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Microbe detection At Genomes 2004, microbial genomics in developing nations

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Genomics is not just for the richest countries anymore, as the recent Genomes 2004 conference at the Wellcome Trust Genome Campus in Hinxton, UK, demonstrated. The poster sessions alone were a veritable United Nations, with teams from Brazil, India, Mexico, Nigeria, Romania, Russia, and Slovenia presenting along with their British, Western European, North American, Japanese, and other Asian colleagues.

A key theme of posters — from developing nations in particular — was the applicability of microbial genomics to solve practical problems in healthcare and agriculture. One poster presented by Indian researchers on identifying nontuberculous mycobacteria strains reminded readers that the underlying research is not “merely a speculative exercise”: appropriate diagnosis of mycobacterial infections in some of India’s 4 million HIV-positive individuals is a life-or-death matter. In this poster, Saba Shahadad and colleagues of the All India Institute of Medical Sciences sequenced a marker gene on standard strains of tuberculosis mycobacteria and sputum samples from HIV-positive patients in New Delhi hospitals. They found that 53.5 percent of the isolates from the HIV-positive patients were nontuberculous mycobacteria, against which standard anti-tuberculosis medications would generally be ineffective. “In conclusion, we believe that there is a need for rapid detection of mycobacteria in clinical samples,” Shahadad and colleagues wrote.

Shahadad’s poster drew a buzz of interest from conference attendees, one of whom wanted to know if the team would be using RT-PCR to confirm findings. But Shahadad said that the institute lacked the funding to use this type of technology.

In another poster with practical implications, Leticia Khater, a doctoral student at the Laboratorio Nacional deLuz Sincrotron in Campinas, Brazil, and colleagues presented on the identification of chaperones for virulence genes in Xanthomonas axonopodis pathovar Citri, a pathogen that causes citrus canker infection in citrus trees. The genome of this pathogen was completed by a team of 13 Brazilian labs in 2002, and since then researchers from the Xanthomonas genome project have been doing standard annotation. When Khater’s team used standard sequence homology searches to look for chaperones, proteins that assist in the secretion of bacterial virulence factors, and came up with little, the team tried a different approach and looked for genes that would encode proteins with similar physico-chemical characteristics to chaperones. They found numerous genes, cloned them, and are now screening them with a yeast two hybrid system based on Gal4 binding and activation domains. These proteins, when identified, could yield promising targets for chemicals designed to kill these pathogens.

“Indeed, the study of Xanthomonas axonopodis biology will benefit from the identification of secretion system chaperone genes,” according to Khater, “since the uncovering of the precise molecular events controlling the delivery of effector proteins will eventually allow the design of compounds that specifically interfere with these processes.”

— Marian Moser Jones

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