By David N. Leff

Genitally invaded girls and women don't even know they're infected. Nor do boys and men know what hit them.

Yet, chlamydial genital-tract infections "are the most commonly reported disease of any kind in the U.S., sexually transmitted or otherwise." So said microbiologist Richard Stephens, public-health professor at the University of California, Berkeley. "Such infections," he added, "often show no symptoms before permanent damage occurs.

"From 60 to 70 percent of new chlamydial infections go undiagnosed in young women," he went on. "It is a very significant disease agent in teenage girls."

Despite its symptomatic silence, the Chlamydia trachomatis bacterium often causes pelvic inflammatory disease, ectopic pregnancy and sterility in women; epididymitis and faux gonorrhea in males; and perinatal eye infection or infant pneumonia.

Chlamydial ocular trachoma is a leading cause of preventable blindness in the developing world. Besides hiding as an artful dodger, the miscreant microbe is also an imposter. For example, in the male genital tract, it often masquerades as gonorrhea, with possible consequent misdiagnosis and mistreatment.

Now, at last, Chlamydia's cover is blown. As reported in today's Science, dated Oct. 23, 1998, its genome has been mapped in full.

Stephens is lead author of the paper, which announces, "Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis."

The shifty bacterium's total chromosomal DNA sequence weighed in at 1,042,519 base pairs, plus a 7,493-bp plasmid sequence. The mappers identified 894 "likely protein-coding genes." These numbers compare with the genome of Haemophilus influenzae, sequenced in 1995, at 1,830,137 base pairs, and 1,743 genes.

The Science article's senior author is gene-mapping biochemist Ronald Davis, who heads the DNA Sequencing and Technology Center at Stanford University, in California.

"When we sat down about three years ago to choose an organism for mapping," Davis told BioWorld Today, "we targeted C. trachomatis, first because its genome is small, so we wouldn't have to fiddle around with it; second [because] it has medical importance; and thirdly [because] it's an organism we know very little about. So, it's hard to work with."

He added, "It was our hope that the Chlamydia [trachomitis] sequence would be a great stimulus to people being able to work with this organism. So, it's more of a test case of how you could go from virtually no understanding, to doing its sequence, to asking: 'What did we learn?'"

Stephens answered that question. "We know more about Chlamydia from this one study than we knew before from 40 years of research," he said. "We found new targets on its surface that could help us develop a vaccine, and new proteins that interact with the host and could help us with diagnostics."

Davis said better antibiotics could result. "Existing antibiotics work quite well against Chlamydia," he pointed out, "but one might want to do something that would be more specifically targeted to this organism and could be taken more often."

Genome Sequencing Starts With Live Culture

Step one in the co-authors' genome-sequencing project was to choose a master strain of the living material they would be mapping.

"We picked the C. trachomatis strain that was considered the standard by workers in the field," Davis said. "So, we were pretty careful about selecting the one that's been worked on in the community for a long time, and also that was still capable of causing disease.

"The bacterium itself," Davis observed, "is very small, and grows only inside of other animal cells. There's a whole collection of them out there that have different specificities. They tend to be selective about the organism and the tissue they infect.

After Davis had nominated C. trachomatis as his genome-sequencing candidate, he recalled, "Stephens at Berkeley made all the DNA, and brought it down to us. Then, we did the sequence and delivered it to him for biological analysis."

Little was previously known about the bug's complex biology, "in part because it only grows inside human cells," Stephens said. "We had no methods of doing genetics with this organism."

Chlamydia holes up in human cells somewhat the way viruses or tuberculosis bacteria, or parasites such as Leishmania do — but with a difference. Instead of bundling into macrophages or lysosomes, the loner C. trachomatis builds its own intracellular safe house.

After invading a eukaryotic cell, it grows inside a vacuole, called an inclusion, that does not merge with lysosomes. After about 20 hours of division and differentiation, the infective microbe emerges from its hole to initiate new rounds of infection.

An individual infectious bacterium is spherical in shape, and about three-tenths of a micron in diameter.

"It usually requires liquid contact," Davis observed, "and usually invades a moist membranous tissue — the eye or the genital tract — as its target. Apparently, it doesn't survive very well airborne."

Chlamydia, Immune System Play Hide-and-Seek

Davis said the body's immune system cells "can't easily kill C. trachomatis. We can fight it off, but it stays pretty well hidden, and sometimes can escape into a neighboring cell before being caught."

A separate chlamydial species, C. pneumoniae, which is particularly good at escaping detection, goes after the lungs and upper respiratory tract.

Davis and his genome-sequencing co-authors have almost finished sequencing C. pneumoniae, "but it's not quite ready for publication yet." They've also finished the Arabidopsis thaliana plant-model genome, and are well along on the infective fungus Candida albicans.

"C. trachomatis doesn't actually cause too many adverse effects on the person," Davis pointed out. "That's why people don't know they're infected. But it probably is an associated factor for other venereal diseases, including the fact that it may increase the chances of acquiring HIV.

"And there may be yet other medical consequences," he continued. "For example, C. pneumoniae has now been associated with atherosclerotic plaque — that is, heart disease. And there are even suspicions that it may be the triggering event.

"As we learn more about these organisms," Davis concluded, "and actually predict where they are, we're learning that they have a bigger impact on human health than we originally thought." *