1
|
Keatley S, Botero A, Fosu-Nyarko J, Pallant L, Northover A, Thompson RCA. Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR). INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2020; 13:261-268. [PMID: 33294365 PMCID: PMC7691731 DOI: 10.1016/j.ijppaw.2020.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/30/2020] [Accepted: 11/11/2020] [Indexed: 10/25/2022]
Abstract
Conventional nested PCR and Sanger sequencing methods are currently the gold standards for detecting trypanosomes in wildlife. However, these techniques are time-consuming and can often overlook mixed infections. True trypanosome prevalence can thus be underrepresented. Here, we designed an 18S rDNA-based real-time quantitative PCR (qPCR) assay coupled with High-Resolution Melting Analysis (HRMA) to detect and discriminate three Trypanosoma species (T. copemani, T. noyesi, and T. vegrandis) commonly infecting Australian marsupials. A total of 68 genetically characterised samples from blood and tissue were used to validate the High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR) assay. A further 87 marsupial samples consisting of blood, tissue and in vitro cultures derived from wildlife blood samples, were screened for the first time using this assay, and species identity confirmed using conventional PCR and Sanger sequencing. All three Trypanosoma species were successfully detected in pure cultures using the HRM-qPCR assay, and in samples containing mixed trypanosome infections. Of the 87 marsupial samples screened using the HRM-qPCR assay, 93.1% were positive for trypanosomes, and 8.0% contained more than one trypanosome species. In addition to the three targeted Trypanosoma species, this assay was also able to detect and identify other native and exotic trypanosomes. The turnaround time for this assay, from sample preparation to obtaining results, was less than 2 h, with a detection limit of 10 copies of the amplicon in a reaction for each of the targeted trypanosome species. This more rapid and sensitive diagnostic tool provides a high throughput platform for the detection, identification and quantification of trypanosome infections. It will also improve understanding of host diversity and parasite relationships and facilitate conservation management decisions.
Collapse
Affiliation(s)
- S Keatley
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - A Botero
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - J Fosu-Nyarko
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia.,Plant Biotechnology Research Group, State Agricultural Biotechnology Center, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - L Pallant
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - A Northover
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - R C A Thompson
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| |
Collapse
|
2
|
Chin KL, Sarmiento ME, Mustapha ZA, Jani J, Jamal NB, Stanis CS, Acosta A. Identification of a Mycobacterium tuberculosis-specific gene marker for diagnosis of tuberculosis using semi-nested melt-MAMA qPCR (lprM-MAMA). Tuberculosis (Edinb) 2020; 125:102003. [PMID: 33099253 DOI: 10.1016/j.tube.2020.102003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) is the deadliest of infectious diseases. TB diagnosis, based on sputum microscopy, culture, and nucleic acid amplification tests (NAATs) to identify its main causative agent, Mycobacterium tuberculosis (MTB), remains challenging. The current available NAATs, endorsed by World Health Organization (WHO), can differentiate MTB from some MTB complex (MTBC) members. Using bioinformatics, we identified a single nucleotide polymorphism (SNP) in lprM (Rv1970) gene that differentiate MTB from other MTBC members. A forward mismatch amplification mutation assay (MAMA) primer was designed for the targeted mutation and was used in a semi-nested melt-MAMA qPCR (lprM-MAMA). Using the optimized protocol, lprM-MAMA was positive with all MTB reference and clinical strains, and negative with other MTBC members, non-tuberculous mycobacteria (NTM) and other non-mycobacterial (NM) reference strains. The limit of detection (LOD) of lprM-MAMA was 76.29 fg. Xpert® MTB/RIF (Xpert)-positive sputum samples were also positive by lprM-MAMA, except for samples classified as having "very low" bacterial load by Xpert. Xpert-negative sputum samples were also negative by lprM-MAMA. In conclusion, lprM-MAMA demonstrated to be a useful tool for specific MTB diagnosis. Further evaluation with higher number of reference strains, including NTM and NM; and sputum samples are required to determine its potential for clinical application.
Collapse
Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Zainal Arifin Mustapha
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Jaeyres Jani
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Norfazirah Binti Jamal
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Cheronie Shely Stanis
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
| |
Collapse
|
3
|
Fatoba AJ, Adeleke MA. Diagnosis and control of chicken coccidiosis: a recent update. J Parasit Dis 2018; 42:483-493. [PMID: 30538344 PMCID: PMC6261147 DOI: 10.1007/s12639-018-1048-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/24/2018] [Indexed: 11/25/2022] Open
Abstract
Coccidiosis is a deadly disease that hampers chicken's productivity and welfare. Thus, the disease is a major menace to the global poultry industry. Coccidiosis which is caused by the apicomplexan parasite of the genus Eimeria has seven known species which affect the different parts of the intestinal tract of chickens. The disease which occurs by ingestion of sporulated oocyst has been associated with poor poultry management system. Mixed infection among the species of this parasite contributes to both pathogenicity and misdiagnosis of the disease. A progress in identification and diagnosis approach which cuts across pathological, morphological and molecular has been reported for this parasite. Control measures which include anticoccidial drugs, vaccines and natural products have dominated literature for this disease. However, the emergence of genetic and antigenic diversity with implication on resistance to anticoccidials among different strains of Eimeria parasite has generated concerns on the effectiveness of the current anticoccidial vaccines. A new look on the control strategy therefore becomes imperative. This study reviews the current trends on the identification and control of chicken coccidiosis with focus on (1) Avian coccidiosis (2) Epidemiology of chicken coccidiosis (3) Eimeria parasite and distribution in poultry (4) Diagnosis of Eimeria parasite (5) Control measures of coccidiosis (6) Threats posed by genetic and antigenic diversity of Eimeria parasite on coccidiosis control. Genomic study on diversity of Eimeria parasite becomes imperative for effective vaccine design against coccidiosis.
Collapse
Affiliation(s)
- Abiodun Joseph Fatoba
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville, P/Bag X54001, Durban, 4000 South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville, P/Bag X54001, Durban, 4000 South Africa
| |
Collapse
|
4
|
Evaluation of the Capacity of PCR and High-Resolution Melt Curve Analysis for Identification of Mixed Infection with Mycoplasma gallisepticum Strains. PLoS One 2015; 10:e0126824. [PMID: 25970590 PMCID: PMC4430288 DOI: 10.1371/journal.pone.0126824] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/07/2015] [Indexed: 11/27/2022] Open
Abstract
Pathogenicity and presentation of Mycoplasma gallisepticum (MG) infection may differ from one strain to another and this may have implications on control measures. Infection of individual birds with more than one MG strain has been reported. A PCR followed by high resolution melt (HRM) curve analysis has been developed in our laboratory and routinely used for detection and differentiation of MG strains. However the potential of this test for identification of MG strains in a mixed specimen has not been evaluated. In the present study, the capability of PCR-HRM curve analysis technique, targeting vlhA and pvpA genes was assessed for identification of individual MG strains in a mixed population. Different DNA ratios of two MG strains from 1 to 10-4 ng were tested with some generated conventional and normalized curves distinct from those of individual strains alone. Using genotype confidence percentages (GCP) generated from HRM curve analysis, it was found that vlhA PCR-HRM was more consistent than pvpA PCR-HRM for the detection of MG ts-11 vaccine strain mixed with any of the MG strains 6/85, F, S6 or a field isolate. The potential of vlhA PCR-HRM to detect mixed MG strains in a specimen was found to be primarily dependent on quantity and proportion of the target DNAs in the mixture. This is the first study examining the capacity of PCR-HRM technique for identification of individual MG strains in a mixed strain population.
Collapse
|
5
|
Pomeroy RS, Balamurugan K, Wong H, Duncan G. High-resolution melt analysis of the minisatellite D1S80: A potential forensic screening tool. Electrophoresis 2014; 35:3020-7. [DOI: 10.1002/elps.201400143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/24/2014] [Accepted: 08/20/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Robert S. Pomeroy
- Department of Chemistry and Biochemistry; University of California; San Diego CA USA
| | | | - Helena Wong
- Department of Chemistry and Biochemistry; University of California; San Diego CA USA
| | - George Duncan
- Oceanographic Institute; Nova Southeastern University; Fort Lauderdale FL USA
| |
Collapse
|
6
|
Chapman HD, Barta JR, Blake D, Gruber A, Jenkins M, Smith NC, Suo X, Tomley FM. A selective review of advances in coccidiosis research. ADVANCES IN PARASITOLOGY 2014; 83:93-171. [PMID: 23876872 DOI: 10.1016/b978-0-12-407705-8.00002-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coccidiosis is a widespread and economically significant disease of livestock caused by protozoan parasites of the genus Eimeria. This disease is worldwide in occurrence and costs the animal agricultural industry many millions of dollars to control. In recent years, the modern tools of molecular biology, biochemistry, cell biology and immunology have been used to expand greatly our knowledge of these parasites and the disease they cause. Such studies are essential if we are to develop new means for the control of coccidiosis. In this chapter, selective aspects of the biology of these organisms, with emphasis on recent research in poultry, are reviewed. Topics considered include taxonomy, systematics, genetics, genomics, transcriptomics, proteomics, transfection, oocyst biogenesis, host cell invasion, immunobiology, diagnostics and control.
Collapse
Affiliation(s)
- H David Chapman
- Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, USA.
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Jabbar A, Gasser RB. Mutation scanning analysis of genetic variation within and among Echinococcus species: implications and future prospects. Electrophoresis 2014; 34:1852-62. [PMID: 23977679 DOI: 10.1002/elps.201300078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tapeworms of the genus Echinococcus (family Taeniidae) occur in the small intestines of carnivorous definitive hosts and are transmitted to particular intermediate mammalian hosts, in which they develop as fluid-filled larvae (cysts) in internal organs (usually lung and liver), causing the disease echinococcosis. Echinococcus species are of major medical importance and also cause losses to the meat and livestock industries, mainly due to the condemnation of infected offal. Decisions regarding the treatment and control of echinococcosis rely on the accurate identification of species and population variants (strains). Conventional, phenetic methods for specific identification have some significant limitations. Despite advances in the development of molecular tools, there has been limited application of mutation scanning methods to species of Echinococcus. Here, we briefly review key genetic markers used for the identification of Echinococcus species and techniques for the analysis of genetic variation within and among populations, and the diagnosis of echinococcosis. We also discuss the benefits of utilizing mutation scanning approaches to elucidate the population genetics and epidemiology of Echinococcus species. These benefits are likely to become more evident following the complete characterization of the genomes of E. granulosus and E. multilocularis.
Collapse
Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | | |
Collapse
|
8
|
Lalonde LF, Gajadhar AA. Detection and differentiation of coccidian oocysts by real-time PCR and melting curve analysis. J Parasitol 2011; 97:725-30. [PMID: 21506835 DOI: 10.1645/ge-2706.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Rapid and reliable detection and identification of coccidian oocysts are essential for animal health and foodborne disease outbreak investigations. Traditional microscopy and morphological techniques can identify large and unique oocysts, but they are often subjective and require parasitological expertise. The objective of this study was to develop a real-time quantitative PCR (qPCR) assay using melting curve analysis (MCA) to detect, differentiate, and identify DNA from coccidian species of animal health, zoonotic, and food safety concern. A universal coccidia primer cocktail was designed and employed to amplify DNA from Cryptosporidium parvum, Toxoplasma gondii, Cyclospora cayetanensis, and several species of Eimeria, Sarcocystis, and Isospora using qPCR with SYBR Green detection. MCA was performed following amplification, and melting temperatures (T(m)) were determined for each species based on multiple replicates. A standard curve was constructed from DNA of serial dilutions of T. gondii oocysts to estimate assay sensitivity. The qPCR assay consistently detected DNA from as few as 10 T. gondii oocysts. T(m) data analysis showed that C. cayetanensis, C. parvum, Cryptosporidium muris, T. gondii, Eimeria bovis, Eimeria acervulina, Isospora suis, and Sarcocystis cruzi could each be identified by unique melting curves and could be differentiated based on T(m). DNA of coccidian oocysts in fecal, food, or clinical diagnostic samples could be sensitively detected, reliably differentiated, and identified using qPCR with MCA. This assay may also be used to detect other life-cycle stages of coccidia in tissues, fluids, and other matrices. MCA studies on multiple isolates of each species will further validate the assay and support its application as a routine parasitology screening tool.
Collapse
Affiliation(s)
- Laura F Lalonde
- Centre for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, 116 Veterinary Road, Saskatoon, S7N 2R3, Canada.
| | | |
Collapse
|
9
|
Ghorashi SA, O'Rourke D, Ignjatovic J, Noormohammadi AH. Differentiation of infectious bursal disease virus strains using real-time RT-PCR and high resolution melt curve analysis. J Virol Methods 2010; 171:264-71. [PMID: 21111004 DOI: 10.1016/j.jviromet.2010.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 11/15/2010] [Accepted: 11/18/2010] [Indexed: 11/15/2022]
Abstract
Differentiation of infectious bursal disease virus (IBDV) strains is crucial for effective vaccination programs and epidemiological investigations. In this study, a combination of real-time RT-PCR and high resolution melt (HRM) curve analysis was developed for simultaneous detection and differentiation of IBDV strains/isolates. The hypervariable region of VP2 gene was amplified from several IBDV strains and subjected to HRM curve analysis. The method could readily differentiate between classical vaccines/isolates and variants. Analysis of the nucleotide sequence of the amplicons from each strain revealed that each melt curve profile was related to a unique DNA sequence. The real-time RT-PCR HRM curve analysis was also able to differentiate IBDV strains/isolates directly in bursal tissues from field submissions and from vaccinated commercial flocks. The differences between melting peaks generated from IBDV strains were significantly different (P<0.0001) demonstrating the high discriminatory power of this technique. The results presented in this study indicated that real-time RT-PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping IBDV isolates/strains and can contribute to effective control of IBDV outbreaks.
Collapse
Affiliation(s)
- Seyed A Ghorashi
- Faculty of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
| | | | | | | |
Collapse
|