Our first genome: Leptospira genome completed

Australian researchers have their first bug in the bank: a full genome map and complete DNA sequence of the 3900-odd genes that make up the spirochete bacterium Leptospira.

It is the first genome for any organism to be completed entirely in Australia. The Australian Genome Research Facility in Brisbane did the sequencing, while the ARC Centre in Microbial Genomics at Monash University performed the analysis.

Monash microbiologist Professor Ben Adler said his team was already searching for genes for conserved surface antigens that might be candidates for inclusion in a vaccine.

Leptospira causes leptospirosis, a potentially lethal bacterial infection commonly known in Australia as 'cane-cutter's disease'.

Adler said that, in the era before mechanical harvesting, workers cutting cane manually were vulnerable to infection when urine from Leptospira-infected rats that infest canefields contaminated skin cuts or scratches. The main pathogenic serovars in Australia -- Hardjo, Zanoni and Pomona -- are named after cane-cutters, or sugar towns.

Banana harvesters, farmers and others who work with animals are the most vulnerable groups in Australia today.

Leptospirosis causes influenza-like symptoms, including severe headache and muscle pains lasting up to two weeks. But in the wake of a severe infection, the victim may be incapable of working for two months,

Adler said Leptospira remains "exquisitely sensitive" to antibiotics, and prompt administration of penicillin rapidly eliminates the infection.

Deaths from leptospirosis in developed nations are rare -- the main serovars in Australia are from a different group to those found in developing nations, where infections are much more severe, and mortality rates approach 20 per cent.

Severe, untreated infection can cause multiple organ failure and permanently damage the kidneys, lungs and liver. Around a million cases of leptospirosis are reported annually around the world, most in developing nations.

"Leptospirosis is a huge problem in countries like Thailand, India, Korea and China, and there was a major outbreak in Nicaragua a few years ago," Adler said.

The microbe's antigenic variation -- 130 serovars have been identified -- has frustrated efforts to develop a vaccine. Some vaccines protect against closely related strains, but Adler said a universally protective vaccine would depend on identifying highly immunogenic proteins that are also highly conserved between strains.

"Like most spirochetes, Leptospira doesn't have many outer membrane proteins," he said. "The genome sequence allows us for the first time to take a global approach to look for every potential vaccine candidate."

Unfortunately, bioinformatics is not yet sufficiently advanced to identify more than 50 per cent of outer-membrane proteins, much less to predict which are likely to be most immunogenic. "We'll just have to go through and do the experiments one-by-one," Adler said. "In the end, the only criterion is wheter the antigen immunises the person or the animal against leptospirosis."

Unusually among bacteria, Leptospira has two circular chromosomes, not one, and lacks plasmids -- the tiny loops of DNA that, in most pathogenic bacteria, are repositories for antibiotic-resistance genes and other genes important for survival in hostile environments.

Adler said the microbe's lack of plasmids may explain why it has not yet acquired resistance to antibiotics, although the genome sequence provides clear evidence that the microbe has acquired gene sequences from other, unrelated microbes by an as-yet unknown mechanism.

The full map and sequence of Leptospira has taken two years, and Adler said he now knew why most geneticists gave genome projects a wide berth. "The sequencing is easy, but doing the sequence assembly and annotating genes is just hard work," he said.

"They're right when they say you get 90 per cent of the data in 10 per cent of the time, and doing the other 10 per cent takes 90 per cent of the time. You have to go through each gene manually and decide what to call it -- even if there's a 99 per cent match to a ribosomal protein from another species, you still have to search the literature to make sure it's correct.

"The problem is that the genomes already out there are riddled with errors. It's becoming a major problem. There's a paper trail, that you have to track through all the previous designations of the gene to find the original -- only to find sometimes that the original designation may have been flawed, and has become fixed in the research literature."