"Many of the bacteria that live on human mucosal surfaces (e.g. those in the ear, nose and throat) are enormously diverse," says Dr Martin Maiden at the University of Oxford. "For example, if you compare two isolates of the meningococcus, the bacterium that causes the most severe form of meningitis, they will be recognisable as members of the same biological group, but genetically they can be as different as humans and mice - this has a major impact on their biology and the ways we study them."

Another example is Streptococcus pneumoniae. Some strains cause pneumonia or middle-ear infections, but others can cause meningitis and blood infections. Similarly, Streptococcus pyogenes is a common cause of throat infections in the developed world, but in the tropics it is an important cause of impetigo (skin lesions) and has 'flesh-eating' variants. Many other medically important bugs are similarly chameleonic.

Diagnosis, therefore, is much more than just knowing what species of bug one is dealing with. It is also important to know what type of bug it is. Multilocus sequence typing, or MLST, a new technique developed by Dr Maiden, Professor Brian Spratt and colleagues, provides just such precision. It provides an unambiguous tag of a strain, based on its DNA sequence (see box below).

Variation

One of the most fundamental differences between ostensibly similar strains of bacteria is their ability to cause disease. Both Dr Maiden and Professor Spratt argue that a focus on disease, although understandable, has distorted our view of bacteria. Says Professor Spratt: "We've always stressed the importance of looking not just at the isolates from disease (a very biased population), but those from the total bacterial population which, depending on the species, might be the throat or gut."

The key difference is that the vast majority of bacteria in such environments will be doing no harm at all. "In many ways one of the most interesting and informative things that bacteria do is to live intimately with host organisms without causing disease," says Dr Maiden. Yet, tiny changes can turn a benign resident into a killer.

MLST provides a valuable way of distinguishing good from bad. "Many Streptococcus pneumoniae isolates rarely cause disease and a few isolates cause most of the disease," explains Professor Spratt. "If a strain is extremely common in the throat, but you never find it in cases of disease, you know that strain is very good at colonizing the throat, but bad at causing disease. If you find a strain that is rare in the throat, but causes a lot of disease, then you know that strain must have a much higher ability to cause disease. We've been trying to identify which of the strains have the highest potential to cause disease. That's important in terms of knowing what types of strains to target in a vaccine, because it's impossible to target all the strains in the population."

There are other practical advantages, too: "If you introduce a vaccine and find that some children are vaccinated and yet still get disease, you can find out whether it's some problem with the child's immune system, or whether there are particular strains which are escaping the vaccine."

MLST is increasingly being used to track the spread of disease, in a range of settings. For example, Dr Maiden's group has examined variants of Campylobacter (a cause of food poisoning) in farm animals and farm wastes, analyses that should aid the understanding of the spread of this bacterium from animals to humans. In Ghana, by contrast, the technique has been used to explore the role of street vendors in the spread of pathogenic E. coli infections among children.

On a wider scale, MLST promises to provide a more richly textured picture of bacteria within human populations. For example, Dr Maiden has been monitoring the effects of a new vaccine against group C meningococci, introduced into the UK immunisation programme in 1999. Conventional typing (based on antibodies against bacterial surface coat proteins) showed that the vaccine was reducing the numbers of group C meningococci, but MLST-based approaches will be able to dig much deeper and reveal what is happening to the meningococcal population in the throats of vaccinated children - how are the meningococci changing, what is taking the place of the group C bacteria, are some variants developing that can escape the vaccine, or is the vaccine altering the bacterial population in ways that are beneficial to humans?

Time line

A further application of MLST technology is in understanding the natural history of the bacterium - how it is now distributed, how it has spread and so on. "If we understand the evolutionary forces that made the bacterium what it is, we will understand more about the biology of the organism," points out Dr Maiden.

For example, while in Professor Spratt's laboratory, Dr Mark Enright (now at Bath) used MLST to characterise an international sample of around 900 strains of MRSA (methicillin-resistant Staphylococcus aureus, a multidrug-resistant bacterium causing significant problems in hospitals).

The analysis showed that the MRSA strains had arisen repeatedly from successful antibiotic-susceptible strains. The results suggest that there is a progression of increasing problems: the successful strains in the community have increasingly becoming hospital-adapted; from these, antibiotic-resistant forms have emerged; and these in turn are giving rise to strains less susceptible to vancomycin - the antibiotic of last resort. From a public health point of view, this is a most troubling scenario.

The future

In the long term, the more refined view of bacteria could point to new ways to intervene to prevent disease, says Dr Maiden. "Ideally, a medical intervention would try to make disease, already a rare event, an even rarer event, so that instead of causing disease very rarely, it never causes disease. If this could be achieved for an organism such as the meningococcus, disease could be dramatically reduced or even eliminated, while leaving the natural bacteria population more or less intact."

Dr Maiden is convinced that new opportunities will emerge. Yet, he cautions, it is still early days. "With genomic techniques including MLST we've managed to open up the diversity of many different and dangerous bacteria. Now we need to develop new phylogenetic, statistical and evolutionary approaches to understand the data that we find in the genomes. We're still only at the very beginning of that."

External links

• Dr Martin Maiden at the University of Oxford: Research Group’s interests
• Professor Brian Spratt at Imperial College London: Research interests
• Dr Mark Enright at the University of Bath: Research interests
• Pneumococcal Network of international laboratories
• Eumenet project
• A central resource for the Neisseria research community
• Multilocus Sequence Typing (MLST) includes instructions and details on methodology and links to databases

Futher reading

Maiden M C J, Bygraves J A, Feil E, Morelli G, Russell J E, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant D A, Feavers I M, Achtman M and Spratt B G (1998) Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA, 95: 3140-3145

Gupta S and Maiden M C J. (2001) Exploring the evolution of diversity in pathogen populations. Trends Microbiol., 9: 181-185

Zhou J, Enright M C and Spratt B G (2000). Identification of the major Spanish clones of penicillin-resistant pneumococci via the internet using multilocus sequence typing. J. Clin. Microbiol., 38: 977-986

Jolley K A, Kalmusova J, Feil E J, Gupta S, Musilek M, Kriz P and Maiden M C J (2000) Carried meningococci in the Czech Republic: A diverse recombining population. J. Clin. Microbiol., 38: 4492-4498

Enright M C, Robinson D A, Randle G, Feil E J, Grundmann H and Spratt B G (2002) Evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc. Natl. Acad. Sci. USA, 99: 7687-7692

Dingle K E, Colles F M, Ure R, Wagenaar J A, Duim B, Bolton F J, Fox A J, Wareing D R and Maiden M C J (2002) Molecular characterization of Campylobacter jejuni clones: A basis for epidemiologic investigation. Emerg. Infect. Dis., 8: 949-955