Table 1.

Tools for drug resistance assessment and parasite diversity monitoring

Tools	Capacity	Resources required	Advantages	Disadvantages
Drug resistance
Ex vivo/in vitro tests	Few samples	BSL2 for parasite culture, refrigerator, freezer, microscope, incubator	Several tests possible on same sample, no heavy equipment	Labor-intensive, expensive, generalization difficult due to different tests/methods, requires advance culture infrastructure
RSA/PSA
TES	Hundreds	Refrigerator, freezer, microscope, incubator, PCR machine, gel electrophoresis, transilluminator	No heavy equipment required	Expensive
Molecular markers	Hundreds	PCR machine, Restriction enzymes, refrigerator, freezer,	Ease of sampling, storage and transport	Markers not always linked to clinical outcome, require good infrastructure and trained personnel
Parasite diversity monitoring
msp/glurp typing	Hundreds	PCR machine, Gel electrophoresis, transilluminator	Simple to implement	Labour-intensive, subjective interpretation
DNA barcodes	Thousands	Real time PCR	Sensitive, robust	Requires relatively sophisticated TaqMan or HRM assay
Microsatellite typing	Thousands	Real time PCR	Very informative from large range of alleles per locus	Requires relatively sophisticated PCR. Lack of standardization in scoring alleles
TDS	Hundreds	Sequencer, Server capacity for data storage	Less subject to inherent bias	High cost, requires large data storage capacity, requires skilled personnel. Target ascertainment bias
Genome wide analysis	Hundreds	Sequencers, Server capacity for data storage	Access to whole genome variants including single nucleotide and structural polymorphisms	As for TDS but need for target DNA enrichment against human DNA, difficulty in constructing haplotypes, and low sensitivity to detect minority clones

BSL2 biosafety level 2, RSA ring stage assay, TES therapeutic efficacy studies, TDS targeted deep sequencing