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ICOPA 2022 Free Living Amoebae Symposia Special Issue
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ICOPA 2022 Free Living Amoebae Symposia Special Issue

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Parasitic Pathogens".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 5197

Special Issue Editors

Dr. Jacob Lorenzo-Morales

E-Mail Website
Guest Editor
Departamento de Obstetricia, Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez, 2, 38206 La Laguna, Tenerife, Spain
Interests: free living amoebae; therapeutics; emerging parasitic protozoa; diagnosis; natural compounds; synthetic compounds
Special Issues, Collections and Topics in MDPI journals
Dr. Sumeeta Khurana

E-Mail Website
Guest Editor
Postgraduate Institute of Medical Education and Research, Chandigarh, India
Interests: free living amoebae; human parasites; protozoa; helminths; malaria; Trichomonas; Giardia; soil transmitted helminths

Special Issue Information

Dear Colleagues,

In the 2022 edition of ICOPA, a Free Living Amoebae symposia will be held. This is the perfect opportunity for experts on the field worldwide to interact. As part of further interactions and due to the emerging number of infections due to Free Living Amoebae worldwide, this special issue of pathogens invites potential authors to contribute. Original research studies focused on all aspects of FLA are welcome.

Dr. Jacob Lorenzo-Morales
Dr. Sumeeta Khurana
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • free living Amoebae
  • therapy
  • diagnostics
  • emerging
  • Acanthamoeba
  • Naegleria

Published Papers (3 papers)

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Research

11 pages, 1284 KiB  
Article
De Novo Transcriptome Profiling of Naegleria fowleri Trophozoites and Cysts via RNA Sequencing
by Hae-Jin Sohn, Jong-Hyun Kim, Kyongmin Kim, Sun Park and Ho-Joon Shin
Pathogens 2023, 12(2), 174; https://doi.org/10.3390/pathogens12020174 - 22 Jan 2023
Cited by 1 | Viewed by 1540
Abstract
Naegleria fowleri is a pathogenic free-living amoeba, commonly found around the world in warm, fresh water and soil. N. fowleri trophozoites can infect humans by entering the brain through the nose and causing usually fatal primary amebic meningoencephalitis (PAM). Trophozoites can encyst to [...] Read more.
Naegleria fowleri is a pathogenic free-living amoeba, commonly found around the world in warm, fresh water and soil. N. fowleri trophozoites can infect humans by entering the brain through the nose and causing usually fatal primary amebic meningoencephalitis (PAM). Trophozoites can encyst to survive under unfavorable conditions such as cold temperature, starvation, and desiccation. Recent technological advances in genomics and bioinformatics have provided unique opportunities for the identification and pre-validation of pathogen-related and environmental resistance through improved understanding of the biology of pathogenic N. fowleri trophozoites and cysts at a molecular level. However, genomic and transcriptomic data on differential expression genes (DEGs) between trophozoites and cysts of N. fowleri are very limited. Here, we report transcriptome Illumina RNA sequencing (RNA-seq) for N. fowleri trophozoites and cysts and de novo transcriptome assembly. RNA-seq libraries were generated from RNA extracted from N. fowleri sampled from cysts, and a reference transcriptome was generated through the assembly of trophozoite data. In the database, the assembly procedure resulted in 42,220 contigs with a mean length of 11,254 nucleotides and a C+G content of 37.21%. RNA sequencing showed that 146 genes in cysts of N. fowleri indicated 2-fold upregulation in comparison with trophozoites of N. fowleri, and 163 genes were downregulated; these genes were found to participate in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The KEGG pathway included metabolic (131 sequences) and genetic information processing (66 sequences), cellular processing (43 sequences), environmental information processing (22 sequences), and organismal system (20 sequences) pathways. On the other hand, an analysis of 11,254 sequences via the Gene Ontology database showed that their annotations contained 1069 biological processes including the cellular process (228 sequences) and metabolic process (214 sequences); 923 cellular components including cells (240 sequences) and cell parts (225 sequences); and 415 molecular functions including catalytic activities (195 sequences) and binding processes (186 sequences). Differential expression levels increased in cysts of N. fowleri compared to trophozoites of N. fowleri, which were mainly categorized as serine/threonine protease, kinase, and lipid metabolism-related proteins. These results may provide new insights into pathogen-related genes or environment-resistant genes in the pathogenesis of N. fowleri. Full article
(This article belongs to the Special Issue ICOPA 2022 Free Living Amoebae Symposia Special Issue)
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13 pages, 2086 KiB  
Article
An Insight into the Genome of Pathogenic and Non-Pathogenic Acanthamoeba
by Chayan Sharma, Sumeeta Khurana, Amit Arora, Alka Bhatia and Amit Gupta
Pathogens 2022, 11(12), 1558; https://doi.org/10.3390/pathogens11121558 - 19 Dec 2022
Cited by 2 | Viewed by 1689
Abstract
Background: Acanthamoeba are amphizoic amoeba majorly responsible for causing Acanthamoeba keratitis (AK) and Granulomatous amoebic encephalitis (GAE). Despite its ubiquitous nature, the frequency of infections is not high, probably due to the existence of non-pathogenic isolates. The whole-genome sequencing and an annotated genome [...] Read more.
Background: Acanthamoeba are amphizoic amoeba majorly responsible for causing Acanthamoeba keratitis (AK) and Granulomatous amoebic encephalitis (GAE). Despite its ubiquitous nature, the frequency of infections is not high, probably due to the existence of non-pathogenic isolates. The whole-genome sequencing and an annotated genome assembly can unravel the biological functions and help in identifying probable genes related to pathogenicity. Methods: Illumina and Nanopore sequencing were performed for keratitis, encephalitis, and non-pathogenic environmental isolates. Hybrid assembly was prepared for the AK and GAE isolates, while only the Illumina reads were utilized for a non-pathogenic environmental isolate. Protein coding genes were identified using the GeneMark-ES program and BLASTx module of Diamond used for gene prediction. Additionally, the Kyoto Encyclopedia of Genes and Genomes annotation and cluster of orthologous group’s annotation using RPS-blast against the CDD database was performed. The subsequent data analysis and validation will help identify probable pathogenic genes. Results: The genome assemblies of 9.67, 8.34, and 8.89 GBs were reported for GAE, AK, and non-pathogenic isolate, respectively. KEGG reported 22,946 in GAE, 24,231 in keratitis, and 9367 genes in the environmental isolate. The COG annotation revealed 3232 in GAE, 3403 in keratitis, and 1314 genes in the non-pathogenic isolate. Conclusion: The present study has attempted to generate de novo hybrid genome assemblies of Acanthamoeba that would help decode the genome of free-living amoeba and will provide genomic data for a better understanding of virulence-related factors. Full article
(This article belongs to the Special Issue ICOPA 2022 Free Living Amoebae Symposia Special Issue)
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10 pages, 2039 KiB  
Article
Molecular Diagnosis of Encephalitis/Meningoencephalitis Caused by Free-Living Amoebae from a Tertiary Center in India
by Sumeeta Khurana, Chayan Sharma, Bishan Dass Radotra, Abhishek Mewara, Parveen Tanwar, Priya Datta and Rakesh Sehgal
Pathogens 2022, 11(12), 1509; https://doi.org/10.3390/pathogens11121509 - 09 Dec 2022
Cited by 1 | Viewed by 1324
Abstract
Background: Pathogenic free-living amoeba (FLA) such as Acanthamoeba spp., Naegleria fowleri, and Balamuthia mandrillaris are causative agents of fatal amoebic encephalitis/meningoencephalitis. The diagnosis of such infections is challenging due to a lack of clinical suspicion and expertise in microscopic identification. We evaluated [...] Read more.
Background: Pathogenic free-living amoeba (FLA) such as Acanthamoeba spp., Naegleria fowleri, and Balamuthia mandrillaris are causative agents of fatal amoebic encephalitis/meningoencephalitis. The diagnosis of such infections is challenging due to a lack of clinical suspicion and expertise in microscopic identification. We evaluated the performance of molecular assays for the timely and accurate detection of FLA-causing central nervous system (CNS) afflictions. Methods: This study included samples from 156 patients with suspected encephalitis/meningoencephalitis, including 149 cerebrospinal fluid (CSF) samples, 5 brain tissue biopsies, and 2 brain abscess samples. All the samples were subjected to PCR-based detection of Acanthamoeba spp., N. fowleri, and B. mandrillaris. The diagnostic characteristics and the inter-rater reliability scores were evaluated for parasite-specific polymerase chain reaction (PCR) using culture on non-nutrient agar (NNA)/microscopy or histopathological examination as a confirmatory test for Acanthamoeba spp. and N. fowleri and histopathology for B. mandrillaris. Results: We detected 11 samples positive for FLA, including 6 Acanthamoeba spp., 3 B. mandrillaris, and 2 N. fowleri. Furthermore, all 11 samples were positive according to the confirmatory tests, i.e., culture on NNA/microscopy/histopathology in the case of Acanthamoeba spp. and N. fowleri and histopathology of tissue biopsies for B. mandrillaris. The inter-rater reliability between the PCRs and the confirmatory tests for the detection of Acanthamoeba spp., N. fowleri, and B. mandrillaris was 100%. Conclusions: The PCR-based detection of FLA in patients suspected of encephalitis/meningoencephalitis was found to be fast, efficient, and reliable in our study. We suggest the use of these PCRs in laboratories to obtain additional data on their efficiency in diagnosing FLA infections of the CNS. The present study was conducted with a small sample size of 156 patient samples, and we found only six Acanthamoeba spp., three B. mandrillaris, and two N. fowleri. The present study should be conducted on a larger sample size for better evaluation of the primer pairs. Full article
(This article belongs to the Special Issue ICOPA 2022 Free Living Amoebae Symposia Special Issue)
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