Pythium insidiosum complex hides a cryptic novel species: Pythium periculosum

Miraglia, Bruno Maltez; Mendoza, Leonel; Rammohan, Ram; Vilela, Luiza; Vilela, Camila; Vilela, Gabriella; Huebner, Marianne; Mani, Rinosh; Vilela, Raquel

doi:10.1016/j.funbio.2022.03.002

Cited by 11 publications

(2 citation statements)

References 46 publications

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“…Typing the ribosomal deoxyribonucleic acid (rDNA) sequence classifies P. insidiosum into three major clades, which are associated with its geographic distributions: clade-I strains from the Americas, clade-II strains from the Americas, Asia, and Australia, and clade-III strains mainly from Thailand and the United States [ 5 , 6 ]. Miraglia et al recently reclassified the P. insidiosum strains in the genotype clade-III as Pythium periculosum based on the population genetic analysis [ 7 ]. So far, the draft genome data of at least 10 strains of P. insidiosum have been sequenced using various next-generation sequencing (NGS) platforms (i.e., 454, Illumina, and PacBio) and deposited in the public databases [ 8 – 15 ].…”

Section: Objectivementioning

confidence: 99%

MGI short-read genome assemblies of Pythium insidiosum (reclassified as Pythium periculosum) strains Pi057C3 and Pi050C3

Krajaejun,

Patumcharoenpol,

Rujirawat

et al. 2023

BMC Res Notes

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Objectives Pythium insidiosum causes a difficult-to-treat infectious condition called pythiosis, with high morbidity and mortality. So far, genome data of at least 10 strains of P. insidiosum, primarily classified in the phylogenetic clades I and II, have been sequenced using various next-generation sequencing platforms. The MGI short-read platform was employed to obtain genome data of 2 clade-III strains of P. insidiosum (recently reclassified as Pythium periculosum) from patients in Thailand and the United States. This work is a part of our attempt to generate a comprehensive genome database from diverse pathogen strains. Data description A 150-bp paired-end library was prepared from a gDNA sample of P. insidiosum (P. periculosum) strains Pi057C3 and Pi050C3 (also known as ATCC90586) to generate draft genome sequences using an MGISEQ-2000RS sequencer. As a result, for the strain Pi057C3, we obtained a 42.5-Mb assembled genome (164x coverage) comprising 14,134 contigs, L50 of 241, N50 of 45,748, 57.6% CG content, and 12,147 ORFs. For the strain Pi050C3, we received a 43.3-Mb draft genome (230x coverage) containing 14,511 contigs, L50 of 245, N50 of 45,208, 57.7% CG content, and 12,249 ORFs. The genome sequences have been deposited in the NCBI/DDBJ databases under the accession numbers JAKCXM000000000.1 (strain Pi057C3) and JAKCXL000000000.1 (strain Pi050C3).

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Section: Objectivementioning

confidence: 99%

MGI short-read genome assemblies of Pythium insidiosum (reclassified as Pythium periculosum) strains Pi057C3 and Pi050C3

Krajaejun,

Patumcharoenpol,

Rujirawat

et al. 2023

BMC Res Notes

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“…Moreover, the advantages and limitations of each assay are provided, making it convenient for healthcare professionals to learn and decide which detection method is suitable for use in their respective laboratory environments. It should be noted that the specific genotypes (i.e., clade III) of P. insidiosum have recently been proposed as a new species called P. periculosum [ 12 ]. However, to avoid confusion, we only referred to the organism as P. insidiosum in this study, as do all the collected publications regarding NATs.…”

Section: Introductionmentioning

confidence: 99%

Nucleic Acid-Based Detection of Pythium insidiosum: A Systematic Review

Sridapan

Krajaejun

2022

JoF

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Pythiosis, a life-threatening infectious condition caused by Pythium insidiosum, has been increasingly reported in humans and animals worldwide. Antifungal drugs usually fail to control the pathogen. The surgical removal of an infected organ is the treatment of choice. Many affected patients die due to advanced infection. A timely and accurate diagnosis could lead to a better prognosis in pythiosis patients and save their lives. Although a standard culture method is available in microbiological laboratories, it is time-consuming, laborious, and insensitive for P. insidiosum identification. Immunological assays have been developed to improve the diagnosis of pythiosis. However, immunological methods are commercially unavailable and primarily detect anti-P. insidiosum antibodies, which constitute indirect evidence of pythiosis, making it challenging to differentiate a past from a recent infection. Moreover, such immunological tests cannot diagnose patients with a local infection, such as in the eye. Nucleic acid-based tests (NATs) are efficient for the direct and rapid detection of P. insidiosum DNA in trace-amount or culture-negative specimens. The reagents and equipment required for NATs are usually available in molecular diagnostic laboratories. Herein, we provide a systematic review to comprehensively present the principal and clinical usages, advantages, and limitations of such NATs in the detection of P. insidiosum. Various NATs have been established to detect P. insidiosum, which can be classified into amplification-based (i.e., PCR assays, isothermal tests, and next-generation sequencing methods) and non-amplification-based (i.e., DNA hybridization) techniques. This concise review on NATs constitutes an up-to-date reference with which healthcare professionals can learn about and decide upon which detection method is suitable for their respective laboratory environments.

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