Single-cell genomics for complex malaria

Single-cell genomics for dissection of complex malaria infections
Genome Res. 2014. Published in Advance May 8, 2014.
Shalini Nair, et al.

Most malaria infections contain complex mixtures of distinct parasite lineages.
These multiple-genotype infections (MGIs) impact virulence evolution, drug resistance, intra-host dynamics, and recombination, but are poorly understood.

To address this we have developed a single-cell genomics approach to dissect MGIs.
By combining cell sorting and whole-genome amplification (WGA), we are able to generate high-quality material from parasite-infected red blood cells (RBCs) for genotyping and next-generation sequencing.
We optimized our approach through analysis of >260 single-cell assays.
To quantify accuracy, we decomposed mixtures of known parasite genotypes and obtained highly accurate (>99%) single-cell genotypes.
We applied this validated approach directly to infections of two major malaria species, Plasmodium falciparum, for which long term culture is possible, and Plasmodium vivax, for which no long-term culture is feasible.

We demonstrate that our single-cell genomics approach can be used to generate parasite genome sequences directly from patient blood in order to unravel the complexity of P. vivax and P. falciparum infections.
These methods open the door for large-scale analysis of within-host variation of malaria infections, and reveal information on relatedness and drug resistance haplotypes that is inaccessible through conventional sequencing of infections.

journalistic version:

Antibiotic Use On The Farm: Are We Flying Blind?

Antibiotic Use On The Farm: Are We Flying Blind?
August 29, 2013

Denmark has led the world in efforts to control antibiotic use and antibiotic resistance.
Every year it publishes a big volume of numbers — and Scott can’t get enough of them. “Diving into these data, and visiting Denmark, is kind of like Disneyland for those of us who like big data,”

There are lots of people who want something similar for farms in the United States.
They include public health experts, but also activist groups like the Union of Concerned Scientists.
Congress is considering a bill that would force the FDA to collect this data and publish it.

… better numbers could actually mean less suspicion and fear.
Many people want to know exactly what meat producers are doing, he says.
When they can’t find the information they want, they’re inclined to assume the worst.