Pathogens Emerging

Oxford Clinical Researcher and molecular microbiologist, Dr. Stephan Baker, gave a talk entitled “A Tale of Two Cities — Genomics Epidemiological in Southeast Asia” last Tuesday, Feb. 11, at the Cal-IT2 Auditorium.

More than 50 students and faculty members attended Baker’s public health talk, where he shared his latest findings on an enteric infection called Typhoid fever and an emerging bacterial pathogen called Shigella.

Baker is head of an enteric infections research unit stationed in Ho Chi Minh City, Vietnam. Since November 2007, his team of clinical researchers has been studying enteric infections, also known as intestinal diseases, plaguing Southeast Asia and has been performing a series of treatment trials to counter such diseases.

Baker began his presentation noting how our society realistically lives in a microbial world in which humans are just purely vectors for moving microbes. This mutualistic relationship between microbes and humans has existed for millions of years and is predicted to exist until the human species becomes extinct.

“There are 100 trillion organisms circulating in a person’s gastrointestinal tract,” Baker said. “About one to three percent of a human’s total body weight actually is made up of bacterial biomass.” He also explained that when it comes to a person’s feces, 60 percent of the dry weight in fecal matter is enormously composed of bacteria.

Baker claims humans come in contact with the bacteria in fecal matter on a fairly regular basis and is commonly the cause of gastrointestinal infections. He explains this is a much bigger problem in developing countries where exposure to fecal matter is more prominent due to contaminated environments, lack of clean water supplies and no access to sustained sanitation systems.

Having worked over 15 years on Typhoid fever in Nepal, India, Baker’s team has conducted the largest clinical trials to study and better diagnose the fever caused by Salmonella. Humans are the only known reservoir to carry the infection. Those carrying the disease can transmit the bacterial pathogens to other people who are not Typhoid fever vaccinated.

He found that one of the main factors to trigger a Typhoid fever outbreak was the sharing of municipal wells. People use these wells to collect water for cooking and drinking. Residents living in close proximity to these wells had a higher risk of getting the infection due to the water being pathogen contaminated as a result of runoff rain water carrying fecal matter and chemical leakage.

Baker’s team plans to introduce a sand-based water filter and randomly distribute filters to 400 households for a period of 12 months to study the effects of reduced exposure to contaminated water.

Part two of Baker’s talk discusses his research on Shigella, a bacterium he describes as a “talled up version of E. coli” with weapons. Just like Typhoid fever, humans are the only vectors for Shigella diseases. Shigella has no flagella, or a tail-like structure similar to what E. coli uses to move. Instead, Shigella uses its host cell’s cytoskeleton to mobilize efficiently between cells.

According to Baker, Shigella is a dynamic organism that is rapidly evolving and emerging worldwide. Thanks to the advancement in genome sequencing technology, Baker’s team is able to sequence genomes at a faster rate with a higher degree of accuracy. Having collected strains of the bacteria in southern Vietnam, his team recently constructed a phylogeny tree to monitor the growing population of Shigella in any location.

Baker believes that Ho Chi Minh City is a relatively huge nursery for Shigella bacteria that are readily spreadable to other new locations and could start their own subset of population.

To combat Shigella outgrowth, Baker’s team plans to study 1000 children starting at birth and following them for three years to understand how their immune system matures after exposure to the organism. With such results, Baker hopes one day to develop novel vaccines and diagnostics of the infection.