1
|
Mohammadi S, Najafzadeh N, Ghafari SM, Hanafi-Bojd AA, Taslimian R, Parvizi P. Geographical and Molecular Analysis of Haplotype Variations in Leishmania major Among Infected Iranian Phlebotomus papatasi. Acta Parasitol 2024; 69:549-558. [PMID: 38231310 DOI: 10.1007/s11686-023-00776-w] [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: 09/21/2022] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
PURPOSE Leishmania major is main causative agent and Phlebotomus papatasi is only proven vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in Iran. Human leishmaniasis is mostly susceptible to climatic conditions and molecular variations of Leishmania parasites within sandflies. METHODS L. major was analyzed based on geographical, environmental, climatic changes and haplotype variations within P. papatasi. Molecular tools and different geographical aspects were employed using Arc-GIS software for mapping the geographic distribution of samples and other statistics tests. Fragments of ITS-rDNA, k-DNA, and microsatellite genes of Leishmania were used for PCR, RFLP, sequencing, and phylogenetic analyses. RESULTS Totally 81 out of 1083 female P. papatasi were detected with Leishmania parasites: 70 and five were L. major and L. turanica, respectively. Golestan and Fars provinces had the highest (13.64%) and lowest (4.55%) infection rates, respectively. The infection rate among female P. papatasi collected from gerbil burrows was significantly higher (15.15%) than animal shelters, yards, and inside houses (4.48%) (P < 0.0%). Microsatellite was more sensitive (22.72%) than k-DNA (18.8%) and ITS-rDNA (7.48%). More molecular variations of L. major were found in Isfahan province. CONCLUSIONS Arc-GIS software and other statistics tests were employed to find Leishmania positive and haplotype variations among sand flies. Geographical situations, altitude, climate, precipitation, humidity, temperature, urbanization, migrations, regional divergences, deforestation, global warming, genome instability, ecology, and biology of the sand flies intrinsically, and the reservoir hosts and neighboring infected locations could be reasons for increasing or decreasing the rate of Leishmania infection and haplotype variations.
Collapse
Affiliation(s)
- Somayeh Mohammadi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave, Tehran, Iran
| | - Narmin Najafzadeh
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave, Tehran, Iran
| | - Seyedeh Maryam Ghafari
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave, Tehran, Iran.
| | - Ahmad Ali Hanafi-Bojd
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Roozbeh Taslimian
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, 69 Pasteur Ave, Tehran, Iran.
| |
Collapse
|
2
|
Gebremeskele BT, Adane G, Adem M, Tajebe F. Diagnostic performance of CL Detect rapid-immunochromatographic test for cutaneous leishmaniasis: a systematic review and meta-analysis. Syst Rev 2023; 12:240. [PMID: 38115138 PMCID: PMC10731771 DOI: 10.1186/s13643-023-02422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Sensitive, robust, and fast point-of-care tests are needed for cutaneous leishmaniasis (CL) diagnosis. The recently developed CL Detect rapid test (InBios) for detecting Leishmania peroxidoxin antigen has been evaluated in several studies. However, diagnostic performances were controversial. Therefore, this systematic review and meta-analysis aimed to determine the pooled sensitivity and specificity of CL Detect for CL diagnosis. METHODS PubMed, Scopus, EMBASE, ScienceDirect, and Google Scholar were sources of articles. We included studies reporting the diagnostic accuracy of CL Detect and CL-suspected patients in the English language. The methodological qualities of the included studies were appraised using the quality assessment of diagnostic accuracy studies-2 (QUADAS-2). Meta-analysis was conducted using Stata 14.2 and R software. RESULTS A total of 9 articles were included. The study sample size ranged from 11 to 274. The sensitivities of the individual studies ranged from 23 to 100%, and the specificities ranged from 78 to 100%. Pooled sensitivity and specificity were 68% (95% CI, 41-86%) and 94% (95% CI, 87-97%), respectively. AUC displayed 0.899. Pooled sensitivity was lower (47%, 95% CI, 34-61%) when PCR was used as a reference than microscopy (83%, 95% CI, 39-97%). Pooled sensitivity was lower (48%, 95% CI, 30-67%) for all lesion durations compared to ≤ 4 months (89%, 95% CI, 43-99%). CONCLUSIONS CL Detect has poor sensitivity and does not meet the minimal sensitivity of 95% of target product profiles designed for CL point-of-care tests. Currently, the CL Detect test looks unsuitable for CL diagnosis, despite its high specificity. Findings are limited by the low number of studies available. Further large-scale studies are recommended. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42022323497.
Collapse
Affiliation(s)
- Behailu Taye Gebremeskele
- Department of Medical Laboratory Science, College of Medicine and Health Science, Dilla University, Dilla, Ethiopia.
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia.
| | - Gashaw Adane
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
| | - Mohammed Adem
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
| | - Fitsumbrhan Tajebe
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
| |
Collapse
|
3
|
Barranco-Gómez O, De Paula JC, Parada JS, Gómez-Moracho T, Marfil AV, Zafra M, Orantes Bermejo FJ, Osuna A, De Pablos LM. Development of a TaqMan qPCR assay for trypanosomatid multi-species detection and quantification in insects. Parasit Vectors 2023; 16:69. [PMID: 36788540 PMCID: PMC9930332 DOI: 10.1186/s13071-023-05687-3] [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: 11/24/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Trypanosomatid parasites are widely distributed in nature and can have a monoxenous or dixenous life-cycle. These parasites thrive in a wide number of insect orders, some of which have an important economic and environmental value, such as bees. The objective of this study was to develop a robust and sensitive real-time quantitative PCR (qPCR) assay for detecting trypanosomatid parasites in any type of parasitized insect sample. METHODS A TaqMan qPCR assay based on a trypanosomatid-conserved region of the α-tubulin gene was standardized and evaluated. The limits of detection, sensitivity and versatility of the α-tubulin TaqMan assay were tested and validated using field samples of honeybee workers, wild bees, bumblebees and grasshoppers, as well as in the human infective trypanosomatid Leishmania major. RESULTS The assay showed a detection limit of 1 parasite equivalent/µl and successfully detected trypanosomatids in 10 different hosts belonging to the insect orders Hymenoptera and Orthoptera. The methodology was also tested using honeybee samples from four apiaries (n = 224 worker honeybees) located in the Alpujarra region (Granada, Spain). Trypanosomatids were detected in 2.7% of the honeybees, with an intra-colony prevalence of 0% to 13%. Parasite loads in the four different classes of insects ranged from 40.6 up to 1.1 × 108 cell equivalents per host. CONCLUSIONS These results show that the α-tubulin TaqMan qPCR assay described here is a versatile diagnostic tool for the accurate detection and quantification of trypanosomatids in a wide range of environmental settings.
Collapse
Affiliation(s)
- Olga Barranco-Gómez
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Jessica Carreira De Paula
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Jennifer Solano Parada
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Tamara Gómez-Moracho
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Ana Vic Marfil
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | - María Zafra
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain
| | | | - Antonio Osuna
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain.,Institute of Biotechnology, University of Granada, Granada, Spain
| | - Luis Miguel De Pablos
- Departamento de Parasitología, Grupo de Bioquímica y Parasitología Molecular CTS-183, Universidad de Granada, Granada, Spain. .,Institute of Biotechnology, University of Granada, Granada, Spain.
| |
Collapse
|
4
|
He P, Chen Z, He Y, Chen J, Hayat K, Pan J, Lin H. A reliable and low-cost deep learning model integrating convolutional neural network and transformer structure for fine-grained classification of chicken Eimeria species. Poult Sci 2022; 102:102459. [PMID: 36682127 PMCID: PMC9876957 DOI: 10.1016/j.psj.2022.102459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Chicken coccidiosis is a disease caused by Eimeria spp. and costs the broiler industry more than 14 billion dollars per year globally. Different chicken Eimeria species vary significantly in pathogenicity and virulence, so the classification of different chicken Eimeria species is of great significance for the epidemiological survey and related prevention and control. The microscopic morphological examination for their classification was widely used in clinical applications, but it is a time-consuming task and needs expertise. To increase the classification efficiency and accuracy, a novel model integrating transformer and convolutional neural network (CNN), named Residual-Transformer-Fine-Grained (ResTFG), was proposed and evaluated for fine-grained classification of microscopic images of seven chicken Eimeria species. The results showed that ResTFG achieved the best performance with high accuracy and low cost compared with traditional models. Specifically, the parameters, inference speed and overall accuracy of ResTFG are 1.95M, 256 FPS and 96.9%, respectively, which are 10.9 times lighter, 1.5 times faster and 2.7% higher in accuracy than the benchmark model. In addition, ResTFG showed better performance on the classification of the more virulent species. The results of ablation experiments showed that CNN or Transformer alone had model accuracies of only 89.8% and 87.0%, which proved that the improved performance of ResTFG was benefit from the complementary effect of CNN's local feature extraction and transformer's global receptive field. This study invented a reliable, low-cost, and promising deep learning model for the automatic fine-grain classification of chicken Eimeria species, which could potentially be embedded in microscopic devices to improve the work efficiency of researchers and extended to other parasite ova, and applied to other agricultural tasks as a backbone.
Collapse
Affiliation(s)
- Pengguang He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China,Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China,Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China
| | - Zhonghao Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China,Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China,Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China
| | - Yefan He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China,Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China,Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China
| | - Jintian Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China,Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China,Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China
| | - Khawar Hayat
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China,Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China,Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China
| | - Jinming Pan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China,Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China,Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China
| | - Hongjian Lin
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Hangzhou 310058, China; Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture, Ministry of Agriculture and Rural Affairs of China, Hangzhou 310058, China.
| |
Collapse
|
5
|
Alaeenovin E, Parvizi P, Ghafari SM. Two Leishmania species separation targeting the ITS-rDNA and Cyt b genes by developing and evaluating HRM- qPCR. Rev Soc Bras Med Trop 2022; 55:S0037-86822022000100342. [PMID: 36542013 PMCID: PMC9757716 DOI: 10.1590/0037-8682-0186-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Incidence of Cutaneous Leishmaniasis as an infectious and neglected disease is increasing, for the diagnosis of which several traditional methods and conventional PCR techniques have been developed, employing different genes for species identification. METHODS Leishmania parasites were sampled, DNA was extracted, and new specific and sensitive primers were designed. Two ITS-rDNA and Cyt b genes were targeted by qPCR using the High- Resolution Melting method to identify Leishmania parasites. The standard curves were drawn, compared, and identified by high-resolution melting curve analysis. RESULTS Melting temperature and Cycle of Threshold of ITS-rDNA was higher than Cyt b but Cyt b was more sensitive than ITS-rDNA when Leishmania major and Leishmania tropica were analyzed and evaluated. By aligning melt curves, normalizing fluorescence curves, and difference plotting melt curves, each Leishmania species was distinguished easily. L. major and L. tropica were separated at 83.6 °C and 84.7 °C, respectively, with less than 0.9 °C of temperature difference. Developing sensitivity and specificity of real-time PCR based on EvaGreen could detect DNA concentration to less than one pmol. CONCLUSIONS Precise identification of Leishmania parasites is crucial for strategies of disease control. Real-time PCR using EvaGreen provides rapid, highly sensitive, and specific detection of parasite's DNA. The modified High-Resolution Melting could determine unique curves and was able to detect single nucleotide polymorphisms according to small differences in the nucleotide content of Leishmania parasites.
Collapse
Affiliation(s)
- Elnaz Alaeenovin
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| | - Parviz Parvizi
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| | - Seyedeh Maryam Ghafari
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| |
Collapse
|
6
|
Gow I, Smith NC, Stark D, Ellis J. Laboratory diagnostics for human Leishmania infections: a polymerase chain reaction-focussed review of detection and identification methods. Parasit Vectors 2022; 15:412. [PMID: 36335408 PMCID: PMC9636697 DOI: 10.1186/s13071-022-05524-z] [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: 07/28/2022] [Accepted: 10/02/2022] [Indexed: 11/08/2022] Open
Abstract
Leishmania infections span a range of clinical syndromes and impact humans from many geographic foci, but primarily the world's poorest regions. Transmitted by the bite of a female sand fly, Leishmania infections are increasing with human movement (due to international travel and war) as well as with shifts in vector habitat (due to climate change). Accurate diagnosis of the 20 or so species of Leishmania that infect humans can lead to the successful treatment of infections and, importantly, their prevention through modelling and intervention programs. A multitude of laboratory techniques for the detection of Leishmania have been developed over the past few decades, and although many have drawbacks, several of them show promise, particularly molecular methods like polymerase chain reaction. This review provides an overview of the methods available to diagnostic laboratories, from traditional techniques to the now-preferred molecular techniques, with an emphasis on polymerase chain reaction-based detection and typing methods.
Collapse
Affiliation(s)
- Ineka Gow
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Nicholas C. Smith
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Damien Stark
- Department of Microbiology, St Vincent’s Hospital Sydney, Darlinghurst, NSW 2010 Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007 Australia
| |
Collapse
|
7
|
Establish an allele-specific real-time PCR for Leishmania species identification. Infect Dis Poverty 2022; 11:60. [PMID: 35655325 PMCID: PMC9164491 DOI: 10.1186/s40249-022-00992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Leishmaniasis is a serious neglected tropical disease that may lead to life-threatening outcome, which species are closely related to clinical diagnosis and patient management. The current Leishmania species determination method is not appropriate for clinical application. New Leishmania species identification tool is needed using clinical samples directly without isolation and cultivation of parasites. Methods A probe-based allele-specific real-time PCR assay was established for Leishmania species identification between Leishmania donovani and L. infantum for visceral leishmaniasis (VL) and among L. major, L. tropica and L. donovani/L. infantum for cutaneous leishmaniasis (CL), targeting hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and spermidine synthase (SPDSYN) gene with their species-specific single nucleotide polymorphisms (SNPs). The limit of detection of this assay was evaluated based on 8 repeated tests with intra-assay standard deviation < 0.5 and inter-assay coefficients of variability < 5%. The specificity of this assay was tested with DNA samples obtained from Plasmodium falciparum, Toxoplasma gondii, Brucella melitensis and Orientia tsutsugamushi. Total 42 clinical specimens were used to evaluate the ability of this assay for Leishmania species identification. The phylogenetic tree was constructed using HGPRT and SPDSYN gene fragments to validate the performance of this assay. Results This new method was able to detect 3 and 12 parasites/reaction for VL and CL respectively, and exhibited no cross-reaction with P. falciparum, T. gondii, B. melitensis, O. tsutsugamushi and non-target species of Leishmania. Twenty-two samples from VL patients were identified as L. donovani (n = 3) and L. infantum (n = 19), and 20 specimens from CL patients were identified as L. major (n = 20), providing an agreement of 100% compared with sequencing results. For further validation, 29 sequences of HGPRT fragment from nine Leishmania species and 22 sequences from VL patients were used for phylogenetic analysis, which agreed with the results of this new method. Similar results were obtained with 43 sequences of SPDSYN fragment from 18 Leishmania species and 20 sequences from CL patients. Conclusions Our assay provides a rapid and accurate tool for Leishmania species identification which is applicable for species-adapted therapeutic schedule and patient management. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40249-022-00992-y.
Collapse
|