Molecular detection of free-living amoebae from Namhangang (southern Han River) in Korea

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Abstract

The free-living amoebae Naegleria spp. and Acanthamoeba spp. exist in the natural environment and are sometimes causal agents of lethal primary amoebic meningoencephalitis (PAM), amoebic keratitis (AK) and granulomatous amebic encephalitis (GAE) in humans, respectively. To ascertain the existence of free-living amoebae in Korea, water samples were collected from the Korean hydrosphere, Namhangang (southern Han River), an active location for water skiing and recreation. Samples underwent two-step filtration and were cultured on non-nutrient agar medium with inactivated E. coli. The remaining samples were subjected to PCR for primarily the 18S small ribosomal RNA gene and gene sequencing. Similarities in 18S rDNA sequences, in comparison with various reference amoebae in GenBank, showed 86~99% homology with N. gruberi, N. philippinensis, N. clarki, A. polyphaga, A. castellannii, and Hartmannella ( Vermamoeba) vermiformis. Therefore, this study will be useful for seasonal detection of free-living amoebae from various Korean hydrospheres in future studies.

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An update on Acanthamoeba keratitis: diagnosis, pathogenesis and treatment

Jacob Lorenzo-Morales, Naveed Khan, Julia Walochnik (2015)

Free-living amoebae of the genus Acanthamoeba are causal agents of a severe sight-threatening infection of the cornea known as Acanthamoeba keratitis. Moreover, the number of reported cases worldwide is increasing year after year, mostly in contact lens wearers, although cases have also been reported in non-contact lens wearers. Interestingly, Acanthamoeba keratitis has remained significant, despite our advances in antimicrobial chemotherapy and supportive care. In part, this is due to an incomplete understanding of the pathogenesis and pathophysiology of the disease, diagnostic delays and problems associated with chemotherapeutic interventions. In view of the devastating nature of this disease, here we present our current understanding of Acanthamoeba keratitis and molecular mechanisms associated with the disease, as well as virulence traits of Acanthamoeba that may be potential targets for improved diagnosis, therapeutic interventions and/or for the development of preventative measures. Novel molecular approaches such as proteomics, RNAi and a consensus in the diagnostic approaches for a suspected case of Acanthamoeba keratitis are proposed and reviewed based on data which have been compiled after years of working on this amoebic organism using many different techniques and listening to many experts in this field at conferences, workshops and international meetings. Altogether, this review may serve as the milestone for developing an effective solution for the prevention, control and treatment of Acanthamoeba infections.

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Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge.

Michael J. M. Hay, Susan J. Schroeder, I Niszl … (2001)

This study identified subgenic PCR amplimers from 18S rDNA that were (i) highly specific for the genus Acanthamoeba, (ii) obtainable from all known genotypes, and (iii) useful for identification of individual genotypes. A 423- to 551-bp Acanthamoeba-specific amplimer ASA.S1 obtained with primers JDP1 and JDP2 was the most reliable for purposes i and ii. A variable region within this amplimer also identified genotype clusters, but purpose iii was best achieved with sequencing of the genotype-specific amplimer GTSA.B1. Because this amplimer could be obtained from any eukaryote, axenic Acanthamoeba cultures were required for its study. GTSA.B1, produced with primers CRN5 and 1137, extended between reference bp 1 and 1475. Genotypic identification relied on three segments: bp 178 to 355, 705 to 926, and 1175 to 1379. ASA.S1 was obtained from single amoeba, from cultures of all known 18S rDNA genotypes, and from corneal scrapings of Scottish patients with suspected Acanthamoeba keratitis (AK). The AK PCR findings were consistent with culture results for 11 of 15 culture-positive specimens and detected Acanthamoeba in one of nine culture-negative specimens. ASA.S1 sequences were examined for 6 of the 11 culture-positive isolates and were most closely associated with genotypic cluster T3-T4-T11. A similar distance analysis using GTSA.B1 sequences identified nine South African AK-associated isolates as genotype T4 and three isolates from sewage sludge as genotype T5. Our results demonstrate the usefulness of 18S ribosomal DNA PCR amplimers ASA.S1 and GTSA.B1 for Acanthamoeba-specific detection and reliable genotyping, respectively, and provide further evidence that T4 is the predominant genotype in AK.

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Origin and evolution of the worldwide distributed pathogenic amoeboflagellate Naegleria fowleri.

Bruna P F Fonseca (2011)

Naegleria fowleri, a worldwide distributed pathogen, is the causative agent of primary amoebic meningoencephalitis. Because it is such a fulminant disease, most patients do not survive the infection. This pathogen is a free-living amoeboflagellate present in warm water. To date, it is well established that there are several types of N. fowleri, which can be distinguished based on the length of the internal transcribed spacer 1 and a one bp transition in the 5.8S rDNA. Seven of the eight known types have been detected in Europe. Three types are present in the USA, of which one is unique to this country. Only one of the eight types occurs in Oceania (Australia and New Zealand) and Japan. In mainland Asia (India, China and Thailand) the two most common types are found, which are also present in Europe and the USA. There is strong indication that the pathogenic N. fowleri evolved from the nonpathogenic Naegleria lovaniensis on the American continent. There is no evidence of virulence differences between the types of N. fowleri. Two other Naegleria spp. are pathogenic for mice, but human infections due to these two other Naegleria spp. are not known. Copyright © 2011 Elsevier B.V. All rights reserved.

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Author and article information

Contributors

Ho-Joon Shin: hjshin@ajou.ac.kr

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 15 January 2020

Publication date PMC-release: 15 January 2020

Publication date Collection: 2020

Volume: 10

Electronic Location Identifier: 335

Affiliations

[1 ]ISNI 0000 0004 0532 3933, GRID grid.251916.8, Department of Microbiology, , Ajou University School of Medicine, ; Suwon, 16499 Republic of Korea

[2 ]ISNI 0000 0004 0532 3933, GRID grid.251916.8, Department of Biomedical Science, , Graduate School of Ajou University, ; Suwon, 16499 Republic of Korea

[3 ]ISNI 0000 0004 0647 1428, GRID grid.443736.1, Department of Biomedical Laboratory Science, Molecular Diagnostics Research Institute, School of Health and Medicine, , Namseoul University, ; Cheonan, 31020 Republic of Korea

[4 ]Division of Vectors and Parasitic Diseases, Korea Centers for Diseases Control and Prevention, Osong, 363-951 Republic of Korea

Article

Publisher ID: 57347

DOI: 10.1038/s41598-019-57347-1

PMC ID: 6962209

PubMed ID: 31942007

SO-VID: 6470ac57-2b89-41c9-9075-25c662e60afc

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 4 July 2019

Date accepted : 20 December 2019

Funding

Funded by: FundRef https://doi.org/10.13039/501100003725, National Research Foundation of Korea (NRF);

Award ID: 2018R1D1A1B07047302

Award Recipient : Ho-Joon Shin

Funded by: FundRef https://doi.org/10.13039/501100003669, Ministry of Health, Welfare and Family Affairs | Korea Centers for Disease Control & Prevention (KCDC);

Award ID: 2015-E5400600

Award Recipient : Ho-Joon Shin

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ScienceOpen disciplines: Uncategorized

Keywords: molecular ecology,parasite biology

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ScienceOpen disciplines: Uncategorized

Keywords: molecular ecology, parasite biology

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Molecular detection of free-living amoebae from Namhangang (southern Han River) in Korea

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Most cited references 34

An update on Acanthamoeba keratitis: diagnosis, pathogenesis and treatment

Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge.

Origin and evolution of the worldwide distributed pathogenic amoeboflagellate Naegleria fowleri.

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