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Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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2
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Mattiucci S, Cipriani P, Levsen A, Paoletti M, Nascetti G. Molecular Epidemiology of Anisakis and Anisakiasis: An Ecological and Evolutionary Road Map. ADVANCES IN PARASITOLOGY 2018. [PMID: 29530312 DOI: 10.1016/bs.apar.2017.12.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review addresses the biodiversity, biology, distribution, ecology, epidemiology, and consumer health significance of the so far known species of Anisakis, both in their natural hosts and in human accidental host populations, worldwide. These key aspects of the Anisakis species' biology are highlighted, since we consider them as main driving forces behind which most of the research in this field has been carried out over the past decade. From a public health perspective, the human disease caused by Anisakis species (anisakiasis) appears to be considerably underreported and underestimated in many countries or regions around the globe. Indeed, when considering the importance of marine fish species as part of the everyday diet in many coastal communities around the globe, there still exist significant knowledge gaps as to local epidemiological and ecological drivers of the transmission of Anisakis spp. to humans. We further identify some key knowledge gaps related to Anisakis species epidemiology in both natural and accidental hosts, to be filled in light of new 'omic' technologies yet to be fully developed. Moreover, we suggest that future Anisakis research takes a 'holistic' approach by integrating genetic, ecological, immunobiological, and environmental factors, thus allowing proper assessment of the epidemiology of Anisakis spp. in their natural hosts, in human populations, and in the marine ecosystem, in both space and time.
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3
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Elelu N, Ferrolho J, Couto J, Domingos A, Eisler MC. Molecular diagnosis of the tick-borne pathogen Anaplasma marginale in cattle blood samples from Nigeria using qPCR. EXPERIMENTAL & APPLIED ACAROLOGY 2016; 70:501-510. [PMID: 27787614 DOI: 10.1007/s10493-016-0081-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
Tick-borne diseases (TBDs) are some of the most important animal health and management problems in Africa, including Nigeria. This study aims to determine the prevalence of an important TBD, anaplasmosis, in a North-central region of Nigeria. Blood samples were collected from cattle and stored on Whatman FTA® cards. Information on village, age and sex associated with each cattle was also recorded. The packed red blood cell volume (PCV) for each blood sample was determined. After DNA extraction, pathogen presence was evaluated by TaqMan® based qPCR of which 75.9 % of the cattle tested positive for Anaplasma marginale. Statistical analysis revealed that the presence of A. marginale infection differed significantly between cattle age groups. However, there was no significant difference in the prevalence of this pathogen between the sexes or among cattle grouped by PCV level. Finally, using a highly sensitive molecular method our pioneer study contributes to the improvement of the current knowledge regarding tick-borne pathogens that seriously affect animal health in specific areas of Nigeria.
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Affiliation(s)
- Nusirat Elelu
- School of Veterinary Science, University of Bristol, Langford, Bristol, BS40 5DU, UK
| | - Joana Ferrolho
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 100, 1349-008, Lisbon, Portugal.
| | - Joana Couto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 100, 1349-008, Lisbon, Portugal
| | - Ana Domingos
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 100, 1349-008, Lisbon, Portugal
| | - Mark C Eisler
- School of Veterinary Science, University of Bristol, Langford, Bristol, BS40 5DU, UK
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4
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Rijsman LH, Monkelbaan JF, Kusters JG. Clinical consequences of polymerase chain reaction-based diagnosis of intestinal parasitic infections. J Gastroenterol Hepatol 2016; 31:1808-1815. [PMID: 27061336 DOI: 10.1111/jgh.13412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022]
Abstract
The implementation of polymerase chain reaction (PCR)-based diagnostics of intestinal protozoa has led to higher sensitivity and (subtype) specificity, more convenient sampling, and the possibility for high-throughput screening. PCR for routine detection of human intestinal protozoa in fecal samples is used by an increasing number of clinical laboratories. This paper discusses the recent developments in the diagnosis of intestinal protozoa, with an emphasis on PCR-based diagnostics. Although many reviews have described the technical aspects of PCR-based diagnostics, this review focuses on the clinical consequences that result from the shift from microscopic toward PCR-based diagnostics. Despite its undisputed superiority, the use of PCR comes with challenges that clinicians should be aware of.
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Affiliation(s)
- Lucas H Rijsman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, CX, The Netherlands
| | - Jan F Monkelbaan
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes G Kusters
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, CX, The Netherlands
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5
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Chahal C, van den Akker B, Young F, Franco C, Blackbeard J, Monis P. Pathogen and Particle Associations in Wastewater: Significance and Implications for Treatment and Disinfection Processes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:63-119. [PMID: 27926432 PMCID: PMC7126130 DOI: 10.1016/bs.aambs.2016.08.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Disinfection guidelines exist for pathogen inactivation in potable water and recycled water, but wastewater with high numbers of particles can be more difficult to disinfect, making compliance with the guidelines problematic. Disinfection guidelines specify that drinking water with turbidity ≥1 Nephelometric Turbidity Units (NTU) is not suitable for disinfection and therefore not fit for purpose. Treated wastewater typically has higher concentrations of particles (1–10 NTU for secondary treated effluent). Two processes widely used for disinfecting wastewater are chlorination and ultraviolet radiation. In both cases, particles in wastewater can interfere with disinfection and can significantly increase treatment costs by increasing operational expenditure (chemical demand, power consumption) or infrastructure costs by requiring additional treatment processes to achieve the required levels of pathogen inactivation. Many microorganisms (viruses, bacteria, protozoans) associate with particles, which can allow them to survive disinfection processes and cause a health hazard. Improved understanding of this association will enable development of cost-effective treatment, which will become increasingly important as indirect and direct potable reuse of wastewater becomes more widespread in both developed and developing countries. This review provides an overview of wastewater and associated treatment processes, the pathogens in wastewater, the nature of particles in wastewater and how they interact with pathogens, and how particles can impact disinfection processes.
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Affiliation(s)
- C Chahal
- Flinders University, Adelaide, SA, Australia
| | - B van den Akker
- Flinders University, Adelaide, SA, Australia; South Australian Water Corporation, Adelaide, SA, Australia
| | - F Young
- Flinders University, Adelaide, SA, Australia
| | - C Franco
- Flinders University, Adelaide, SA, Australia
| | | | - P Monis
- Flinders University, Adelaide, SA, Australia; South Australian Water Corporation, Adelaide, SA, Australia
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6
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Zhang B, Sambono JL, Morgan JAT, Venus B, Rolls P, Lew-Tabor AE. An Evaluation of Quantitative PCR Assays (TaqMan ® and SYBR Green) for the Detection of Babesia bigemina and Babesia bovis, and a Novel Fluorescent-ITS1-PCR Capillary Electrophoresis Method for Genotyping B. bovis Isolates. Vet Sci 2016; 3:vetsci3030023. [PMID: 29056732 PMCID: PMC5606575 DOI: 10.3390/vetsci3030023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/17/2022] Open
Abstract
Babesia spp. are tick-transmitted haemoparasites causing tick fever in cattle. In Australia, economic losses to the cattle industry from tick fever are estimated at AUD$26 Million per annum. If animals recover from these infections, they become immune carriers. Here we describe a novel multiplex TaqMan qPCR targeting cytochrome b genes for the identification of Babesia spp. The assay shows high sensitivity, specificity and reproducibility, and allows quantification of parasite DNA from Babesia bovis and B. bigemina compared to standard PCR assays. A previously published cytochrome b SYBR Green qPCR was also tested in this study, showing slightly higher sensitivity than the Taqman qPCRs but requires melting curve analysis post-PCR to confirm specificity. The SYBR Green assays were further evaluated using both diagnostic submissions and vaccinated cattle (at 7, 9, 11 and 14 days post-inoculation) showed that B. bigemina can be detected more frequently than B. bovis. Due to fewer circulating parasites, B. bovis detection in carrier animals requires higher DNA input. Preliminary data for a novel fluorescent PCR genotyping based on the Internal Transcribed Spacer 1 region to detect vaccine and field alleles of B. bovis are described. This assay is capable of detecting vaccine and novel field isolate alleles in a single sample.
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Affiliation(s)
- Bing Zhang
- Department of Agriculture & Fisheries, Agri-Science Queensland, Animal Science, Dutton Park QLD 4102, Australia.
| | - Jacqueline L Sambono
- Department of Agriculture & Fisheries, Biosecurity Queensland, Tick Fever Centre, Wacol QLD 4076, Australia.
| | - Jess A T Morgan
- Department of Agriculture & Fisheries, Agri-Science Queensland, Animal Science, Dutton Park QLD 4102, Australia.
| | - Bronwyn Venus
- Queensland Alliance for Agriculture & Food Innovation, University of Queensland, Centre for Animal Science, St Lucia QLD 4072, Australia.
| | - Peter Rolls
- Department of Agriculture & Fisheries, Biosecurity Queensland, Tick Fever Centre, Wacol QLD 4076, Australia.
| | - Ala E Lew-Tabor
- Queensland Alliance for Agriculture & Food Innovation, University of Queensland, Centre for Animal Science, St Lucia QLD 4072, Australia.
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7
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A review of methods for nematode identification. J Microbiol Methods 2016; 138:37-49. [PMID: 27262374 DOI: 10.1016/j.mimet.2016.05.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 12/15/2022]
Abstract
Nematodes are non-segmented roundworms found in soil, aquatic environment, plants, or animals. Either useful or pathogenic, they greatly influence environmental equilibrium, human and animal health, as well as plant production. Knowledge on their taxonomy and biology are key issues to answer the different challenges associated to these organisms. Nowadays, most of the nematode taxonomy remains unknown or unclear. Several approaches are available for parasite identification, from the traditional morphology-based techniques to the sophisticated high-throughput sequencing technologies. All these techniques have advantages or drawbacks depending on the sample origin and the number of nematodes to be processed. This review proposes an overview of all newly available methods available to identify known and/or unknown nematodes with a specific focus on emerging high-throughput molecular techniques.
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Evaluation of the efficiency of nested q-PCR in the detection of Mycobacterium tuberculosis complex directly from tuberculosis-suspected lesions in post-mortem macroscopic inspections of bovine carcasses slaughtered in the state of Mato Grosso, Brazil. Meat Sci 2015; 106:11-5. [DOI: 10.1016/j.meatsci.2015.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/30/2014] [Accepted: 03/19/2015] [Indexed: 11/24/2022]
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Roeber F, Kahn L. The specific diagnosis of gastrointestinal nematode infections in livestock: larval culture technique, its limitations and alternative DNA-based approaches. Vet Parasitol 2014; 205:619-28. [PMID: 25182210 DOI: 10.1016/j.vetpar.2014.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/01/2014] [Accepted: 08/09/2014] [Indexed: 11/29/2022]
Abstract
The specific diagnosis of gastrointestinal nematode infections in ruminants is routinely based on larval culture technique and on the morphological identification of developed third-stage larvae. However, research on the ecology and developmental requirements of different species suggests that environmental conditions (e.g., temperature and humidity) for optimal development to occur vary between the different species. Thus, employing a common culture protocol for all species will favour the development of certain species over others and can cause a biased result in particular when species proportions in a mixed infection are to be determined. Furthermore, the morphological identification of L3 larvae is complicated by a lack of distinctive, obvious features that would allow the identification of all key species. In the present paper we review in detail the potential limitations of larval culture technique and morphological identification and provide account to some modern molecular alternatives to the specific diagnosis of gastrointestinal nematode infection in ruminants.
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Affiliation(s)
- Florian Roeber
- AusDiagnostics Pty. Ltd., Beaconsfield 2015, NSW, Australia.
| | - Lewis Kahn
- Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
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A review of molecular approaches for investigating patterns of coevolution in marine host-parasite relationships. ADVANCES IN PARASITOLOGY 2014; 84:209-52. [PMID: 24480315 DOI: 10.1016/b978-0-12-800099-1.00004-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Parasites and their relationships with hosts play a crucial role in the evolutionary pathways of every living organism. One method of investigating host-parasite systems is using a molecular approach. This is particularly important as analyses based solely on morphology or laboratory studies of parasites and their hosts do not take into account historical evolutionary interactions that can shape the distribution, abundance and population structure of parasites and their hosts. However, the predominant host-parasite coevolution literature has focused on terrestrial hosts and their parasites, and there still is a lack of studies in marine environments. Given that marine systems are generally more open than terrestrial ones, they provide fascinating opportunities for large-scale (as well as small-scale) geographic studies. Further, patterns and processes of genetic structuring and systematics are becoming more available across many different taxa (but especially fishes) in many marine systems, providing an excellent basis for examining whether parasites follow host population/species structure. In this chapter, we first highlight the factors and processes that challenge our ability to interpret evolutionary patterns of coevolution of hosts and their parasites in marine systems at different spatial, temporal and taxonomic scales. We then review the use of the most commonly utilized genetic markers in studying marine host-parasite systems. We give an overview and discuss which molecular methodologies resolve evolutionary relationships best and also discuss the applicability of new approaches, such as next-generation sequencing and studies utilizing functional markers to gain insights into more contemporary processes shaping host-parasite relationships.
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11
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Koehler AV, Jex AR, Haydon SR, Stevens MA, Gasser RB. Giardia/giardiasis — A perspective on diagnostic and analytical tools. Biotechnol Adv 2014; 32:280-9. [DOI: 10.1016/j.biotechadv.2013.10.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 10/08/2013] [Accepted: 10/27/2013] [Indexed: 12/28/2022]
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12
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Jex AR, Gasser RB. Diagnostic and analytical mutation scanning ofCryptosporidium: utility and advantages. Expert Rev Mol Diagn 2014; 9:179-85. [DOI: 10.1586/14737159.9.2.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Roeber F, Jex AR, Gasser RB. Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants. Biotechnol Adv 2013; 31:1135-52. [PMID: 23376340 PMCID: PMC7126997 DOI: 10.1016/j.biotechadv.2013.01.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 12/19/2022]
Abstract
Parasitic nematodes (roundworms) of livestock have major economic impact globally. In spite of the diseases caused by these nematodes and some advances in the design of new therapeutic agents (anthelmintics) and attempts to develop vaccines against some of them, there has been limited progress in the establishment of practical diagnostic techniques. The specific and sensitive diagnosis of gastrointestinal nematode infections of livestock underpins effective disease control, which is highly relevant now that anthelmintic resistance (AR) is a major problem. Traditional diagnostic techniques have major constraints, in terms of sensitivity and specificity. The purpose of this article is to provide a brief background on gastrointestinal nematodes (Strongylida) of livestock and their control; to summarize conventional methods used for the diagnosis and discuss their constraints; to review key molecular-diagnostic methods and recent progress in the development of advanced amplification-based and sequencing technologies, and their implications for epidemiological investigations and the control of parasitic diseases.
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Affiliation(s)
| | | | - Robin B. Gasser
- Faculty of Veterinary Science, The University of Melbourne, Victoria 3010, Australia
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14
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Llarena-Reino M, Abollo E, Pascual S. A scoring system approach for the parasite predictive assessment of fish lots: a proof of concept with anisakids. Foodborne Pathog Dis 2013; 10:1067-74. [PMID: 24147656 DOI: 10.1089/fpd.2013.1553] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A total of 982 individuals distributed in 11 lots belonging to 10 fish species from three Atlantic FAO fishing areas were sampled and examined to detect the presence of anisakid larvae in fish muscle. After hazard identification by genetic sequencing and exposure assessment by anatomic extent and demographic characterization of infection, all data were fitted for each fish species to a new proposed scoring schema of parasite prediction. In the absence of a criterion standard method for inspection and precise definition of the quantum satis for parasites in contaminated fish lots, the inspection rating scheme called SADE (Site of infection, Assurance of quality, Demography, Epidemiology) may help fish industries to precisely handle and to evaluate the likely outcome of infected fish lots after being diagnosed. For this purpose, a supporting flow diagram for decision was defined and suggested. This new performance assessment tool has the aim of staging fish lots, thus helping in planning manufacture, commercial, and research decisions during self-management programs. This novel scoring system provides an improved inspection format by implementing the occurrence stratification for parasites to guide Hazard Analysis and Critical Control Points (HACCP) programs for the uniform exchange of information among fish industries, administration and researchers, thus facilitating standardization and communication. In the future, this scoring version could be validated (in terms of classification and wording) for similar overall predictive purposes in other muscular parasites infecting seafood products.
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Affiliation(s)
- María Llarena-Reino
- 1 Ecobiomar, Instituto de Investigaciones Marinas de Vigo , Consejo Superior de Investigaciones Científicas (CSIC), Bouzas-Vigo, Spain
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15
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Peckle M, Pires MS, Dos Santos TM, Roier ECR, da Silva CB, Vilela JAR, Santos HA, Massard CL. Molecular epidemiology of Theileria equi in horses and their association with possible tick vectors in the state of Rio de Janeiro, Brazil. Parasitol Res 2013; 112:2017-25. [PMID: 23474658 PMCID: PMC3625414 DOI: 10.1007/s00436-013-3360-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/15/2013] [Indexed: 10/27/2022]
Abstract
The aim of this study was to detect Theileria equi (Laveran 1901) DNA in horses and ticks using real-time PCR and to list the factors associated with infection in animals located in the Seropedica and Petropolis municipalities of the state of Rio de Janeiro. We tested blood samples from 314 horses and samples from 300 ticks, including 191 Amblyomma cajennense, 104 Dermacentor nitens, and 5 Ixodida larvae. Factors inherent to the horse, the ownership, and animal management were obtained from an epidemiological questionnaire and were evaluated in association with the presence of T. equi DNA in the animals. Among the horses in the study, 81 % (n = 253/314) presented T. equi DNA, and the animals of the Seropedica municipality had the highest infection frequency (91 %, n = 128/141, p < 0.001). The factors that had significantly different infection frequencies by chi-squared or Fisher's exact tests (p < 0.2) were included in a logistic regression model using the R programming package. Work and walking activity (odds ratio [OR] = 5.7, CI = 2.3-14.4), reproductive activity (OR = 3.8, CI = 1.3-11.5), and tick infestation (OR = 2.6, CI = 1.1-6.2) were factors that favored the presence of T. equi DNA in the animals (p < 0.05). Among the tick samples, A. cajennense and D. nitens were the identified species. The presence of T. equi DNA was observed in 9.9 % (n = 19/191) of the A. cajennense samples and 3.8 % (n = 4/104) of the D. nitens samples. A multivariate analysis revealed that the presence of A. cajennense on the animals (OR = 4.1, CI = 1.8-9.1) was associated with the presence of T. equi DNA in the horses. In the studied municipalities, activities related to work, walking, and reproduction and the presence of ticks on the horses, particularly an intense infestation of A. cajennense, are factors that lead to infection with T. equi in the horses.
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Affiliation(s)
- Maristela Peckle
- Animal Parasitology Department, Veterinary Institute, Universidade Federal Rural do Rio de Janeiro, BR 465, Km 7, Seropédica, Rio de Janeiro, 23897-000, Brazil
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Roeber F, Jex AR, Gasser RB. Next-generation molecular-diagnostic tools for gastrointestinal nematodes of livestock, with an emphasis on small ruminants: a turning point? ADVANCES IN PARASITOLOGY 2013; 83:267-333. [PMID: 23876874 PMCID: PMC7150098 DOI: 10.1016/b978-0-12-407705-8.00004-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Parasitic nematodes of livestock have major economic impact worldwide. Despite the diseases caused by these nematodes, some advances towards the development of new therapeutic agents and attempts to develop effective vaccines against some of them, there has been limited progress in the development of practical diagnostic methods. The specific and sensitive diagnosis of parasitic nematode infections of livestock underpins effective disease control, which is now particularly important given the problems associated with anthelmintic resistance in parasite populations. Traditional diagnostic methods have major limitations, in terms of sensitivity and specificity. This chapter provides an account of the significance of parasitic nematodes (order Strongylida), reviews conventional diagnostic techniques that are presently used routinely and describes advances in polymerase chain reaction (PCR)-based methods for the specific diagnosis of nematode infections. A particular emphasis is placed on the recent development of a robotic PCR-based platform for high-throughput diagnosis, and its significance and implications for epidemiological investigations and for use in control programmes.
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Affiliation(s)
| | | | - Robin B. Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
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17
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Optimization of the pepsin digestion method for anisakids inspection in the fishing industry. Vet Parasitol 2012; 191:276-83. [PMID: 23044250 DOI: 10.1016/j.vetpar.2012.09.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 09/05/2012] [Accepted: 09/11/2012] [Indexed: 11/20/2022]
Abstract
During the last 50 years human anisakiasis has been rising while parasites have increased their prevalence at determined fisheries becoming an emergent major public health problem. Although artificial enzymatic digestion procedure by CODEX (STAN 244-2004: standard for salted Atlantic herring and salted sprat) is the recommended protocol for anisakids inspection, no international agreement has been achieved in veterinary and scientific digestion protocols to regulate this growing source of biological hazard in fish products. The aim of this work was to optimize the current artificial digestion protocol by CODEX with the purpose of offering a faster, more useful and safer procedure for factories workers, than the current one for anisakids detection. To achieve these objectives, the existing pepsin chemicals and the conditions of the digestion method were evaluated and assayed in fresh and frozen samples, both in lean and fatty fish species. Results showed that the new digestion procedure considerably reduces the assay time, and it is more handy and efficient (the quantity of the resulting residue was considerably lower after less time) than the widely used CODEX procedure. In conclusion, the new digestion method herein proposed based on liquid pepsin format is an accurate reproducible and user-friendly off-site tool, that can be useful in the implementation of screening programs for the prevention of human anisakiasis (and associated gastroallergic disorders) due to the consumption of raw or undercooked contaminated seafood products.
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18
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Ahmed M, Singh MN, Bera AK, Bandyopadhyay S, Bhattacharya D. Molecular basis for identification of species/isolates of gastrointestinal nematode parasites. ASIAN PAC J TROP MED 2012; 4:589-93. [PMID: 21914532 DOI: 10.1016/s1995-7645(11)60152-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/17/2011] [Accepted: 06/15/2011] [Indexed: 11/18/2022] Open
Abstract
Gastrointestinal (GI) parasitism is the most serious constraint throughout the world in small ruminants which causes significant production loss in animals. GI parasites are major contributor to reduce productivity in terms of meat, milk and wool in animals. Control of GI parasite is done primarily by anthelmintic treatment where choice and schedule of treatment is done after identification and quantitation of individual parasite. Identification of GI parasites is done through microscopic method by identifying specific morphological characteristics of egg and larva (L(3)). Since most of parasite eggs are having similar morphological characteristics, identification up to species level through microscopy is not possible in most of cases. To address this issue, molecular techniques are the viable alternative for identification of species as well as molecular level differences within a species (isolates) of parasites. Different DNA based molecular techniques viz. PCR, AFLP, RAPD, RFLP, PCR-SSCP, real time PCR, DNA microarray etc. have been used for identification and to assess the genetic diversity among parasite population. For identification of species, the characteristic sequence of genomic DNA of different species should differ to allow the delineation of species, but at the same time, no/minor variation within the species should exist. In contrast, for purpose of identifying population variants (strains/isolates), a considerable degree of variation in the sequence should exist within a species. Various target regions, including nuclear ribosomal DNA (rDNA), mitochondrial DNA (mtDNA) or repetitive DNA elements (microsatellite loci), which show considerable variation in the number of repeats within individuals have been employed to achieve the identification of parasites species or strain.
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Affiliation(s)
- M Ahmed
- Eastern Regional Station of Indian veterinary Research Institute, 37 Belgachia Road, Kolkata, West Bengal, India
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19
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Lymbery AJ, Thompson RCA. The molecular epidemiology of parasite infections: tools and applications. Mol Biochem Parasitol 2011; 181:102-16. [PMID: 22027028 DOI: 10.1016/j.molbiopara.2011.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 10/16/2022]
Abstract
Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.
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Affiliation(s)
- A J Lymbery
- Fish Health Unit, School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch WA 6150, Australia.
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Schmid-Hempel R, Salathé R, Tognazzo M, Schmid-Hempel P. Genetic exchange and emergence of novel strains in directly transmitted trypanosomatids. INFECTION GENETICS AND EVOLUTION 2011; 11:564-71. [PMID: 21252000 DOI: 10.1016/j.meegid.2011.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Revised: 12/24/2010] [Accepted: 01/04/2011] [Indexed: 10/18/2022]
Abstract
The breeding structure of protozoan infections, i.e. whether and how frequently parasites exchange genes ("sexual reproduction"), is a crucially important parameter for many important questions; it also matters for how new virulent strains might emerge. Whether protozoan parasites are clonal or sexual is therefore a hotly debated issue. For trypanosomatids, few experimental tests of breeding structure exist to date and are limited to the vector-borne human diseases Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. We infected the natural host (Bombus terrestris) of the monoxenous parasite Crithidia bombi (Trypanosomatida) either with a single strain of the parasite or in mixed infections and tested for genetic exchange among co-infecting strains using microsatellite markers. We show that strains regularly exchange genetic material, with occasional self-crossing during mixed infections. Most offspring clones fit the expected allelic pattern from a standard Mendelian segregation. In some cases, alleles are lost or gained, leading to an entirely new genotype different from either parent. Genetic exchange in C. bombi therefore does occur and the process also leads to allelic loss or gain that could result from slippage during recombination. The majority of novel offspring types correspond to a recombination of parental alleles. The case of C. bombi demonstrates that directly transmitted, monoxenic trypanosomatids can also exchange genes. Sex therefore seems to be found in very different lineages of the trypanosomatids. Furthermore, the data allowed estimating a frequency at which C. bombi shows genetic exchange in populations.
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Affiliation(s)
- Regula Schmid-Hempel
- ETH Zürich, Institute of Integrative Biology (IBZ), ETH-Zentrum CHN, Universitätsstrasse 16, Zürich, Switzerland.
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Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A. Identification of species by multiplex analysis of variable-length sequences. Nucleic Acids Res 2010; 38:e203. [PMID: 20923781 PMCID: PMC3001097 DOI: 10.1093/nar/gkq865] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing.
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Affiliation(s)
- Filipe Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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Battocchi C, Totti C, Vila M, Masó M, Capellacci S, Accoroni S, Reñé A, Scardi M, Penna A. Monitoring toxic microalgae Ostreopsis (dinoflagellate) species in coastal waters of the Mediterranean Sea using molecular PCR-based assay combined with light microscopy. MARINE POLLUTION BULLETIN 2010; 60:1074-1084. [PMID: 20188383 DOI: 10.1016/j.marpolbul.2010.01.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 01/19/2010] [Accepted: 01/25/2010] [Indexed: 05/28/2023]
Abstract
A molecular PCR-based assay was developed and applied to macrophyte and seawater samples containing mixed microphytobenthic and phytoplanktonic assemblages, respectively, in order to detect toxic Ostreopsis species in Mediterranean Sea. The specificity and sensitivity of the molecular PCR assay were assessed with both plasmidic and genomic DNA of the target genus or species using taxon-specific primers in the presence of background macrophyte DNA. The PCR molecular technique allowed rapid detection of the Ostreopsis cells, even at abundances undetectable within the resolution limit of the microscopy technique. Species-specific identification of Ostreopsis was determined only by PCR-based assay, due to the inherent difficulty of morphological identification in field samples. In the monitoring of the toxic Ostreopsis blooms PCR-based methods proved to be effective tools complementary to microscopy for rapid and specific detection of Ostreopsis and other toxic dinoflagellates in marine coastal environments.
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Affiliation(s)
- Cecilia Battocchi
- Dipartimento di Scienze Biomolecolari, Sez. Biol. Amb., Università di Urbino, Viale Trieste 296, 61100 Pesaro, Italy
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Identification of forensically important blowfly species (Diptera: Calliphoridae) by high-resolution melting PCR analysis. Int J Legal Med 2010; 124:277-85. [DOI: 10.1007/s00414-009-0396-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 11/18/2009] [Indexed: 10/20/2022]
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Comparison of the susceptibility of brown trout (Salmo trutta) and four rainbow trout (Oncorhynchus mykiss) strains to the myxozoan Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD). Vet Parasitol 2009; 165:200-6. [PMID: 19683396 DOI: 10.1016/j.vetpar.2009.07.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 06/17/2009] [Accepted: 07/15/2009] [Indexed: 11/22/2022]
Abstract
Differences in susceptibility to the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD), between four strains of rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta) were evaluated. Fish were exposed to water enzootic for the parasite in the field for 5 days and were subsequently transferred to the laboratory. Relative parasite load was determined after 2, 3 and 4 weeks post-exposure (wpe) by quantitative real-time PCR (qPCR) of kidney samples and number of parasite stages was determined in immunohistochemical stained sections of kidney, liver and spleen tissues. According to qPCR results, the highest amount of parasite DNA per equal amount of host tissue at all time points was measured in brown trout. Two of the rainbow trout strains showed lower relative parasite load than all other groups at the beginning of the experiment, but the parasite multiplied faster in these strains resulting in an equal level of relative parasite load for all rainbow trout strains at 4 wpe. A weak negative correlation of fish size and parasite load was detected. Only in samples of a few fish, single stages of T. bryosalmonae were found in sections stained by immunohistochemistry impeding quantitative evaluation of parasite numbers by this method. The results indicate a differential resistance to T. bryosalmonae between the rainbow trout strains investigated and between rainbow trout and brown trout.
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Bott NJ, Campbell BE, Beveridge I, Chilton NB, Rees D, Hunt PW, Gasser RB. A combined microscopic-molecular method for the diagnosis of strongylid infections in sheep. Int J Parasitol 2009; 39:1277-87. [PMID: 19328802 DOI: 10.1016/j.ijpara.2009.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 03/16/2009] [Accepted: 03/18/2009] [Indexed: 11/29/2022]
Abstract
We evaluated a combined microscopic-molecular approach for the diagnosis of key strongylid infections in sheep using panels of well-defined control and test samples. The method established is based on the separation of nematode eggs from faecal samples using a salt flotation procedure, the extraction and column-purification of genomic DNA, followed by real-time PCR and melting-curve analysis. Specific and semi-quantitative amplification from (a minimum of 0.1-2.0pg) genomic DNA of Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus spp., Cooperia oncophora, Oesophagostomum columbianum, Oesophagostomum venulosum or Chabertia ovina is achieved using a specific, forward oligonucleotide primer located in the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) together with a conserved reverse primer in the large subunit of rDNA. Using a panel of well-defined genomic DNA samples from eggs from sheep monospecifically infected with H. contortus or Te. circumcincta, there was a correlation between cycle threshold (Ct) values in the PCR and numbers of egg per gram of faeces, thus allowing the semi-quantitation of parasite DNA in faeces. The findings of the present study indicate that a microscopic-molecular approach provides a useful tool for diagnosis, for epidemiological and ecological surveys as well as for integration into parasite monitoring, drug resistance (i.e. 'egg count reduction') testing or control programmes, particularly following semi- or full-automation.
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Affiliation(s)
- Nathan J Bott
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Vic. 3030, Australia
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Biotechnological advances in the diagnosis of little-known parasitoses of pets. Parasitol Res 2008; 104:209-16. [DOI: 10.1007/s00436-008-1290-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 11/13/2008] [Indexed: 11/25/2022]
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Toward practical, DNA-based diagnostic methods for parasitic nematodes of livestock — Bionomic and biotechnological implications. Biotechnol Adv 2008; 26:325-34. [DOI: 10.1016/j.biotechadv.2008.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/06/2008] [Accepted: 03/14/2008] [Indexed: 11/22/2022]
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Jex AR, Smith HV, Monis PT, Campbell BE, Gasser RB. Cryptosporidium--biotechnological advances in the detection, diagnosis and analysis of genetic variation. Biotechnol Adv 2008; 26:304-17. [PMID: 18430539 DOI: 10.1016/j.biotechadv.2008.02.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 01/29/2008] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
Abstract
Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.
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Affiliation(s)
- A R Jex
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
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Corradi N, Gangaeva A, Keeling PJ. Comparative profiling of overlapping transcription in the compacted genomes of microsporidia Antonospora locustae and Encephalitozoon cuniculi. Genomics 2008; 91:388-93. [PMID: 18280697 DOI: 10.1016/j.ygeno.2007.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 11/26/2007] [Accepted: 12/17/2007] [Indexed: 11/30/2022]
Abstract
Microsporidia are highly adapted parasites related to fungi with compact, gene-dense genomes. It has previously been shown in the microsporidian Antonospora locustae that transcripts from any given gene overlap with adjacent genes at a high frequency, perhaps due to the compact nature of its genome. However, it is still not known if this phenomenon is widespread among microsporidia or conserved between species, or even whether it is strictly correlated with compaction. To address these questions, we performed a comparison of transcription profiles in two microsporidian species, A. locustae and Encephalitozoon cuniculi. Transcription overlap was characterized at many A. locustae loci representing a range of gene densities, to determine if overlapping transcription correlates with the length of intergenic spacers. In parallel, we examined the first cases of transcription overlap in E. cuniculi. Using regions of the genome where the order of genes is conserved between A. locustae and E. cuniculi, we identified the transcriptional processing points in both species to determine how the process changes through evolutionary time. We show that there is little conservation of processing points between species and indeed that the process differs in important ways in the two genomes. Overall, A. locustae transcripts generally start just upstream of the start codon, but terminate well within or beyond downstream genes. In contrast, E. cuniculi transcripts often initiate within upstream genes, but more frequently terminate prior to the downstream gene. This process appears to have predictable characteristics within a given genome, but to be relatively flexible between species, presenting further challenges to the study of gene expression in these obligately intracellular parasites.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, Canada
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PCR Techniques as Diagnostic Tools for the Identification and Enumeration of Toxic Marine Phytoplankton Species. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8480-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
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31
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Leetz AS, Sotiriadou I, Ongerth J, Karanis P. An evaluation of primers amplifying DNA targets for the detection of Cryptosporidium spp. using C. parvum HNJ-1 Japanese isolate in water samples. Parasitol Res 2007; 101:951-62. [PMID: 17514380 DOI: 10.1007/s00436-007-0567-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
The performance of polymerase chain reaction (PCR) procedures for the detection of Cryptosporidium parvum HNJ-1 strain (genotype II) oocysts purified from mice using published protocols was evaluated. Oocysts were concentrated from fecal samples of infected severe combined immunodeficiency (SCID) mice by sucrose flotation and were then purified by immunomagnetic separation method. The genotype of C. parvum was established as type II by restriction fragment length polymorphism (RFLP) analysis. Water samples were spiked with different numbers of oocysts, determined by limiting dilution. Genomic DNA was extracted and used for PCR assays targeting various Cryptosporidium species genes (Beta-Tubulin, COWP, 70 kDa HSP, SSU rRNA, ITS1, TRAP-C1 and TRAP-C2 gene). DNA from oocyst numbers of more than 1 x 10(4) was detected using each of the primers. However, when using lower oocyst numbers, the tools based on 9 of the 16 different primer assays gave sufficient results. Assays using the remaining seven primers gave less than satisfactory results. A new primer set, named VKSS-F1/2 and VKSS-R1/2, that target the 18 SSU rRNA gene of C. parvum was constructed and applied. The VKSS-F1/2 and VKSS-R1/2 assays amplified DNA isolated from spiked samples in 206 of 211 trials (97.6%). This illustrates the difficulty of detecting low numbers of Cryptosporidium spp. oocysts by molecular methods when working with environmental samples.
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Affiliation(s)
- Anna Susanne Leetz
- Medical and Molecular Parasitology Laboratory, University of Cologne, Medical School, Center of Anatomy, Institute II, Cologne, Germany
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Biologie moléculaire et microbiologie clinique en 2007. IMMUNO-ANALYSE & BIOLOGIE SPÉCIALISÉE 2007. [PMCID: PMC7148721 DOI: 10.1016/j.immbio.2006.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
La biologie moléculaire est omniprésente en biologie médicale et plus particulièrement en microbiologie. De nombreux articles démontrent son importance tant dans le domaine du diagnostic que du pronostic, de l'évaluation thérapeutique, de l'épidémiologie ou des risques biologiques naturels ou non. La quantité considérable d'articles sur ce sujet n'apporte pas toujours une réponse évidente sur le rôle de la biologie moléculaire dans un laboratoire de microbiologie qu'il soit hospitalier ou non. Cette revue constitue une synthèse des apports de cette discipline en microbiologie. À partir de cet état des lieux, certaines questions se posent, par exemple : la biologie moléculaire constitue-t-elle un réel apport en microbiologie ? Dans quelles indications prescrire un examen de biologie moléculaire ? Les réponses ne sont pas toujours simples. Elles sont évidentes dans certains cas (l'hépatite C par exemple) et le sont moins dans d'autres, la tuberculose par exemple. Dans la première partie de l'article, nous avons parlé des généralités appliquées à la microbiologie. Dans cette deuxième partie, nous abordons certaines applications, reflets de l'importance prise par la biologie moléculaire en microbiologie.
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Behets J, Declerck P, Delaedt Y, Verelst L, Ollevier F. Quantitative Detection and Differentiation of Free-Living Amoeba Species Using SYBR Green–Based Real-Time PCR Melting Curve Analysis. Curr Microbiol 2006; 53:506-9. [PMID: 17106802 DOI: 10.1007/s00284-006-0241-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 08/14/2006] [Indexed: 11/28/2022]
Abstract
Real-time polymerase chain reaction melting curve analysis (MCA) allows differentiation of several free-living amoebae species. Distinctive characteristics were found for Naegleria fowleri, N. lovaniensis, N. australiensis, N. gruberi, Hartmanella vermiformis, and Willaertia magna. Species specificity of the amplicons was confirmed using agarose gel electrophoresis and sequence-based approaches. Amplification efficiency ranged from 91% to 98%, indicating the quantitative potential of the assay. This MCA approach can be used for quantitative detection of free-living amoebae after cultivation but also as a culture-independent detection method.
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Affiliation(s)
- Jonas Behets
- Laboratory of Aquatic Ecology, Katholieke Universiteit Leuven (KUL), Charles Deberiotstraat 32, 3000, Leuven, Belgium.
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Morris GM, Gasser RB. Biotechnological advances in the diagnosis of avian coccidiosis and the analysis of genetic variation in Eimeria. Biotechnol Adv 2006; 24:590-603. [PMID: 16901674 DOI: 10.1016/j.biotechadv.2006.06.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Revised: 06/18/2006] [Accepted: 06/18/2006] [Indexed: 11/17/2022]
Abstract
Coccidiosis is an intestinal disease of chickens caused by various species of protozoan parasites within the genus Eimeria. This disease has a major economic impact to growers and to the poultry industry world-wide. The diagnosis and genetic characterization of the different species of Eimeria are central to the prevention, surveillance and control of coccidiosis, particularly now given the major problems with wide-spread resistance of Eimeria species against anticoccidial drugs (coccidiostats) and the residue problems associated with these compounds. While traditional methods have had major limitations in the specific diagnosis of coccidiosis, there have been significant advances in the development of molecular-diagnostic tools. The present article provides a background on coccidiosis, reviews the main molecular methods which have been used and describes recent advances in the establishment of polymerase chain reaction (PCR)-coupled electrophoretic approaches for the specific diagnosis of coccidiosis as well as the genetic characterization of species of Eimeria. These biotechnological advances are considered to represent a significant step toward the improved prevention and control of this important disease of poultry.
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Affiliation(s)
- G M Morris
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
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King CH, Sturrock RF, Kariuki HC, Hamburger J. Transmission control for schistosomiasis - why it matters now. Trends Parasitol 2006; 22:575-82. [PMID: 17030017 DOI: 10.1016/j.pt.2006.09.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 08/30/2006] [Accepted: 09/26/2006] [Indexed: 11/30/2022]
Abstract
Current population-based schistosomiasis treatment programs are a first step to reducing the global burden of Schistosoma-related disease; however, they might not dramatically reduce parasite transmission in highly endemic areas. Consequently, the benefits of these programs remain in doubt because recurring low-level reinfection is likely to be associated with subtle but persistent morbidities such as anemia, undernutrition and diminished performance status. The real health benefits of transmission control need to be reconsidered and attention given to more aggressive and, ultimately, more affordable parasite elimination strategies. The next generation of schistosomiasis control can be optimized using new monitoring tools and effective transmission containment.
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Affiliation(s)
- Charles H King
- Center for Global Health and Diseases, Case Western Reserve University, Wolstein 4126, 10900 Euclid Avenue, Cleveland, OH 44106-7286, USA.
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Abstract
Modern molecular technologies are having a substantial impact in many fundamental and applied areas of parasitology. In particular, polymerase chain reaction (PCR)-coupled approaches have found broad applicability because their sensitivity permits the enzymatic amplification of gene fragments from minute quantities of nucleic acids from tiny amounts of parasite material. Also, high-resolution electrophoretic and genomic methods are finding increased utility. This paper briefly discusses some developments and applications of DNA methods to parasites and highlights their usefulness or potential for those of veterinary importance. Selected examples of applications with implications in fundamental (systematics, population genetics, epidemiology and ecology) and applied (diagnosis, prevention and control) areas are presented. The focus is mainly on tools for the accurate identification of parasitic nematodes and protozoa of socio-economic importance, the diagnosis of infections and the detection of genetic variability using PCR-coupled mutation scanning technology.
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Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria 3030, Australia.
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Traub RJ, Monis PT, Robertson ID. Molecular epidemiology: A multidisciplinary approach to understanding parasitic zoonoses. Int J Parasitol 2005; 35:1295-307. [PMID: 16143334 DOI: 10.1016/j.ijpara.2005.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/21/2005] [Accepted: 06/23/2005] [Indexed: 10/25/2022]
Abstract
Sound application of molecular epidemiological principles requires working knowledge of both molecular biological and epidemiological methods. Molecular tools have become an increasingly important part of studying the epidemiology of infectious agents. Molecular tools have allowed the aetiological agent within a population to be diagnosed with a greater degree of efficiency and accuracy than conventional diagnostic tools. They have increased the understanding of the pathogenicity, virulence, and host-parasite relationships of the aetiological agent, provided information on the genetic structure and taxonomy of the parasite and allowed the zoonotic potential of previously unidentified agents to be determined. This review describes the concept of epidemiology and proper study design, describes the array of currently available molecular biological tools and provides examples of studies that have integrated both disciplines to successfully unravel zoonotic relationships that would otherwise be impossible utilising conventional diagnostic tools. The current limitations of applying these tools, including cautions that need to be addressed during their application are also discussed.
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Affiliation(s)
- R J Traub
- WHO Collaborating Centre for the Molecular Epidemiology of Parasitic Infections, School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia.
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