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Additional file 1. Schematic of Richard Toll sample analysis. A total of 759 samples were received and genotyping yielded 649 samples that passed genotyping (5 or fewer missing alleles in the 24-SNP barcode). Of these 649 samples, 473 were monogenomic (0, or 1 mixed allele in the 24-SNP barcode).

Additional file 8. Map of infections. A. Map of infections collected in 2015 and relative location of Thiès. The distance between Richard Toll and Thiès is approximately 150 miles. The sites of households from which samples were collected in 2015 are shown, with red indicating infections in individuals with a travel history and blue indicating infections from individuals with no travel history (see B). No household locations were collected in any other year. B. Inset from panel A is shown enlarged to indicate the relative locations of households from which parasite infections were identified in 2015. Infections identified in individuals who reported a travel history are shown in red, while those from individuals who reported no recent travel are shown in blue. Tear drop markers indicate infections identified through reactive active case detection (RACD), with index case marked red for positive travel history or blue for no travel history. All of these RACD households with a travel history (red teardrops) had parasites that were different from one another; and all these RACD households with no travel history (blue teardrops) shared genotype infections, with one exception being the household in dark blue in the center of Richard Toll (identified with an asterisk). This household had parasites that were genetically distinct but the index case reported no recent travel. C. Location of passive case detection infections that share a parasite genotype. To provide an example of household location where shared infections were identified by passive case detection at four households with the same parasite genotype are shown in blue teardrops, and a different parasite genotype found among two households are shown in red teardrops. The two infections from the red household were both detected on the same date at the clinic. The infections for the blue households occurred on different dates: (1) September 7; (2) September 12; (3) November 8; (4) November 10. Note that household 4 was positive for additional infections and corresponds to the household in panel B as indicated by the red arrow. The geographic distance between household 1 and 2 is 3.3 miles; between household 2 and 3 is 14 miles and between household 3 and 4 is 0.8 miles.

Additional file 3. SNP genetic barcode; Genotyped SNPs arrange according to the place of collection.

Additional file 1: Table S1. Number of samples by year of PfRh2b polymorphism in Thiès and Western Gambia. Column N shows the number of samples analysed. n = the number of samples of each allele. PfRh2bdel = deletion present; PfRh2bfull = full-length sequence; Mix = PfRh2bDel/PfRh2bfull.

Additional file 1. Participant questionnaire.

Additional file 2: Figure S2. Plasmodium falciparum detection in Kédougou by health center, 2013–2014 (n = 475).

Additional file 1: Figure S1. Plasmodium spp. detection in Kédougou, 2013–2014 (n = 475 samples).

Table S1. Prevalence of dhfr and dhps alleles in Comoros over time. Prevalences in dhfr and dhps mutations were compared from Rebaudet et al. in 2010 and this study in 2012â 2013.

Additional file 1. Additional tables and figures.

Additional file 1. Additional tables and figures.

Additional file 1. Culture-adaptation of TRAC parasites.

Additional file 5. Association between percent survival RSA0â 3h and clearance time. Correlation between clearance time on the x-axis and percent survival RSA0â 3h on the y-axis. Each dot represents an isolate. Samples represented by color were used for in vitro drug testing and for pfmdr1 copy number variation determinationâ green for ART sensitive; blue for discordant; and red for ART resistant parasites. The grey dot marks the isolate with an E270K mutation. The dotted lines represent the cut off used to discriminate between resistant and sensitive parasites (1% for RSA0â 3h, 4 or 5% for clearance).

Additional file 1. Culture-adaptation of TRAC parasites.

Additional file 2. Parallel amplicon sequencing error correction (PASEC) workflow.

Additional file 4. Distribution of C580Y mutations in Cambodian isolates. Parasites from Pursat (round symbols) or Pailin (square symbols) were classified according to their Pfkelch13 alleles. Comparison of clearance half-life values (hours, h) from parasites harboring the wild-type (C) or mutant (Y) allele at amino acid position 580 in the Pfkelch13 locus, with culture-adapted parasites represented by black outlined symbols. C580 parasites harboring a mutation in the Pfkelch13 propeller domain other than C580Y are indicated by grey filled symbols. An unpaired t test was performed between the C580 and C580Y carrying parasites from Pursat (p

Table S1. Prevalence of dhfr and dhps alleles in Comoros over time. Prevalences in dhfr and dhps mutations were compared from Rebaudet et al. in 2010 and this study in 2012â 2013.

Additional file 5. Association between percent survival RSA0â 3h and clearance time. Correlation between clearance time on the x-axis and percent survival RSA0â 3h on the y-axis. Each dot represents an isolate. Samples represented by color were used for in vitro drug testing and for pfmdr1 copy number variation determinationâ green for ART sensitive; blue for discordant; and red for ART resistant parasites. The grey dot marks the isolate with an E270K mutation. The dotted lines represent the cut off used to discriminate between resistant and sensitive parasites (1% for RSA0â 3h, 4 or 5% for clearance).

Additional file 3. Schematic shows distribution of parasites obtained from Pursat (blue star on map, KH1 parasites indicated in blue) and Pailin (red star, KH4 parasites indicated in red) from Cambodia (map modified from https://commons.wikimedia.org/wiki/File:Cambodia_provinces_en.svg ).

Additional file 2. Parallel amplicon sequencing error correction (PASEC) workflow.

Additional file 4. Distribution of C580Y mutations in Cambodian isolates. Parasites from Pursat (round symbols) or Pailin (square symbols) were classified according to their Pfkelch13 alleles. Comparison of clearance half-life values (hours, h) from parasites harboring the wild-type (C) or mutant (Y) allele at amino acid position 580 in the Pfkelch13 locus, with culture-adapted parasites represented by black outlined symbols. C580 parasites harboring a mutation in the Pfkelch13 propeller domain other than C580Y are indicated by grey filled symbols. An unpaired t test was performed between the C580 and C580Y carrying parasites from Pursat (p