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Cantin LJ, Gregory V, Blum LN, Foster JM. Dual RNA-seq in filarial nematodes and Wolbachia endosymbionts using RNase H based ribosomal RNA depletion. Front Microbiol 2024; 15:1418032. [PMID: 38832111 PMCID: PMC11144916 DOI: 10.3389/fmicb.2024.1418032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024] Open
Abstract
Lymphatic filariasis is caused by parasitic nematodes and is a leading cause of disability worldwide. Many filarial worms contain the bacterium Wolbachia as an obligate endosymbiont. RNA sequencing is a common technique used to study their molecular relationships and to identify potential drug targets against the nematode and bacteria. Ribosomal RNA (rRNA) is the most abundant RNA species, accounting for 80-90% of the RNA in a sample. To reduce sequencing costs, it is necessary to remove ribosomal reads through poly-A enrichment or ribosomal depletion. Bacterial RNA does not contain a poly-A tail, making it difficult to sequence both the nematode and Wolbachia from the same library preparation using standard poly-A selection. Ribosomal depletion can utilize species-specific oligonucleotide probes to remove rRNA through pull-down or degradation methods. While species-specific probes are commercially available for many commonly studied model organisms, there are currently limited depletion options for filarial parasites. Here, we performed total RNA sequencing from Brugia malayi containing the Wolbachia symbiont (wBm) and designed ssDNA depletion probes against their rRNA sequences. We compared the total RNA library to poly-A enriched, Terminator 5'-Phosphate-Dependent Exonuclease treated, NEBNext Human/Bacteria rRNA depleted and our custom nematode probe depleted libraries. The custom nematode depletion library had the lowest percentage of ribosomal reads across all methods, with a 300-fold decrease in rRNA when compared to the total RNA library. The nematode depletion libraries also contained the highest percentage of Wolbachia mRNA reads, resulting in a 16-1,000-fold increase in bacterial reads compared to the other enrichment and depletion methods. Finally, we found that the Brugia malayi depletion probes can remove rRNA from the filarial worm Dirofilaria immitis and the majority of rRNA from the more distantly related free living nematode Caenorhabditis elegans. These custom filarial probes will allow for future dual RNA-seq experiments between nematodes and their bacterial symbionts from a single sequencing library.
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Affiliation(s)
- Lindsey J. Cantin
- Biochemistry and Microbiology Division, New England BioLabs, Ipswich, MA, United States
| | - Vanessa Gregory
- Biochemistry and Microbiology Division, New England BioLabs, Ipswich, MA, United States
| | - Laura N. Blum
- Applications and Product Development, New England BioLabs, Ipswich, MA, United States
| | - Jeremy M. Foster
- Biochemistry and Microbiology Division, New England BioLabs, Ipswich, MA, United States
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Huggins LG, Atapattu U, Young ND, Traub RJ, Colella V. Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans. BMC Microbiol 2024; 24:28. [PMID: 38245715 PMCID: PMC10799534 DOI: 10.1186/s12866-023-03159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Filarial worms are important vector-borne pathogens of a large range of animal hosts, including humans, and are responsible for numerous debilitating neglected tropical diseases such as, lymphatic filariasis caused by Wuchereria bancrofti and Brugia spp., as well as loiasis caused by Loa loa. Moreover, some emerging or difficult-to-eliminate filarioid pathogens are zoonotic using animals like canines as reservoir hosts, for example Dirofilaria sp. 'hongkongensis'. Diagnosis of filariasis through commonly available methods, like microscopy, can be challenging as microfilaremia may wane below the limit of detection. In contrast, conventional PCR methods are more sensitive and specific but may show limited ability to detect coinfections as well as emerging and/or novel pathogens. Use of deep-sequencing technologies obviate these challenges, providing sensitive detection of entire parasite communities, whilst also being better suited for the characterisation of rare or novel pathogens. Therefore, we developed a novel long-read metabarcoding assay for deep-sequencing the filarial nematode cytochrome c oxidase subunit I gene on Oxford Nanopore Technologies' (ONT) MinION™ sequencer. We assessed the overall performance of our assay using kappa statistics to compare it to commonly used diagnostic methods for filarial worm detection, such as conventional PCR (cPCR) with Sanger sequencing and the microscopy-based modified Knott's test (MKT). RESULTS We confirmed our metabarcoding assay can characterise filarial parasites from a diverse range of genera, including, Breinlia, Brugia, Cercopithifilaria, Dipetalonema, Dirofilaria, Onchocerca, Setaria, Stephanofilaria and Wuchereria. We demonstrated proof-of-concept for this assay by using blood samples from Sri Lankan dogs, whereby we identified infections with the filarioids Acanthocheilonema reconditum, Brugia sp. Sri Lanka genotype and zoonotic Dirofilaria sp. 'hongkongensis'. When compared to traditionally used diagnostics, such as the MKT and cPCR with Sanger sequencing, we identified an additional filarioid species and over 15% more mono- and coinfections. CONCLUSIONS Our developed metabarcoding assay may show broad applicability for the metabarcoding and diagnosis of the full spectrum of filarioids from a wide range of animal hosts, including mammals and vectors, whilst the utilisation of ONT' small and portable MinION™ means that such methods could be deployed for field use.
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Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia.
| | - Ushani Atapattu
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
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Al-Jawabreh R, Lastik D, McKenzie D, Reynolds K, Suleiman M, Mousley A, Atkinson L, Hunt V. Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220437. [PMID: 38008117 PMCID: PMC10676819 DOI: 10.1098/rstb.2022.0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 11/28/2023] Open
Abstract
Among nematodes, the free-living model organism Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Reem Al-Jawabreh
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Dominika Lastik
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | - Kieran Reynolds
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Mona Suleiman
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | | | - Vicky Hunt
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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Matapo BB, Mpabalwani EM, Kaonga P, Simuunza MC, Bakyaita N, Masaninga F, Siyumbwa N, Siziya S, Shamilimo F, Muzongwe C, Mwase ET, Sikasunge CS. Lymphatic Filariasis Elimination Status: Wuchereria bancrofti Infections in Human Populations after Five Effective Rounds of Mass Drug Administration in Zambia. Trop Med Infect Dis 2023; 8:333. [PMID: 37505629 PMCID: PMC10383567 DOI: 10.3390/tropicalmed8070333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 07/29/2023] Open
Abstract
Lymphatic filariasis (LF), also commonly known as elephantiasis, is a neglected tropical disease (NTD) caused by filarial parasites. The disease is transmitted via a bite from infected mosquitoes. The bites of these infected mosquitoes deposit filarial parasites, Wuchereria or Brugia, whose predilection site is the lymphatic system. The damage to the lymph system causes swelling in the legs, arms, and genitalia. A mapping survey conducted between 2003 and 2011 determined LF as being endemic in Zambia in 96 out of 116 districts. Elimination of LF is known to be possible by stopping the spread of the infection through large-scale preventive chemotherapy. Therefore, mass drug administration (MDA) with diethylcarbamazine citrate (DEC) (6 mg/kg) and Albendazole (400 mg) for Zambia has been conducted and implemented in all endemic districts with five effective rounds. In order to determine whether LF prevalence has been sufficiently reduced to levels less than 2% antigenemia and less than 1% microfilaremia, a pre-transmission assessment survey (pre-TAS) was conducted. Therefore, post-MDA pre-TAS was conducted between 2021 and 2022 in 80 districts to determine the LF prevalence. We conducted a cross-sectional seroprevalence study involving 600 participants in each evaluation unit (EU) or each district. The study sites (sentinel and spot-check sites) were from districts that were the implementation units (IUs) of the LF MDA. These included 80 districts from the 9 provinces. A total of 47,235 people from sentinel and spot-check locations were tested. Of these, valid tests were 47,052, of which 27,762 (59%) were females and 19,290 (41%) were males. The survey revealed in the 79/80 endemic districts a prevalence of Wb antigens of 0.14% and 0.0% prevalence of microfilariae. All the surveyed districts had an optimum prevalence of less than 2% for antigenaemia, except for Chibombo district. The majority of participants that tested positive for Wuchereria bancrofti (Wb) Antigens (Ag) were those that had 2, 3, and 4 rounds of MDA. Surprisingly, individuals that had 1 round of MDA were not found to have circulating antigens of Wb. The study showed that all the surveyed districts, except for Chibombo, passed pre-TAS. This further implies that there is a need to conduct transmission assessment surveys (TASs) in these districts.
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Affiliation(s)
- Belem Blamwell Matapo
- School of Public Health, University of Zambia, Ridgeway Campus, Lusaka P.O. Box 50516, Zambia
- World Health Organization, Corner Andrew Mwenya/Beit Road, Lusaka P.O. Box 32346, Zambia
| | - Evans Mwila Mpabalwani
- School of Medicine, University of Zambia, Ridgeway Campus, Lusaka P.O. Box 50516, Zambia
| | - Patrick Kaonga
- School of Public Health, University of Zambia, Ridgeway Campus, Lusaka P.O. Box 50516, Zambia
| | - Martin Chitolongo Simuunza
- School of Veterinary Medicine, University of Zambia, Great East Road Campus, Lusaka P.O. Box 32379, Zambia
| | - Nathan Bakyaita
- World Health Organization, Corner Andrew Mwenya/Beit Road, Lusaka P.O. Box 32346, Zambia
| | - Freddie Masaninga
- World Health Organization, Corner Andrew Mwenya/Beit Road, Lusaka P.O. Box 32346, Zambia
| | - Namasiku Siyumbwa
- Ministry of Health Headquarters Ndeke House, Lusaka P.O. Box 30205, Zambia
| | - Seter Siziya
- Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola P.O. Box 71191, Zambia
| | - Frank Shamilimo
- Ministry of Health Headquarters Ndeke House, Lusaka P.O. Box 30205, Zambia
| | - Chilweza Muzongwe
- Ministry of Health Headquarters Ndeke House, Lusaka P.O. Box 30205, Zambia
| | - Enala T. Mwase
- School of Veterinary Medicine, University of Zambia, Great East Road Campus, Lusaka P.O. Box 32379, Zambia
| | - Chummy Sikalizyo Sikasunge
- School of Veterinary Medicine, University of Zambia, Great East Road Campus, Lusaka P.O. Box 32379, Zambia
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Wu T, Ma X, Wang F, Xie L, Lv Q, Zeng M, Xu Y, Qin S, Chang Q. First Description of the Mitogenome Features of Neofoleyellides Genus (Nematoda: Onchocercidae) Isolated from a Wild Bird (Pyrrhocorax pyrrhocorax). Animals (Basel) 2022; 12:ani12202854. [PMID: 36290239 PMCID: PMC9597759 DOI: 10.3390/ani12202854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Filarioidea, a superfamily of nematodes, presently includes 42 species divided into six genera, mainly in the family Onchocercidae, which have been reported to infect a wide range of hosts, including reptiles, birds, and mammals. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. Thus, the objective of the present study was to sequence and analyze the complete mt genome of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and to assess its phylogenetic position in the Onchocercidae family. The evaluated Neofoleyellides sp. mt genome was consistent with the molecular pattern of the Onchocercidae family: 36 subunits consisting of 12 PCGs, 2 rRNAs, and 22 tRNAs. Phylogenetic analyses based on the 18S rRNA gene, cox1 gene, and 12 PCGs showed consistent results, which strongly supported monophyly of the genus Neofoleyellides. These findings enriched the gene database and improved our knowledge of the molecular characteristics of the Onchocercidae family, which provide useful genetic markers to study the population genetics, molecular biology, and phylogenetics of these Onchocercidae nematodes. Abstract The Onchocercidae family is composed of more than 30 valid nematode species with notable zoonotic potential. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. This study describes for the first time the complete mitochondrial (mt) genome sequence of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and belonging to the Neofoleyellides genus (Nematoda: Onchocercidae). The mt genome of Neofoleyellides sp. (GenBank accession number: ON641583) was a typical circular DNA molecule of 13,628 bp in size with an AT content of 76.69%. The complete mt genome comprised 36 functional subunits, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The most common start codon was ATT/ATG except for nad2 with TTG, and TAA was the termination codon for all protein-coding genes (PCGs). Phylogenetic analysis of the concatenated and aligned amino acid sequences of the 12 PCGs showed that the trees generated using different methods (Bayesian inference and maximum likelihood) with different partition schemes shared similar topologies. The isolated Neofoleyellides sp. was placed in the Onchocercidae family and formed a sister branch with the genera Onchocerca and Dirofilaria. The entire mt genome of Neofoleyellides sp. presented in this study could provide useful data for studying the population genetics and phylogenetic relationships of Onchocercidae species.
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Affiliation(s)
- Tingting Wu
- School of Public Health, Shantou University, Shantou 515063, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoxiao Ma
- School of Public Health, Shantou University, Shantou 515063, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Fengfeng Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Linhong Xie
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Qingbo Lv
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Minhao Zeng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yu Xu
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Siyuan Qin
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Qiaocheng Chang
- School of Public Health, Shantou University, Shantou 515063, China
- Correspondence:
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Abstract
Glaucoma is an intraocular pressure-related ophthalmic disease with multiple causes that results in an optic neuropathy and vision loss. Intraocular pressure elevation is among its strongest risk factors. While glaucoma is mostly primary in etiology, secondary glaucoma is not infrequent. Recognizing its cause is imperative, since treatment is often different depending on the pathophysiologic mechanism. Numerous clinically relevant ophthalmic infections can result in robust inflammatory responses that may result in pressure elevation or intraocular anatomic configurations that predispose to pressure elevation. Knowing the mechanisms by which these infections can lead to glaucoma is critical in treating, and we consolidate what is currently known in regards to how infectious diseases lead to glaucoma.
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7
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Hedtke SM, Zendejas-Heredia PA, Graves PM, Sheridan S, Sheel M, Fuimaono SD, Lau CL, Grant WN. Genetic epidemiology of lymphatic filariasis in American Samoa after mass drug administration. Int J Parasitol 2020; 51:137-147. [PMID: 33166540 DOI: 10.1016/j.ijpara.2020.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022]
Abstract
Over 892 million people in 48 countries are at risk of infection by nematodes that cause lymphatic filariasis. As part of the Global Programme to Eliminate Lymphatic Filariasis, mass drug administration is distributed to communities until surveillance indicates infection rates are below target prevalence thresholds. In some countries, including American Samoa, lymphatic filariasis transmission persists despite years of mass drug administration and/or has resurged after cessation. Nothing is known about the population genetics of Wuchereria bancrofti worms in Polynesia, or whether local transmission is persisting and/or increasing due to inadequate mass drug administration coverage, expansion from residual hotspots, reintroduction from elsewhere, or a combination. We extracted DNA from microfilariae on blood slides collected during prevalence surveys in 2014 and 2016, comprising 31 pools of five microfilariae from 22 persons living in eight villages. We sequenced 1104 bp across three mitochondrial markers (ND4, COI, CYTB). We quantified parasite genetic differentiation using variant calls and estimated haplotypes using principal components analysis, F-statistics, and haplotype networks. Of the variants called, all but eight were shared across the main island of Tutuila, and three of those were from a previously described hotspot village, Fagali'i. Genotypic data did not support population genetic structure among regions or villages in 2016, although differences were observed between worms collected in Fagali'i in 2014 and those from 2016. Because estimated haplotype frequency varied between villages, these statistics suggested genetic differentiation, but were not consistent among villages. Finally, haplotype networks demonstrated American Samoan sequence clusters were related to previously published sequences from Papua New Guinea. These are, to our knowledge, the first reports of W. bancrofti genetic variation in Polynesia. The resurgent parasites circulating on the main island of American Samoa represent a single population. This study is the first step towards investigating how parasite population structure might inform strategies to manage resurgence and elimination of lymphatic filariasis.
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Affiliation(s)
- Shannon M Hedtke
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia.
| | - Patsy A Zendejas-Heredia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Patricia M Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, Queensland, Australia
| | - Sarah Sheridan
- Department of Global Health, Research School of Population Health, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Meru Sheel
- National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Acton, Australian Capital Territory, Australia
| | | | - Colleen L Lau
- Department of Global Health, Research School of Population Health, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Warwick N Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia; Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
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Hedtke SM, Kuesel AC, Crawford KE, Graves PM, Boussinesq M, Lau CL, Boakye DA, Grant WN. Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions. Front Genet 2020; 10:1282. [PMID: 31998356 PMCID: PMC6964045 DOI: 10.3389/fgene.2019.01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites-i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment-or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.
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Affiliation(s)
- Shannon M. Hedtke
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Annette C. Kuesel
- Unicef/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Katie E. Crawford
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Patricia M. Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Michel Boussinesq
- Unité Mixte Internationale 233 "TransVIHMI", Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Colleen L. Lau
- Department of Global Health, Research School of Population Health, Australian National University, Acton, ACT, Australia
| | - Daniel A. Boakye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Warwick N. Grant
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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Fauver JR, Martin J, Weil GJ, Mitreva M, Fischer PU. De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell. Sci Rep 2019; 9:19521. [PMID: 31863009 PMCID: PMC6925183 DOI: 10.1038/s41598-019-55908-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/28/2019] [Indexed: 11/15/2022] Open
Abstract
Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous. Single molecule sequencing technologies can reduce the cost of genome sequencing and long reads produced from these devices can improve the contiguity and completeness of genome assemblies. In addition, these new technologies can make generation and analysis of large numbers of field isolates feasible. In this study, we assessed the performance of the Oxford Nanopore Technologies MinION for sequencing and assembling the genome of Brugia malayi, a human parasite widely used in filariasis research. Using data from a single MinION flowcell, a 90.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb. This assembly covered 96.9% of the well-defined B. malayi reference genome with 99.2% identity. The complete mitochondrial genome was obtained with individual reads and the nearly complete genome of the endosymbiotic bacteria Wolbachia was assembled alongside the nuclear genome. Long-read data from the MinION produced an assembly that approached the quality of a well-established reference genome using comparably fewer resources.
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Affiliation(s)
- Joseph R Fauver
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.
| | - John Martin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Gary J Weil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Peter U Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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Prado IC, Mendes VG, Souza AL, Dutra RF, De-Simone SG. Electrochemical immunosensor for differential diagnostic of Wuchereria bancrofti using a synthetic peptide. Biosens Bioelectron 2018; 113:9-15. [DOI: 10.1016/j.bios.2018.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
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Potential of cell-free DNA as a screening marker for parasite infections in dog. Genomics 2018; 111:906-912. [PMID: 29860031 DOI: 10.1016/j.ygeno.2018.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/17/2018] [Accepted: 05/25/2018] [Indexed: 11/21/2022]
Abstract
Parasitic infections are common in stray dogs and accurate knowledge of parasite communities in dogs would provide insight into the epidemiology of parasitic diseases. In this study, we used Illumina sequencing technology to evaluate cell-free DNA (cfDNA) as a marker for screening of parasitic infections in dogs. Plasma samples from 14 stray dogs captured in Bangladesh were used in the experiments. An average of 2.3 million reads was obtained for each sample. BLASTn analysis identified 150 reads with high similarity with parasites from 19 different genera. In particular, we detected sequences of Babesia spp. in five dogs; consistent with this, a previous study using conventional PCR showed that four of these dogs were positive for B. gibsoni. Several reads with similarity to Leishmania and filarial nematodes were also identified. These findings indicate that cfDNA in blood can be a potential screening marker for identifying parasite diversity in dogs.
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Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO-1 barcoding. Sci Rep 2018; 8:6158. [PMID: 29670192 PMCID: PMC5906601 DOI: 10.1038/s41598-018-24382-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/15/2018] [Indexed: 11/26/2022] Open
Abstract
Despite the broad distribution of M. ozzardi in Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite’s epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene’s barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts. Here, we have used shot-gun Illumina-HiSeq sequencing to recover the first complete Mansonella genus mitogenome and to identify several mitochondrial-origin pseudogenes. Mitogenome phylogenetic analysis placed M. ozzardi in the Onchocercidae “ONC5” clade and suggested that Mansonella parasites are more closely related to Wuchereria and Brugia genera parasites than they are to Loa genus parasites. DNA sequence alignments, BLAST searches and conceptual translations have been used to compliment phylogenetic analysis showing that M. ozzardi from the Amazon and Caribbean regions are near-identical and that previously reported Peruvian M. ozzardi CO1 reference sequences are probably of pseudogene origin. In addition to adding a much-needed resource to the Mansonella genus’s molecular tool-kit and providing evidence that some M. ozzardi CO1 sequence deposits are pseudogenes, our results suggest that all Neotropical M. ozzardi parasites are closely related.
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Wallau GL, Vieira C, Loreto ÉLS. Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome. Mob DNA 2018; 9:6. [PMID: 29422954 PMCID: PMC5791352 DOI: 10.1186/s13100-018-0112-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Background All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes. Main body For some time now, it has been a scientific consensus that HT events were rare and non-relevant for evolution of eukaryotic species, but there is growing evidence supporting that HT is an important and frequent phenomenon in eukaryotes as well. Conclusion Here, we will discuss the latest findings regarding HT among eukaryotes, mainly HT of transposons (HTT), establishing HTT once and for all as an important phenomenon that should be taken into consideration to fully understand eukaryotes genome evolution. In addition, we will discuss the latest development methods to detect such events in a broader scale and highlight the new approaches which should be pursued by researchers to fill the knowledge gaps regarding HTT among eukaryotes.
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Affiliation(s)
- Gabriel Luz Wallau
- 1Entomology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE Brazil
| | - Cristina Vieira
- 2Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, F-69622 Villeurbanne, France
| | - Élgion Lúcio Silva Loreto
- 3Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS Brazil
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Abdel-Shafi IR, Shoieb EY, Attia SS, Rubio JM, Ta-Tang TH, El-Badry AA. Molecular identification and phylogenetic analysis of Wuchereria bancrofti from human blood samples in Egypt. Parasitol Res 2017; 116:963-970. [DOI: 10.1007/s00436-017-5372-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
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15
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Lv W, Xu Y, Guo Y, Yu Z, Feng G, Liu P, Luan M, Zhu H, Liu G, Zhang M, Lv H, Duan L, Shang Z, Li J, Jiang Y, Zhang R. The drug target genes show higher evolutionary conservation than non-target genes. Oncotarget 2016; 7:4961-71. [PMID: 26716901 PMCID: PMC4826257 DOI: 10.18632/oncotarget.6755] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/26/2015] [Indexed: 01/10/2023] Open
Abstract
Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.
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Affiliation(s)
- Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongdeng Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yiying Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ziqi Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guanglong Feng
- Department of Radiology, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Panpan Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Meiwei Luan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongjie Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guiyou Liu
- Genome Analysis Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lian Duan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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16
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Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nat Commun 2016; 7:11396. [PMID: 27097561 PMCID: PMC4844689 DOI: 10.1038/ncomms11396] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/21/2016] [Indexed: 02/08/2023] Open
Abstract
Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. Lymphatic filariasis and loiasis are diseases caused by insect-borne filarial nematodes. Here, Suh et al. identify a retrotransposon that is present in the genomes of these nematodes and seven tropical bird lineages, indicating two waves of horizontal gene transfer around 17–25 million years ago.
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Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Juliana Menger
- Department of Conservation Biology, Helmholtz Centre for Environmental Research (UFZ), D-04318 Leipzig, Germany.,Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany.,Instituto Nacional de Pesquisas da Amazônia (INPA), AM 69067-375 Manaus, Brazil
| | - Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Lars Podsiadlowski
- Institute of Evolutionary Biology and Ecology, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gerth
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany.,Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico 87505, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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