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Hemming-Schroeder E, Umukoro E, Lo E, Fung B, Tomás-Domingo P, Zhou G, Zhong D, Dixit A, Atieli H, Githeko A, Vardo-Zalik A, Yan G. Impacts of Antimalarial Drugs on Plasmodium falciparum Drug Resistance Markers, Western Kenya, 2003-2015. Am J Trop Med Hyg 2018; 98:692-699. [PMID: 29363453 PMCID: PMC5930917 DOI: 10.4269/ajtmh.17-0763] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Antimalarial drug resistance has threatened global malaria control since chloroquine (CQ)-resistant Plasmodium falciparum emerged in Asia in the 1950s. Understanding the impacts of changing antimalarial drug policy on resistance is critical for resistance management. Plasmodium falciparum isolates were collected from 2003 to 2015 in western Kenya and analyzed for genetic markers associated with resistance to CQ (Pfcrt), sulfadoxine-pyrimethamine (SP) (Pfdhfr/Pfdhps), and artemether-lumefantrine (AL) (PfKelch13/Pfmdr1) antimalarials. In addition, household antimalarial drug use surveys were administered. Pfcrt 76T prevalence decreased from 76% to 6% from 2003 to 2015. Pfdhfr/Pfdhps quintuple mutants decreased from 70% in 2003 to 14% in 2008, but increased to near fixation by 2015. SP "super resistant" alleles Pfdhps 581G and 613S/T were not detected in the 2015 samples that were assessed. The Pfmdr1 N86-184F-D1246 haplotype associated with decreased lumefantrine susceptibility increased significantly from 4% in 2005 to 51% in 2015. No PfKelch13 mutations that have been previously associated with artemisinin resistance were detected in the study populations. The increase in Pfdhfr/Pfdhps quintuple mutants that associates with SP resistance may have resulted from the increased usage of SP for intermittent preventative therapy in pregnancy (IPTp) and for malaria treatment in the community. Prevalent Pfdhfr/Pfdhps mutations call for careful monitoring of SP resistance and effectiveness of the current IPTp program in Kenya. In addition, the commonly occurring Pfmdr1 N86-184F-D1246 haplotype associated with increased lumefantrine tolerance calls for surveillance of AL efficacy in Kenya, as well as consideration for a rotating artemisinin-combination therapy regimen.
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Affiliation(s)
| | | | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina
| | - Becky Fung
- Program in Public Health, University of California, Irvine, California
| | | | - Guofa Zhou
- Program in Public Health, University of California, Irvine, California
| | - Daibin Zhong
- Program in Public Health, University of California, Irvine, California
| | - Amruta Dixit
- Program in Public Health, University of California, Irvine, California
| | - Harrysone Atieli
- Centre for Vector Biology and Control Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Andrew Githeko
- Centre for Vector Biology and Control Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California
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Simple detection of single nucleotide polymorphism in Plasmodium falciparum by SNP-LAMP assay combined with lateral flow dipstick. Parasitol Int 2016; 66:964-971. [PMID: 27816495 DOI: 10.1016/j.parint.2016.10.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 11/20/2022]
Abstract
The significant strides made in reducing global malaria burden over the past decades are being threatened by the emergence of multi-drug resistant malaria. Mechanisms of resistance to several classes of antimalarial drugs have been linked to key mutations in the Plasmodium falciparum genes. Pyrimethamine targets the dihydrofolate reductase of the bifunctional dihydrofolate reductase thymidylate synthase (DHFR-TS), and specific point mutations in the dhfr-ts gene have been assigned to resistant phenotypes. Several molecular methods are available to detect the mutant genotypes including DNA sequencing and PCR-based methods. In this study, we report the development of PfSNP-LAMP to detect nucleotide polymorphism in the dhfr gene associated with N51I mutation and antifolate resistance. The PfSNP-LAMP method was validated with genomic DNA samples and parasite lysates prepared from sensitive and pyrimethamine resistant strains of P. falciparum.
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Lo E, Nguyen J, Oo W, Hemming-Schroeder E, Zhou G, Yang Z, Cui L, Yan G. Examining Plasmodium falciparum and P. vivax clearance subsequent to antimalarial drug treatment in the Myanmar-China border area based on quantitative real-time polymerase chain reaction. BMC Infect Dis 2016; 16:154. [PMID: 27084511 PMCID: PMC4833920 DOI: 10.1186/s12879-016-1482-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 03/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent emergence of artemisinin-resistant P. falciparum has posed a serious hindrance to the elimination of malaria in the Greater Mekong Subregion. Parasite clearance time, a measure of change in peripheral parasitaemia in a sequence of samples taken after treatment, can be used to reflect the susceptibility of parasites or the efficiency of antimalarials. The association of genetic polymorphisms and artemisinin resistance has been documented. This study aims to examine clearance time of P. falciparum and P. vivax parasitemia as well as putative gene mutations associated with residual or recurred parasitemia in Myanmar. METHODS A total of 63 P. falciparum and 130 P. vivax samples collected from two internally-displaced populations and one surrounding village were examined for parasitemia changes. At least four samples were taken from each patient, at the first day of diagnosis up to 3 months following the initial treatment. The amount of parasite gene copy number was estimated using quantitative real-time PCR based on a species-specific region of the 18S rRNA gene. For samples that showed residual or recurred parasitemia after treatment, microsatellites were used to identify the 'post-treatment' parasite genotype and compared such with the 'pre-treatment' genotype. Mutations in genes pfcrt, pfmdr1, pfatp6, pfmrp1 and pfK13 that are potentially associated with ACT resistance were examined to identify if mutation is a factor for residual or persistent parasitemia. RESULTS Over 30% of the P. falciprium infections showed delayed clearance of parasitemia after 2-3 days of treatment and 9.5% showed recurred parasitemia. Mutations in codon 876 of the pfmrp1 corroborated significance association with slow clearance time. However, no association was observed in the variation in pfmdr1 gene copy number as well as mutations of various codonsinpfatp6, pfcrt, and pfK13 with clearance time. For P. vivax, over 95% of the infections indicated cleared parasitemia at days 2-3 of treatment. Four samples were found to be re-infected with new parasite strains based on microsatellite genotypes after initial treatment. CONCLUSION The appearance of P.falciparum infected samples showing delayed clearance or recurred parasitemia after treatment raises concerns on current treatment and ACT drug resistance.
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Affiliation(s)
- Eugenia Lo
- />Program in Public Health, University of California at Irvine, Irvine, CA 92697-4050 USA
| | - Jennifer Nguyen
- />Program in Public Health, University of California at Irvine, Irvine, CA 92697-4050 USA
| | - Winny Oo
- />Program in Public Health, University of California at Irvine, Irvine, CA 92697-4050 USA
| | | | - Guofa Zhou
- />Program in Public Health, University of California at Irvine, Irvine, CA 92697-4050 USA
| | - Zhaoqing Yang
- />Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Liwang Cui
- />Department of Entomology, Pennsylvania State University, University Park, PA USA
| | - Guiyun Yan
- />Program in Public Health, University of California at Irvine, Irvine, CA 92697-4050 USA
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Li J, Chen J, Xie D, Eyi UM, Matesa RA, Ondo Obono MM, Ehapo CS, Yang L, Yang H, Lin M. Limited artemisinin resistance-associated polymorphisms in Plasmodium falciparum K13-propeller and PfATPase6 gene isolated from Bioko Island, Equatorial Guinea. Int J Parasitol Drugs Drug Resist 2016; 6:54-59. [PMID: 27054064 PMCID: PMC4805774 DOI: 10.1016/j.ijpddr.2015.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/03/2015] [Accepted: 11/25/2015] [Indexed: 02/05/2023]
Abstract
OBJECTIVE With emergence and geographically expanding of antimalarial resistance worldwide, molecular markers are essential tool for surveillance of resistant Plasmodium parasites. Recently, single-nucleotide polymorphisms (SNPs) in the PF3D7_1343700 kelch propeller (K13-propeller) domain are shown to be associated with artemisinin (ART) resistance in vivo and in vitro. This study aims to investigate the ART resistance-associated polymorphisms of K13-propeller and PfATPase6 genes in Plasmodium falciparum isolates from Bioko Island, Equatorial Guinea (EG). METHODS A total of 172 samples were collected from falciparum malaria patients on Bioko Island between 2013 and 2014. The polymorphisms of K13-propeller and PfATPase6 genes were analyzed by Nest-PCR and sequencing. RESULTS Sequences of K13-propeller and PfATPase6 were obtained from 90.74% (98/108) and 91.45% (139/152) samples, respectively. The 2.04% (2/98) cases had non-synonymous K13-propeller A578S mutation but no found the mutations associated with ART resistance in Southeast Asia. For PfATPase6, the mutations were found at positions N569K and A630S with the mutation prevalence of 7.91% (11/139) and 1.44% (2/139), respectively. In addition, a sample with the mixed type at position I723V was discovered (0.72%, 1/139). CONCLUSIONS This study initially offers an insight of K13-propeller and PfATPase6 polymorphisms on Bioko Island, EG. It suggests no widespread ART resistance or tolerance in the region, and might be helpful for developing and updating guidance for the use of ART-based combination therapies (ACTs).
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Affiliation(s)
- Jian Li
- Institute of Basic Medical Sciences, College of Basic Medicine, Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Jiangtao Chen
- Laboratory Medical Center, Huizhou Municipal Central Hospital, Huizhou 516001, People's Republic of China; The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou 510000, People's Republic of China
| | - Dongde Xie
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou 510000, People's Republic of China
| | - Urbano Monsuy Eyi
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo 999115, Equatorial Guinea
| | - Rocio Apicante Matesa
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo 999115, Equatorial Guinea
| | - Maximo Miko Ondo Obono
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo 999115, Equatorial Guinea
| | - Carlos Sala Ehapo
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo 999115, Equatorial Guinea
| | - Liye Yang
- Laboratory Medical Center, Chaozhou Central Hospital, Southern Medical University, Chaozhou 521021, People's Republic of China
| | - Huitian Yang
- Laboratory Medical Center, Chaozhou Central Hospital, Southern Medical University, Chaozhou 521021, People's Republic of China
| | - Min Lin
- Laboratory Medical Center, Chaozhou Central Hospital, Southern Medical University, Chaozhou 521021, People's Republic of China; Department of Histology and Embryology, Shantou University Medical College, Shantou 515000, Guangdong, People's Republic of China.
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LI Y. Establishment and Application of a Visual DNA Microarray for the Detection of Food-borne Pathogens. ANAL SCI 2016; 32:215-8. [DOI: 10.2116/analsci.32.215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yongjin LI
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, Huzhou University
- College of Life Science, Yangtze University
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Li J, Chen J, Xie D, Eyi UM, Matesa RA, Obono MMO, Ehapo CS, Yang L, Yang H, Lin M, Wu W, Wu K, Li S, Chen Z. Molecular mutation profile of Pfcrt and Pfmdr1 in Plasmodium falciparum isolates from Bioko Island, Equatorial Guinea. INFECTION GENETICS AND EVOLUTION 2015; 36:552-556. [PMID: 26325683 DOI: 10.1016/j.meegid.2015.08.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/11/2015] [Accepted: 08/27/2015] [Indexed: 01/03/2023]
Abstract
BACKGROUND Antimalarial drug resistance is a primary public health problem. Haplotypes of pfcrt and pfmdr1 gene have been implicated to be molecular markers of chloroquine (CQ) resistance. This study aims to explore mutation distribution of Pfcrt and Pfmdr1 in Bioko Island, Equatorial Guinea (EG). METHODS Blood samples were collected from different districts of Bioko. The single nucleotide polymorphisms in Pfcrt (codons 72 to 76) and Pfmdr1 (codons 86, 130, 184, 1034, 1042, 1109 and 1246) were assessed by nested PCR with DNA sequencing and haplotype prevalences were also determined. RESULTS Analysis of Pfcrt and Pfmdr1 mutations was successful in 151 and 157 samples respectively out of the 172 samples taken for this study. The mutations of Pfcrt and Pfmdr1 were found in 98.67% and 89.81% isolates, respectively. The Pfcrt 74-76, Pfmdr1 86, and Pfmdr1 184 were 92.05%, 50.32%, and 87.26% found mostly of mutation type, respectively. Three haplotypes coding 72-76 of Pfcrt were found including CVMNK, CVIET, and CVM/I N/E K/T, which accounted for 1.33%, 92.05%, and 6.62%, respectively. No mutation in Pfmdr1-N1 codon at 130 and Pfmdr1-N2 (S1034C, N1042D, V1109I, and D1246Y) was detected. The types coding 86 and 184 in Pfmdr1 were found including NY, YY, NF, YF, NY/F and YY/F, which accounted for 10.19%, 2.55%, 33.76%, 45.22%, 5.73% and 2.55%, respectively. CONCLUSION High prevalence of Pfcrt CVIET and Pfmdr1 86Y, 184F double mutations confirm high-level CQ resistance (CQR) and might suggest reduced susceptibility of Plasmodium falciparum isolates to AQ in Bioko, EG. It establishes fundamental data for detection of P. falciparum CQR with molecular markers and will promotes the surveillance level of drug resistance in Bioko, EG.
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Affiliation(s)
- Jian Li
- Department of Parasitology, College of Basic Medicine, Department of Infectious Diseases, Shiyan Renmin Hospital, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Jiangtao Chen
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou 510000, People's Republic of China
| | - Dongde Xie
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou 510000, People's Republic of China
| | - Urbano Monsuy Eyi
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo, Equatorial Guinea
| | - Rocio Apicante Matesa
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo, Equatorial Guinea
| | - Maximo Miko Ondo Obono
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo, Equatorial Guinea
| | - Carlos Sala Ehapo
- Central Blood Transfusion Service, Department of Medical Laboratory Science, Malabo Regional Hospital, Malabo, Equatorial Guinea
| | - Liye Yang
- Laboratory Medical Center, Chaozhou Central Hospital, Southern Medical University, Chaozhou 521021, People's Republic of China
| | - Huitian Yang
- Laboratory Medical Center, Chaozhou Central Hospital, Southern Medical University, Chaozhou 521021, People's Republic of China
| | - Min Lin
- Laboratory Medical Center, Chaozhou Central Hospital, Southern Medical University, Chaozhou 521021, People's Republic of China.
| | - Wanjun Wu
- Department of Parasitology, College of Basic Medicine, Department of Infectious Diseases, Shiyan Renmin Hospital, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Kai Wu
- Department of Schistosomiasis and Endemic Diseases, Wuhan City Center for Disease Control and Prevention, Wuhan 430015, People's Republic of China
| | - Shan Li
- Department of Parasitology, College of Basic Medicine, Department of Infectious Diseases, Shiyan Renmin Hospital, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Zongyun Chen
- Department of Parasitology, College of Basic Medicine, Department of Infectious Diseases, Shiyan Renmin Hospital, Hubei University of Medicine, Shiyan 442000, People's Republic of China
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Abdul-Ghani R, Al-Maktari MT, Al-Shibani LA, Allam AF. A better resolution for integrating methods for monitoring Plasmodium falciparum resistance to antimalarial drugs. Acta Trop 2014; 137:44-57. [PMID: 24801884 DOI: 10.1016/j.actatropica.2014.04.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/25/2014] [Accepted: 04/27/2014] [Indexed: 12/16/2022]
Abstract
Effective chemotherapy is the mainstay of malaria control. However, resistance of falciparum malaria to antimalarial drugs compromised the efforts to eliminate the disease and led to the resurgence of malaria epidemics. Three main approaches are used to monitor antimalarial drug efficacy and drug resistance; namely, in vivo trials, in vitro/ex vivo assays and molecular markers of drug resistance. Each approach has its implications of use as well as its advantages and drawbacks. Therefore, there is a need to use an integrated approach that would give the utmost effect to detect resistance as early as its emergence and to track it once spread. Such integration becomes increasingly needed in the era of artemisinin-based combination therapy as a forward action to deter resistance. The existence of regional and global networks for the standardization of methodology, provision of high quality reagents for the assessment of antimalarial drug resistance and dissemination of open-access data would help in approaching an integrated resistance surveillance system on a global scale.
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Boubaker G, Macchiaroli N, Prada L, Cucher MA, Rosenzvit MC, Ziadinov I, Deplazes P, Saarma U, Babba H, Gottstein B, Spiliotis M. A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex. PLoS Negl Trop Dis 2013; 7:e2017. [PMID: 23350011 PMCID: PMC3547860 DOI: 10.1371/journal.pntd.0002017] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 12/04/2012] [Indexed: 12/29/2022] Open
Abstract
Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1–G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1–G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6–G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%). Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus. The dog tapeworm Echinococcus granulosus (E. granulosus) is a cosmopolitan parasite. The adult worms reside in the small intestine of their definitive hosts (dogs). Infective eggs are shed with the feces into the environment and are orally ingested by intermediate hosts where they develop into the metacestode (larval) stage, causing cystic echinococcosis (CE) in humans and livestock. Ten intraspecific genotypes of E. granulosus (G1 to G10) have been reported from different intermediate host species. Based on the recently established molecular phylogeny, E. granulosus is now considered a complex consisting of four species: E. granulosus sensu stricto (G1/G2/G3), E. equinus (G4), E. ortleppi (G5) and E. canadensis (G6–G10). Simple and highly discriminative molecular epidemiological approaches are needed to explore dynamics, life cycle patterns, and the pathogenicity of the members of this complex. We here introduce a one-step multiplex PCR (mPCR) protocol for the genotyping and discrimination of the different members of the E. granulosus complex, allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex, and (iii) genetic variants within the E. granulosus complex. The relatively complicated task of E. granulosus complex speciation and genotyping is clearly simplified by mPCR, and this technique therefore represents a useful tool for routine practice.
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Affiliation(s)
- Ghalia Boubaker
- Institute of Parasitology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- University of Monastir, Faculty of Pharmacy, Department of Clinical Biology B, Laboratory of Parasitology and Mycology, Monastir, Tunisia
| | - Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, Buenos Aires, Argentina
| | - Laura Prada
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, Buenos Aires, Argentina
| | - Marcela A. Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, Buenos Aires, Argentina
| | - Mara C. Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, Buenos Aires, Argentina
| | - Iskender Ziadinov
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Peter Deplazes
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Hamouda Babba
- University of Monastir, Faculty of Pharmacy, Department of Clinical Biology B, Laboratory of Parasitology and Mycology, Monastir, Tunisia
| | - Bruno Gottstein
- Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Markus Spiliotis
- Institute of Parasitology, University of Bern, Bern, Switzerland
- * E-mail:
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Cai H, Hong C, Gu J, Lilburn TG, Kuang R, Wang Y. Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. BMC SYSTEMS BIOLOGY 2012; 6 Suppl 3:S5. [PMID: 23282319 PMCID: PMC3524314 DOI: 10.1186/1752-0509-6-s3-s5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background Malaria causes over one million deaths annually, posing an enormous health and economic burden in endemic regions. The completion of genome sequencing of the causative agents, a group of parasites in the genus Plasmodium, revealed potential drug and vaccine candidates. However, genomics-driven target discovery has been significantly hampered by our limited knowledge of the cellular networks associated with parasite development and pathogenesis. In this paper, we propose an approach based on aligning neighborhood PPI subnetworks across species to identify network components in the malaria parasite P. falciparum. Results Instead of only relying on sequence similarities to detect functional orthologs, our approach measures the conservation between the neighborhood subnetworks in protein-protein interaction (PPI) networks in two species, P. falciparum and E. coli. 1,082 P. falciparum proteins were predicted as functional orthologs of known transcriptional regulators in the E. coli network, including general transcriptional regulators, parasite-specific transcriptional regulators in the ApiAP2 protein family, and other potential regulatory proteins. They are implicated in a variety of cellular processes involving chromatin remodeling, genome integrity, secretion, invasion, protein processing, and metabolism. Conclusions In this proof-of-concept study, we demonstrate that a subnetwork alignment approach can reveal previously uncharacterized members of the subnetworks, which opens new opportunities to identify potential therapeutic targets and provide new insights into parasite biology, pathogenesis and virulence. This approach can be extended to other systems, especially those with poor genome annotation and a paucity of knowledge about cellular networks.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Dong Y, Sheng H, Zeng X, Yan J, Li H, Xiao H, Li X, Yang S. Investigation of Genetic Diversity of theblaSHVGene and Development of an Oligonucleotide Microarray to Detect Mutations in theblaSHVGene. Microb Drug Resist 2012; 18:539-45. [DOI: 10.1089/mdr.2012.0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yuanyuan Dong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Haihui Sheng
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Xainting Zeng
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Jufen Yan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Haiyan Li
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, China
| | - Huasheng Xiao
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Xiaokun Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, China
| | - Shulin Yang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
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Cai H, Zhou Z, Gu J, Wang Y. Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium.. Curr Bioinform 2012; 7. [PMID: 24298232 DOI: 10.2174/157489312803900965] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quantum leap in our understanding of the fundamental processes of the parasite life cycle and mechanisms of drug resistance and immune evasion.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Molecular Approaches for Diagnosis of Malaria and Characterization of Genetic Markers of Drug Resistance. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Since 1977, >2000 research papers described attempts to detect, identify and/or quantify parasites, or disease organisms carried by ecto-parasites, using DNA-based tests and 148 reviews of the topic were published. Despite this, only a few DNA-based tests for parasitic diseases are routinely available, and most of these are optional tests used occasionally in disease diagnosis. Malaria, trypanosomiasis, toxoplasmosis, leishmaniasis and cryptosporidiosis diagnosis may be assisted by DNA-based testing in some countries, but there are very few cases where the detection of veterinary parasites is assisted by DNA-based tests. The diagnoses of some bacterial (e.g. lyme disease) and viral diseases (e.g. tick borne encephalitis) which are transmitted by ecto-parasites more commonly use DNA-based tests, and research developing tests for these species makes up almost 20% of the literature. Other important uses of DNA-based tests are for epidemiological and risk assessment, quality control for food and water, forensic diagnosis and in parasite biology research. Some DNA-based tests for water-borne parasites, including Cryptosporidium and Giardia, are used in routine checks of water treatment, but forensic and food-testing applications have not been adopted in routine practice. Biological research, including epidemiological research, makes the widest use of DNA-based diagnostics, delivering enhanced understanding of parasites and guidelines for managing parasitic diseases. Despite the limited uptake of DNA-based tests to date, there is little doubt that they offer great potential to not only detect, identify and quantify parasites, but also to provide further information important for the implementation of parasite control strategies. For example, variant sequences within species of parasites and other organisms can be differentiated by tests in a manner similar to genetic testing in medicine or livestock breeding. If an association between DNA sequence and phenotype has been demonstrated, then qualities such as drug resistance, strain divergence, virulence, and origin of isolates could be inferred by DNA-based tests. No such tests are in clinical or commercial use in parasitology and few tests are available for other organisms. Why have DNA-based tests not had a bigger impact in veterinary and human medicine? To explore this question, technological, biological, economic and sociological factors must be considered. Additionally, a realistic expectation of research progress is needed. DNA-based tests could enhance parasite management in many ways, but patience, persistence and dedication will be needed to achieve this goal.
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Abstract
PURPOSE OF REVIEW The purpose of this article is to review the molecular methods commonly used in medical microbiology as well as to update the clinician as to newer molecular technologies that show promise in the identification of microorganisms as well as evaluation of the presence of virulence factors and antibiotic resistance determinants. RECENT FINDINGS Numerous molecular assays have been developed recently using a variety of technologies. Direct hybridization techniques have allowed analysis of blood culture bottles for organisms such as methicillin-resistant Staphylococcus aureus. Target amplification methods allow postamplification analysis using a variety of technologies depending on the clinical needs for the assay. Postamplification analysis includes methods such as Sanger sequencing, pyrosequencing, reverse hybridization, and Luminex analysis, which are becoming more widely utilized. In the future, whole genome sequencing, mass spectrometry, and microarray analysis may provide a wealth of information that can be used to specifically tailor the treatment of infectious diseases. SUMMARY The implications of current trends in molecular infectious diseases are moving towards high-throughput, simple, array-type technologies that will provide a wealth of data regarding types of organisms present in a sample and the virulence factors/resistance determinants that influence the severity of disease. As a result of these developments, infectious diseases will be more accurately and effectively treated.
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