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

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

In our study we present an overview of the use of Oxford Nanopore Technologies (ONT) sequencing technology on the background of Enteric fever. Unlike traditional methods (e.g., qPCR, serological tests), the nanopore sequencing technology enables virtually real-time data generation and highly accurate pathogen identification and characterization. Blood cultures were obtained from a 48-year-old female patient suffering from a high fever, headache and diarrhea. Nevertheless, both the initial serological tests and stool culture appeared to be negative. Therefore, the bacterial isolate from blood culture was used for nanopore sequencing (ONT). This technique in combination with subsequent bioinformatic analyses allowed for prompt identification of the disease-causative agent as Salmonella enterica subsp. enterica serovar Paratyphi A. The National Reference Laboratory for Salmonella (NIPH) independently reported this isolate also as serovar Paratyphi A on the basis of results of biochemical and agglutination tests. Therefore, our results are in concordance with certified standards. Furthermore, the data enabled us to assess some basic questions concerning the comparative genomics, i.e., to describe whether the isolated strain differs from the formerly published ones or not. Quite surprisingly, these results indicate that we have detected a novel and so far, unknown variety of this bacteria.


This study was supported by funding from projects of the Ministry of the Interior of the Czech Republic (VH20172020012: Preparation of the collection of biologically significant toxins with the support of European Biological European Biodefence Laboratory Network), Ministry of Defence of the Czech Republic through a Long-term organization development plan 907930101413 and a project MO1012, and a project of Charles University SVV 260 520.


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