Table 1 Tools for drug resistance assessment and parasite diversity monitoring

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