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Graumans W, Ayo D, van Lieshout N, Lanke K, Bousema T, Arinaitwe E. Plasmodium malariae and Plasmodium ovale-Prevalent and Relevant. J Infect Dis 2024; 229:1239-1240. [PMID: 38243611 PMCID: PMC11011154 DOI: 10.1093/infdis/jiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Affiliation(s)
- Wouter Graumans
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, the Netherlands
| | - Daniel Ayo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Nadeche van Lieshout
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, the Netherlands
| | - Kjerstin Lanke
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, the Netherlands
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, the Netherlands
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, United Kingdom
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Dos Santos EH, Barreira GA, Yamamoto L, Rocha MC, Rodrigues KA, Cruz MCP, Kanunfre KA, Okay TS. New Allele-Specific Oligonucleotide (ASO) amplifications for Toxoplasma gondii rop18 allele typing: Analysis of 86 human congenital infections in Brazil. Acta Trop 2023; 247:107011. [PMID: 37652181 DOI: 10.1016/j.actatropica.2023.107011] [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: 03/30/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
This study aimed to detect and differentiate Toxoplasma gondii by the allele typing of its polymorphic rop18 gene. For this purpose, a novel genotyping system using allele-specific oligonucleotides (ASOs) was designed, consisting of three ASO pairs. The first and third pairs specifically amplify rop18 allele I and allele III, while the second pair amplify both allele I and II. Genomic DNA from 86 congenital infections was analyzed by ASO-PCRs, successfully typing 82 (95.35%) samples. The remaining 4 samples (4.65%) required sequencing and single nucleotide polymorphism (SNP) analysis of the amplification products. The distribution of samples according to rop18 alleles was: 39.5% of allele III, 38.4% of allele II, 19.8% of mixed rop18 alleles (I/III or II/III), and 2.3% of allele I. The six severely compromised infants exhibited the highest parasite load levels and were infected during the first and early second trimesters of pregnancy. Among these cases, two were associated with rop18 allele I parasites, two with mixed rop18 alleles (I/III), one with allele II, and one with allele III parasites. In conclusion, all severe cases of congenital toxoplasmosis were infected during early pregnancy, but they were not exclusively associated with rop18 allele I parasites, as observed in murine toxoplasmosis. Furthermore, nearly one-fifth of parasites were non-archetypal, exhibiting more than one rop18 allele, indicating a higher genetic diversity of Toxoplasma gondii in this South American sample. Overall, a robust T. gondii rop18 allele typing was developed and suggested that congenital toxoplasmosis in humans involves complex mechanisms beyond the parasite genotype.
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Affiliation(s)
- Emilly Henrique Dos Santos
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brasil; Departamento de Pediatria, Faculdade de Medicina, Universidade de São Paulo, Brasil
| | - Gabriel Acca Barreira
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brasil; Faculdade Israelita de Ciências da Saúde Albert Einstein (FICSAE), São Paulo, Brasil
| | - Lidia Yamamoto
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brasil
| | - Mussya Cisotto Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brasil
| | - Karen Alessandra Rodrigues
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brasil; Departamento de Pediatria, Faculdade de Medicina, Universidade de São Paulo, Brasil
| | | | | | - Thelma Suely Okay
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brasil; Departamento de Pediatria, Faculdade de Medicina, Universidade de São Paulo, Brasil.
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Xu H, Sun Y, Zhang X, Chen R, Cai Z, Zhao B, Liu X, Liu J. Universal two-dimensional labelled probe-mediated melting curve analysis based on multiplex PCR for rapid typing of Plasmodium in a single closed tube. Microb Biotechnol 2023; 16:838-846. [PMID: 36745663 PMCID: PMC10034624 DOI: 10.1111/1751-7915.14232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/07/2023] Open
Abstract
Currently, malaria is still one of the major public health problems commonly caused by the four Plasmodium species. The similar symptoms of malaria and the COVID-19 epidemic of fever or fatigue lead to frequent misdiagnosis. The disadvantages of existing detection methods, such as time-consuming, costly, complicated operation, need for experienced technicians, and indistinguishable typing, lead to difficulties in meeting the clinical requirements of rapid, easy, and accurate typing of common Plasmodium species. In this study, we developed and optimized a universal two-dimensional labelled probe-mediated melting curve analysis (UP-MCA) assay based on multiplex and asymmetric PCR for rapid and accurate typing of five Plasmodium species, including novel human Plasmodium, Plasmodium knowlesi (Pk), in a single closed tube following genome extraction. The assay showed a limit of detection (LOD) of 10 copies per reaction and could accurately distinguish Plasmodium species from intra-plasmodium and other pathogens. Additionally, we proposed and validated different methods of fluorescence quenching and tag design for probes that are suitable for UP-MCA assays. Moreover, the clinical performance of the Plasmodium UP-MCA assay using a base-quenched universal probe was evaluated using 226 samples and showed a sensitivity of 100% (164/164) and specificity of 100% (62/62) at a 99% confidence interval, with the microscopy method as the gold standard. In summary, the UP-MCA assay showed excellent sensitivity, specificity, and accuracy for genotyping Plasmodium species spp. Additionally, it facilitates convenient and rapid Plasmodium detection in routine clinical practice and has great potential for clinical translation.
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Affiliation(s)
- Haipo Xu
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yupeng Sun
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Xiaolong Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Ronghua Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Xiaolong Liu
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Jingfeng Liu
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
- Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, China
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Gimenez AM, Marques RF, Regiart M, Bargieri DY. Diagnostic Methods for Non-Falciparum Malaria. Front Cell Infect Microbiol 2021; 11:681063. [PMID: 34222049 PMCID: PMC8248680 DOI: 10.3389/fcimb.2021.681063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is a serious public health problem that affects mostly the poorest countries in the world, killing more than 400,000 people per year, mainly children under 5 years old. Among the control and prevention strategies, the differential diagnosis of the Plasmodium-infecting species is an important factor for selecting a treatment and, consequently, for preventing the spread of the disease. One of the main difficulties for the detection of a specific Plasmodium sp is that most of the existing methods for malaria diagnosis focus on detecting P. falciparum. Thus, in many cases, the diagnostic methods neglect the other non-falciparum species and underestimate their prevalence and severity. Traditional methods for diagnosing malaria may present low specificity or sensitivity to non-falciparum spp. Therefore, there is high demand for new alternative methods able to differentiate Plasmodium species in a faster, cheaper and easier manner to execute. This review details the classical procedures and new perspectives of diagnostic methods for malaria non-falciparum differential detection and the possibilities of their application in different circumstances.
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Affiliation(s)
- Alba Marina Gimenez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodolfo F. Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Matías Regiart
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Daniel Youssef Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Varliero G, Wray J, Malandain C, Barker G. PhyloPrimer: a taxon-specific oligonucleotide design platform. PeerJ 2021; 9:e11120. [PMID: 33986979 PMCID: PMC8098674 DOI: 10.7717/peerj.11120] [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: 11/13/2020] [Accepted: 02/25/2021] [Indexed: 11/26/2022] Open
Abstract
Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
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Affiliation(s)
- Gilda Varliero
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jared Wray
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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Aschar M, Levi JE, Farinas MLRN, Montebello SC, Mendrone-Junior A, Di Santi SM. The hidden Plasmodium malariae in blood donors: a risk coming from areas of low transmission of malaria. Rev Inst Med Trop Sao Paulo 2020; 62:e100. [PMID: 33331519 PMCID: PMC7748032 DOI: 10.1590/s1678-9946202062100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Malaria is an infectious vector-borne disease with other important routes of
transmission, such as blood transfusion and organ/tissue transplantation, due to
asymptomatic reservoirs of Plasmodium presenting with low
parasitemia. Reports of transfusion-transmitted malaria have shown that in
immunosuppressed recipients, infections can be fatal if they are not diagnosed
and timely treated. All Plasmodium species can survive on blood
components at temperatures from 2 to 6 °C for some days or even weeks. This
report describes two candidates for blood donation harboring
Plasmodium, infected in an area considered non-endemic.
Blood samples were collected from donors who attended a blood bank in Sao Paulo
and tested by microscopy, qPCR for Plasmodium genus-specific
amplification, targeting the parasite 18S ribosomal subunit gene and a multiplex
qPCR based on mtDNA of the five species. Under microscopy, only structures
resembling Plasmodium were observed. The qPCR whose standard
curve tested parasites varying from 2 to 0.1 parasites/ µL, showed the presence
of Plasmodium DNA in the two blood donors, as did the multiplex
qPCR that revealed the presence of P. malariae. The prevalence
of positive donors varies according to the level of transmission, ranging from
0.7 to 55% in endemic areas. In non-endemic regions, prevalences are lower,
however, transfusion malaria can evolve to severe cases, due to the lack of
suspicion of this transmission route. Asymptomatic donors from low transmission
regions pose a risk to blood banks, with particular emphasis on those located in
areas with malaria elimination goals.
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Affiliation(s)
- Mariana Aschar
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - José Eduardo Levi
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Laboratório de Virologia, São Paulo, São Paulo, Brazil
| | - Maria L R N Farinas
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Sandra C Montebello
- Secretaria da Saúde de São Paulo, Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, São Paulo, Brazil
| | - Alfredo Mendrone-Junior
- Secretaria da Saúde de São Paulo, Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, São Paulo, Brazil
| | - Silvia Maria Di Santi
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil.,Secretaria da Saúde de São Paulo, Superintendência de Controle de Endemias, Núcleo de Estudos em Malária, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
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