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Defence Health

Army Malaria Institute

Department of Drug Resistance Diagnostics

Culicine mosquito


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.

In collaboration with MERLIN, the department has performed molecular analysis on parasite diversity and allelic types for a chloroquine and Fansidar trial in East Timor, providing information on malaria transmission in the area and more accurate efficacy data by distinguishing new infections from recrudescences.

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.


  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



  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.


  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


  • Alyson Auliff: Australian American Fulbright Queensland Scholar 2009 – 2010
  • Alyson Auliff: Chief of Army Scholarship 2009-2010
  • Alyson Auliff: Gregory Schwartz Enrichment Grant – Australian American Fulbright Commission 2009
  • Alyson Auliff: Vivax Malaria Research III: 2009 and Beyond conference travel scholarship, Panama City, Panama, 2009
  • Joanne Baker: Conference Travel Award, 58th Annual Meeting of the American Society of Tropical Medicine and Hygiene, Washington, 2009
  • Joanne Baker: Young Investigator Award, 58th Annual Meeting of the American Society of Tropical Medicine and Hygiene, Washington, 2009


(Current and past staff names in bold)


Joanne Baker, Michelle L Gatton, Jennifer Peters, Mei-Fong Ho,  James McCarthy and Qin Cheng. Transcription and Expression of Plasmodium falciparum Histidine-Rich Proteins in Different Stages and Strains: Implications for the Performance of Rapid Diagnostic Tests. PLoS One, 2011: manuscript in review.

Codd A, Teuscher F, Kyle D, Cheng Q, Gatton M. Artemisinin-induced parasite dormancy: a plausible mechanism for treatment failure. Malar J. 2011; 10:56.

Alyson M Auliff, Bharath Balu, Michael T O’Neil, Qin Cheng, John H Adams. Stable integration of Plasmodium vivax dihydrofolate reductase-thymidylate synthase Gene using the piggyBac transposon. 2011: manuscript in preparation.

Fukuda MM, Klein TA, Kochel T, Quandelacy TM, Smith BL, Villinski J, Bethell D, Tyner S, Se Y, Lon C, Saunders D, Johnson J, Wagar E, Walsh D, Kasper M, Sanchez1 JL, Witt CJ, Cheng Q, Waters N, Shrestha SK, Pavlin JA, Lescano AG, Graf PCF, Richardson JH, Durand S, Rogers WO, Blazes DL, Russell KL, the AFHSC-GEIS Malaria and Vector Borne Infections Writing Group. Malaria and other vector-borne infection surveillance in the U.S. Department of Defense Armed Forces Health Surveillance Center-Global Emerging Infections Surveillance program: review of 2009 accomplishments. BMC Public Health, 2011; 11(Suppl 2):S9.


Teuscher F, Gatton M, Chen N, Peters J, Kyle D, Cheng Q. Artemisinin induced dormancy in Plasmodium falciparum: Duration, recovery rates and implications in treatment failure. J Inf Dis, 2010; 202: 1362-1368.

Baker J, Ho MF, Pelecanos A, Gatton M, Chen N, Abdullah S, Albertini A, Ariey F, Barnwell J, Bell D, Cunningham J, Djalle D, Echeverry DF, Gamboa D, Hii J, Kyaw MP, Luchavez J, Membi C, Menard D, Murillo C, Nhem S, Ogutu B, Onyor P, Oyibo W, Wang SQ, McCarthy J, Cheng Q. Global sequence variation in the histidine-rich proteins 2 and 3 of Plasmodium falciparum: implications for the performance of rapid diagnostic tests. Malar J, 2010; 9:129.

Alyson M Auliff, John H Adams, Michael T O’Neil, Qin Cheng. Defining the role of mutations in Plasmodium vivax dihydrofolate reductase-thymidylate synthase Gene using an episomal Plasmodium falciparum transfection system. Antimicrob. Agents Chemother. 2010; 54(9):3927-32.

Nasveld PE, Edstein MD, Reid M, Brennan L, Harris IE, Kitchener SJ, Leggat PA, Pickford P, Kerr C, Orht C, Prescott W, Tafenoquine Study Team. Randomised, double-blind study of the safety, tolerability, and efficacy of tafenoquine versus mefloquine for malaria prophylaxis in nonimmune subjects. Antimicrob Agents Chemother. 2010; 54(2):792-8.

Chavchich M, Gerena L, Peters J, Chen N, Cheng Q, Kyle DE. Induction of resistance to artemisinin derivatives in Plasmodium falciparum: role of pfmdr1 amplification and expression. Antimicrob Agent Chemother, 2010; 54:2455-2464.

Chen N, Chavchich M, Peters JM, Kyle DE, Gatton ML, Cheng, Q. De-amplification of pfmdr1-containing amplicon on chromosome 5 in Plasmodium falciparum is associated with reduced resistance to artelinic acid in vitro. Antimicrob Agent Chemother, 2010; 54:3395-3401.

Gamboa D, Ho MF, Bendezu J, Torres K, Chiodini PL, Barnwell JW,  Incardona S, Perkins M, Bell D,  McCarthy J, Cheng, Q. A large proportion of Plasmodium falciparum isolates in the Amazon region of Peru lack pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test (RDT) performance in the region. PLoS One, 2010; 5(1):e8091.

Figtree M, Lee R, Bain L, Kennedy B, Mackertich S, Urban M, Cheng Q, Hudson BJ, Plasmodium knowlesi acquired in Indonesian Borneo. Emerg Infect Dis, 2010; 16(4):672-674. 

Taleo GA, Bobogare A, A Auliff, L Bain, L Boaz, Q Cheng,  A Clements, A Ebringer, MD Edstein, N Elmes, S Forsyth, K Gray, I Harris, H Iata, Jennifer Iavro, K Lilley, H Reid, WW Sharrock, A Vallely, NC Waters, S Yama, GD Shanks. Pacific Malaria Initiative Survey Group (PMISG) on behalf of the Ministries of Health of Vanuatu and Solomon Islands. Malaria on Isolated Melanesian Islands Prior to the Initiation of Malaria Elimination Activities. Malar J, 2010; 9:218.

Harris I, Sharrock W, Bain L, Gray K, Bobogare A, Boaz L, Lilley K, Krause D, Vallely A, Gatton M, Cheng Q. A large proportion of asymptomatic malaria infections with low and sub-microscopic parasite densities in Temotu province, Solomon Islands: challenges for malaria diagnostics in an elimination setting.  Malar J, 2010; 9:254.

Gatton ML, Cheng Q. Interrupting Malaria Transmission: Quantifying the Impact of Interventions in Regions of Low to Moderate Transmission.  PLoS One, 2010; 5(12):e15149.

McGowan S, Porter C, Lowther J, Stack C, Golding S, Skinner-Adams T, Trenholme K,  Teuscher F, Donnelly S, Grembecka J, Mucha A, Kafarski P, DeGori R, Buckle A, Gardiner D, Whisstock J, Dalton J. Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase: a new route for antimalarial compounds. PNA , 2009; 106 (8): 2537-2542.

Alyson M Auliff, John H Adams, Michael T O’Neil, Qin Cheng. Investigation of genetic mutations in Plasmodium vivax dihdrofolate reductase and susceptibility to conventional and new antifolates antimalarials using a Plasmodium falciparum expression system. Am J Trop Med Hyg, 2009; 81 (5): supp 1.

Upcroft JA, Kraue, KG, Burgess AG, Dunn LA, Chen N, Upcroft P. Sequence map of the 3-Mb Giardia duodenalis assemblage A chromosome. Chromosome Res, 2009; 17:1001-1014.

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.

Gatton, ML. and Cheng Q.  (2008) Therapeutic efficacy of anti-malarials: parasite diversity, PCR-genotyping and statistics Trends Parasitol.  24(2):68-73.

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.

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.

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.

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 P. vivax. J Infect Dis, 2008; 198 (10): 1558-64.

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.


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.

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.

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.

Baker J, McCarthy J, Gatton M, Lee N, Bell D, Peters J, Cheng Q. Rapid Diagnostic Tests for malaria: are they sufficiently reliable? Journal of the Australian Defence Health Service, 2007; 8: 12-17.

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.

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.


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.

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.

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.

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.

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.

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.

21 September, 2011