Army Malaria Institute -
Department of Drug Resistance Diagnostics

Mission

To improve our knowledge in the development, survival and spread of drug resistance in malaria parasites and to monitor the extent of drug resistance and efficacy of standard and new antimalaral drugs in areas of interest to ADF. The department explores and evaluates novel malaria detection/diagnosis methods including molecular and various rapid diagnostic kits. The department is engaged in studies investigating P. vivax genetics that determine or correlate with relapses of infections.

Current Research Projects

1. Mechanisms of resistance to standard and newly developed antimalarial drugs:

• Chloroquine resistance in P. falciparum: mutations in P. falciparum chloroquine resistant transporter (Pfcrt) and their roles in conferring chloroquine resistance
• Chloroquine resistance in P. vivax: searching for molecular correlates for chloroquine resistance in P. vivax and its correlation with in vivo and in vitro susceptibility to chloroquine (in collaboration with Menzies School of Health Research)
• Atovaquone resistance in P. falciparum: established that genetic mutations resulted from atovaquone selection are located in the drug binding site in cytochrome b and correlate with resistance to atovaquone. The implications of these mutations in resistance to Malarone are under investigation.
• Sulfa resistance in P. vivax: Using molecular biology methods and molecular modelling, we established that mechanism of innate resistance to sulfa drugs in P. vivax is determined by a single amino acid in the drug binding site in pvDHPS. P. vivax can also acquire resistance to sulfa drugs by changing several other amino acids at the drug binding site. Further investigations are under way to examine the effect of these mutations in P. falciparum systems and to test a variety of sulfa drugs on PvDHPS in this system.
• Antifolate resistance in P. vivax. Investigations of genetic mutations in P.vivax DHFR and DHPS and their impact on the susceptibilities to conventional and new antimalarial antifolate drugs are underway using the state of art transfaction technology.
• Artemisinin resistance: Investigating the development of parasites following exposures to artemisinin derivatives and possible linkage with treatment failures (in collaboration with University of South Florida, USA).
• Primaquine tolerance in P. vivax: genetic analysis on parasites breaking through primaquine radical cure.

2. Molecular evaluation of antimalarial drugs and drug combinations trailing in various settings.

3. Evolution of drug resistance

• Monitor chloroquine resistance and investigate the evolution of chloroquine resistance in Asia-Pacific Region and other regions of interest (in collaboration with WRAIR , JIPD and HPITD China).

• Monitor the extent of sulfadoxine and pyrimethamine (SP) resistance in P. vivax: investigate mutations in P. vivax DHFR and DHPS in parasites collected from Asia, South-East Asia and Pacific regions and their association with in vitro susceptibility to SP.

• Role of antigenic variation in the development, survival and spread of drug resistance (NIH funded project): Investigating antigenic switch rates and switch processes in P. falciparum, and the influence of antigenic variation on the development, survival and spread of drug resistance by using molecular biology methods and mathematical modelling.

4. P. vivax genetics and relapses

Despite the use of radical cure regimens, post operational relapses of P. vivax infections in ADF personnel have become a major health problem. Studies in parasite genetics are under way to investigate factors that associated with increased risk of relapses.

5. Improve rapid malaria diagnostic tests.

Many rapid diagnostic tests (RDTs) for P. falciparum have been developed and are commercially available. Most of these RDTs are based on detecting parasite antigens in patient's blood. The detection sensitivity of these kits is highly variable. In collaboration with WPRO/WHO and FIND we are investigating the possible causes of the sensitivity variation. Our research focus on defining genetic diversity in parasite antigens, difference in the level of antigens produced by parasites and the variation in epitopes recognised by monoclonal antibodies. The study outcome will help the selection and quality control of RDTs, as well as help to improve the detection sensitivity of malaria RDTs .

6. Molecular Diagnosis

For assisting microscopic confirmation of malaria infections, we have established PCR-based detection for 4 human malaria species. We will continue to improve out capacity to perform multiplex PCR and develop field adaptable PCR methods. Currently, the department is actively involved in the AusAID Pacific Malaria Initiatives. We are investigating the prevalence of the malaria infections and the transmission parameters in Vanuatu and Solomon Islands using molecular tools.

Training

1. Postgraduates: Hons, Masters and PhD;
2. Short term training for scientists from developing countries: Molecular- based techniques: PCR, genotyping, and resistance mutation detections;
3. Microscopic confirmation of malaria infections for ADF

Collaborators

Australian

1. Malaria Drug Resistance and Chemotherapy, Clinical Tropical Medicine, and Malaria Biology, Queensland Institute of Medical Research
2. School of Population Health, the University of Queensland.
3. Tropical Medicine and International Health Unit, Menzies School of Health Research, Darwin.

International

1. WPRO/WHO/FIND
2. National Institutes of Health
3. Department of Global Health, University of South Florida, Tampa, USA
4. Division of Experimental Therapeutics, Walter Reed Army Institute of Research, USA.
5. Research Institute for Tropical Medicine, Manila, Philippines
6. Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
7. Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
8. Genome Sciences, University of Washington, Seattle, WA, USA.
9. Malaria Department, Jiangsu Institute for Parasitic Diseases, China
10. Hainan Provincial Institute for Tropical Diseases, Hainan CDC, China
11. Malaria Department, Henan CDC, Zhengzhou, China
12. National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia

External Grants

• NIH, RO1, 2000-2003; 2004-2007; 2005-2009
• WPRO/WHO, 2004-2005, 2005 - 2007
• WHO/ FIND, 2007- 2008
• TDR/WHO, 2002-2004

Awards

Peters J. Second prize for best publications at QIMR for 2002
Peters, J., Fowler, E., Gatton, M., Chen, N., Saul, A. and Cheng, Q. (2002) High diversity and rapid changeover of expressed var genes during acute phase of Plasmodium falciparum infections in human volunteers. Proc. Nat. Acad. Sci. USA. 99(16):10689-10694.
Qin Cheng, Suncorp 2007 Queenslander of the year Finalist, June 2007.

Publications

(Current and past staff names in bold)

1. Chen, N. and Cheng, Q. (1999) Codon usage in Plasmodium vivax nuclear genes. International Journal for parasitology 29,445-449.
2. Lawrance, G., Cheng, Q., Reed, C., Taylor, D., Stowers, A., Cloonan, N., C., Smillie, A., Anderson, K., Pombo, D., Allworth, A., Eisen, D., Anders, R. and Saul, A. (2000) Efficacy trial in human volunteers of 3 recombinant asexual stage malaria antigens. Vaccine 18(18):1925-1931.
3. Figtree M., Pasay C.J., Slade R., Cheng Q., Cloonan N., Walker J. and Saul A. (2000) Plasmodium vivax synonymus substitution frequencies, evolution and population structure deduced from diversity in AMA 1 and MSP 1. Mol. Biochem. Parasitol. 108:53-66.
4. Korsinczky M., Chen N., Kotecka B., Saul A., Rieckmann K. and Cheng Q. (2000) Mutations in Plasmodium falciparum cytochrome b that are associated with atovaquone resistance are located in a putative drug-binding site. Antimicrob. Agent Chemocher. 44(8):2100-2108.
5. Taylor D, Cloonan N, Mann V, Cheng Q and Saul A. (2000). Sequence diversity in rodent malaria of the Pfs28 ookinete surface antigen homologs. Mol. Biochem. Parasitol. 110(2):429-434.
6. Yuesheng, L., Auliff, A., Jones, M.K. & McManus, D.P. (2000). Immunogeneicity and immunolocalisation of the 22.6-kDa antigen of Schistosoma japonicum. Parasite Immunology. 22 pp 415-
7. Kitchener, S.J., Auliff, A. M. & Rieckmann K.H. (2000). Malarai in the Australian Defence Force during and after participation in the International Force in East Timor (INTERFET). The Medical Journal of Australia. 173. pp 583-585.
8. Cloonan, N., Fischer, K., Cheng, Q. and Saul, A (2001). Aldolase genes of Plasmodium species. Mol. Biochem Parasitol. 113(2): 327-330.
9. Chen, N., Russel, B., Staley, J., Kotecka, B., Nasveld, P. and Cheng, Q. (2001) Sequence polymorphisms in pfcrt are strongly associated with chloroquine resistance in Plasmodium falciparum. J. Infect. Dis. 183(10):1543-1545.
10. Frances, S.P., Cooper, R.D., Chen, N and Cheng, Q. (2001) Surveillance of potential arbovirus vectors at Shoal Water Bay military training area, Queensland. Arbovirus Research in Australia 8:160-163.
11. Fowler, E., Peters, J., Gatton, M., Chen, N. and Cheng, Q. (2002) Genetic diversity of the DBLa region in Plasmodium falciparum var genes among Asia-Pacific isolates. Mol Biochem Parasitol 120(1):117-126.
12. Chen, N., Russel, B., Fowler, E., Peters, J. and Cheng, Q. (2002) Levels of chloroquine resistance in Plasmodium falciparum are determined by loci apart from Pfcrt and Pfmdr1. J. Infect. Dis. 185 (3):405-406.
13. Gatton, M.L.and Cheng, Q. (2002) Evaluation of the pyrogenic threshold for P. falciparum malaria in naïve individuals. Am. J. Trop. Med. Hyg. 66(5):467-473.
14. Rieckmann, K. and Cheng, Q (2002) Pyrimethamin-sulfadoxine resistance in Plasmodium falciparum must be delayed in Africa. Trends in Parasitology. 18(7):293-294.
15. Peters, J., Chen, N., Gatton, M., Korsinczky, M., Fowler, E., Manzetti, S., Saul, A. and Cheng. Q. (2002) Mutations in cytochrome b resulting atovaquone resistance are associated with a loss of fitness in Plasmodium falciparum. Antimicrobial Agents and Chemotherapy 46(8):2435-2441.
16. Peters, J., Fowler, E., Gatton, M., Chen, N., Saul, A. and Cheng, Q. (2002) High diversity and rapid changeover of expressed var genes during acute phase of Plasmodium falciparum infections in human volunteers. Proc. Nat. Acad. Sci. USA. 99(16):10689-10694.
17. Chen, N., Baker, J., Ezard, N., Burns, M., Edstein, M. and Cheng, Q. (2002) Molecular evaluation of the efficacy of chloroquine treatment of uncomplicated Plasmodium falciparum in East Timor. Am. J. Trop. Med. Hyg. 67(1):64-66.
18. Tjitra, E., Baker, J., Cheng, Q and Anstey, N. (2002) The therapeutic efficacy of artesunate plus sulfadoxine-pyrimethamine and chloroquine plus sulfadoxine-pyrimethamine for vivax malaria: relationship with Plasmodium vivax dhfr mutations. Antimicrobial Agents and Chemotherapy 46(12):3947-3953.
19. Bragonier R, Reyburn H, Nasveld P, Edstein M, Auliffe A. (2002). Rainy-season prevalence of malaria in Bobonaro district, East Timor. Ann Trop Med Parasitol 96: 739-43.
20. Bragonier R., Nasveld P. & Auliff A. (2002) Plasmodium malariae in East Timor. Southeast Asian Journal of Tropical Medicine and Public Health. 33. pp 689-90.
21. Gatton, M.L., Peters, J., Fowler, E. and Cheng, Q. (2003) The switching rates of Plasmodium falciparum var genes: faster than we thought? Trends in Parasitology 19(5):202-208.
22. Ezard, N., Burns, M, Lynch, C., Cheng, Q. and Edstein, M. (2003) Efficacy of chloroquine in the treatment of uncomplicated Plasmodium falciparum infection in East Timor, 2000. Acta Trop 88(1):87-90.
23. Chen, N., Kyle, D.E., Pasay, C.M. Fowler, E.V., Peters, J. M. and Cheng, Q. (2003) Pfcrt allelic types with novel amino acid mutations in chloroquine resistant Plasmodium falciparum from the Philippines. Antimicrobial Agents and Chemotherapy 47(11):3500-3505.
24. Frances SP, Cooper RD, Auliff AM, Edstein MD. (2003) Survey of Personal Protection Measures against Mosquitoes among Australian Defence Force personnel deployed to East Timor. Mil Med 168: 227-30.
25. Gatton, M. L. and Cheng. Q. (2004) Investigating parasite-host interactions in Plasmodium falciparum infections in naïve hosts using a simulation model. Parasitololgy (in press).
26. Frances, S.P., Cooper, R.D., Rowcliffe, K.L., Chen, N. and Cheng, Q. (2004) Occurrence of Ross River virus and Barmah Forest Virus in mosquitoes at Shoalwater Bay Military Training Area, Queensland, Australia. J Med Ento 41(1):115-120.
27. Korsinczky, M., Fisher, K., Chen, N., Rieckmann and Cheng, Q. (2004) Sulfadoxine resistance in Plasmodium vivax is associated with a DHPS sequence polymorphism altering the putative drug-binding site. Antimicrobial Agents and Chemotherapy 48(6):2214-2222.
28. Gatton, M.L., Martin, L.B. & Cheng, Q.(2004) The Evolution of Resistance to Sulfadoxine / Pyrimethamine in Plasmodium falciparum parasites. Antimicrob. Agent. Chemother 48 (6):2116-2123.
29. Gatton, M.L. and Cheng, Q (2004) Modelling the development of acquired clinical immunity to Plasmodium falciparum. Infection and Immunity 72(11),6538-6545.
30. Boutlis,C.S., Weinberg,J.B., Baker, J., Bockarie, M.J., Mgone, C.S., Cheng, Q. and Anstey, N.M. (2004) Nitric oxide production and nitric oxide synthase activity in malaria-exposed Papua New Guinean children and adults shows longitudinal stability and no association with parasitemia.  Infection and Immunity 72(12): 6932-6938.
31. Chen, N., Wilson, D., Pasay, C.M., Bell, D., Martin, L., Kyle, D. and Cheng, Q.  (2005) The origin and dissemination of novel mutant Pfcrt allelic Types of Plasmodium falciparum in the Philippines.  Antimicrob. Agent. Chemother 49(5): 2102-2105.
32. Baker, J., McCarthy, J., Gatton, M.L., Kyle, D., Belizario, V., Luchavez, J., Bell D and Cheng, Q.  (2005) Genetic Diversity of Plasmodium falciparum Histidine-Rich Protein 2 and Its Effect on the Performance of PfHRP2-Based Rapid Diagnostic Tests.  J. Infect. Dis.  192:870-877.
33. Gatton, M.L., Peters, J.M, Gresty, K., Fowler, E.V., Chen, N. & Cheng Q. (2006) Detection sensitivity and quantitation of Plasmodium falciparum var gene transcripts by real-time RT-PCR in comparison with conventional RT-PCR.  Am. J. Trop. Med. Hyg. 75(2):212-218.
34. Fowler, E.V., Chavchich, M., Chen, N., Peters, J.M., Kyle, D., Gatton, M.L and Cheng, Q. (2006)  Physical linkage to drug resistance genes results in conservation of var genes among West Pacific Plasmodium falciparum isolates.   J. Infect. Dis. 194:939-948.
35. Gatton, M.L and Cheng, Q. (2006) Plasmodium falciparum infection dynamics and transmission potential following treatment with sulfadoxine-pyrimethamine.  J. Antimicrob. Agent. Chemother. 58(1):47-51.
36. Lee, N., Baker, J., Andrews, K., Gatton, M., Bell, D., Cheng, Q. and McCarthy, J.  (2006) The effect of sequence variation in Plasmodium falciparum Histidine-Rich Protein 2 on the binding of specific monoclonal antibodies: implications for Rapid Diagnostic Tests for malaria. J. Clin. Microb 44(8):2773-2778.
37. Auliff, A., Wilson, D., Russell, B., Gao, Q., Chen, N., Anh, L.N., Maguire, J., O'Neil, M. and Cheng, Q. (2006)  Amno acid mutations in Plasmodium vivax DHFR and DHPS from several geographical rerions and susceptibility to antifolate drugs.   Am. J. Trop. Med. Hyg 75(4): 617-621.
38. Lee, N., Baker, J., Bell, D., McCarthy, J. and Cheng, Q.  (2006) Assessing the genetic diversity of Plasmodium falciparum and Plasmodium vivax aldolases and its potential effect on the performance of Aldolase-based Rapid Diagnostic Tests (RDTs). J Clin Microb 44(12):4547-4549.
39. Jennifer M. Peters, Elizabeth V. Fowler, Darren Krause, Qin Cheng, Michelle L. Gatton (2007) Differential changes in Plasmodium falciparum var transcription during adaptation to culture.  J. Infect. Dis. 195:748-755.
40. Chen, N., Auliff, A., Rieckmann, K., Gatton, L.M. and Cheng, Q.  (2007)  Relapses of Plasmodium vivax infection result from clonal hypnozoites activated at predetermined intervals. J. Infect. Dis.  195(7):934-941.
41. O’Neil, M.T., Korsinczky, M.L.J, Gresty, K., Auliff, A. and Cheng Q. (2007) A P. falciparum heterologous expression system for the assessment of antifolate resistance caused by mutant P. vivax dihydrofolate reductase-thymidylate synthase. J. Infect. Dis. 196:467-474.
42. Baker, J., McCarthy, J., Gatton, M., Lee, N., Bell, D., Peters, J., Cheng, Q. (2007) Rapid diagnostic tests for malaria: are they sufficiently reliable?  ADF Health 8:12-17.
43. Suwanarusk R, Russell B, Chavchich M, Chalfein F, Kenangalem E, Kosaisavee V,  Prasetyorini B, Piera KA, Barends M, Brockman A, Lek-Uthai U, Anstey NM, Tjitra, E, Nosten F, Cheng Q, Price RN.  Chloroquine resistant Plasmodium vivax: in vitro characterisation and association with molecular polymorphisms. PLoS ONE. 2007 Oct 31;2(10):e1089.
44. Krause, D., Gatton, M.L., Frankland, S., Eisen, D.P., Good, M.F. Lilley, L. and Cheng, Q. (2007) Characterisation of the antibody response against Plasmodium falciparum erythrocyte membrane protein-1 in human volunteers.  Infect. Immun. 75(12): 5967-5973.
45. Chen N, Gao Q, Wang SQ, Wang GZ, Gatton M and Cheng Q. (2008) No genetic bottle-neck in Plasmodium falciparum wild type pfcrt alleles re-emerging in Hainan Island, China following high-level Chloroquine resistance.  Antimicrob. Agent. Chemother 52(1): 345-347.
46. Gatton, ML. and Cheng Q.  (2008) Therapeutic efficacy of anti-malarials: parasite diversity, PCR-genotyping and statistics.  Trends Parasitol.  24(2):68-73.
47. Russell B, Chalfien F, Prasetyorini B, Kenangalem E, Piera K, Suwanarusk R, Brockman A, Prayoga, Sugiarto P, Cheng Q, Tjitra E,  Anstey NM, Price RN  (2008) Determinates of in vitro drug susceptibility testing of Plasmodium vivax.  Antimicrob. Agent. Chemother  52(3): 1040-1045.
48. Appleyard B, Tuni M, Cheng Q, Chen N, Bryan J, McCarthy JS.  Malaria in pregnancy in the Solomon islands: barriers to prevention and control. Am J Trop Med Hyg. 2008 Mar;78(3):449-54.
49. Hawkins VN, Auliff A, Prajapati SK, Rungsihirunrat K, Hapuarachchi HC, Maestre A, O'Neil MT, Cheng Q, Joshi H, Na-Bangchang K, Sibley CH.  Multiple origins of resistance-conferring mutations in Plasmodium vivax dihydrofolate reductase. Malar J. 2008 Apr 28;7:72.
50. Suwanarusk R, Chavchich M, Russell B, Jaidee A, Chalfein F, Barends M, Prasetyorini B, Kenangalem E, Piera KA, Lek-Uthai U, Anstey NM, Tjitra E, Nosten F, Cheng Q, Price RN.  Amplification of pvmdr1 Associated with Multidrug-Resistant Plasmodium vivax. J Infect Dis. 2008 Sep 22.
51. Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM.  Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 2008 Oct 9;455(7214):757-63.

     

13 October, 2008