria: past, present, and future. Chem. Soc. Rev. 46(16), 4818–4832. <https://doi.org/10.1039/C6CS00693K>
26. Wain, J., Diep, T. S., Ho, V. A., Walsh, A. M., Hoa, N. T. T., Parry, C. M., White, N. J. (1998) Quantitation of bacteria in blood of typhoid fever patients and relationship between counts and clinical features, transmissibility, and antibiotic resistance. J. Clin. Microbiol. 36(6), 1683–1687. <https://doi.org/10.1128/JCM.36.6.1683-1687.1998>
27. Watsa, M., Erkenswick, G. A., Pomerantz, A., Prost, S. (2019) Genomics in the jungle: Using portable sequencing as a teaching tool in field courses. bioRxiv.
28. Zhang, Z., Schwartz, S., Wagner, L., Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7(1–2), 203–214. <https://doi.org/10.1089/10665270050081478>
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