OKLAHOMA CITY—Shortly after publication of the first complete sequences of the human genome, other researchers announced success in projects of a less grandiose scale—namely, analyzing the gene sequences of pathogenic bacteria. These genomes prove to be not only extremely complex but also highly dynamic. The research provides insights into the mechanisms of the organisms’ pathogenicity as well as alarming evidence of rapid acquisition of resistance to antibiotics.

In early April, Joseph Ferretti, PhD, and colleagues at the University of Oklahoma Health Sciences Center in Oklahoma City published the genome of Streptococcus pyogenes (group A streptococci [GAS]).[1] A few weeks later, Keiichi Hiramatsu and colleagues at Juntendo University in Tokyo described their analysis of another microbial genome, that of Staphylococcus aureus.[2]

CHARTING THE LANDSCAPE OF STREPTOCOCCUS PYOGENES

While sequencing the S pyogenes genome, Dr. Ferretti and colleagues found more than 40 possible virulence-associated genes. Some encode superantigen-like proteins that trigger shock-inducing immune responses. Others encode products that seem to mimic human proteins, thus representing potential autoimmune triggers. One GAS gene encodes a protein resembling collagen. “In rheumatic fever, one of the symptoms is polyarthritis, and patients have antibodies that cross-react to collagen,” said Dr. Ferretti, the George Lynn Cross Research Professor at the University of Oklahoma. This suggests, he added, “that some of the bacterial proteins stimulate an immune response to the patient’s joints.”

In addition, the S pyogenes genome contained the inserted genomes of at least four viral bacteriophages. “When a bacterium is stressed, the bacteriophages can be induced to reproduce, taking genetic material that can then be transferred ‘laterally’ to another bacterium,” Dr. Ferretti explained.

“Each of the bacteriophage-prophage sequences we found within the genome contained superantigen sequences. So bacteriophages may represent a major way for microbes to acquire virulence.”

This “lateral transfer” of genes from other strains or even from other species may also provide the means of rapid development of antibiotic resistance.

STAPHYLOCOCCUS AUREUS: GENES ON THE MOVE

Dr. Hiramatsu and colleagues sequenced the genome of S aureus, which can cause pneumonia, sepsis, toxic shock syndrome, and staphylococcal scarlet fever. Efforts to control S aureus infection have been complicated by the emergence in 1961 of resistance to methicillin and, in 1997, to the only known effective agent, vancomycin.

Analysis of the methicillin-resistant N315 and the vancomycin-resistant Mu50 strains revealed three “islands,” or mobile genetic elements, containing pathogenicity genes that apparently were introduced by lateral transfer from other species of bacteria and even from organisms as distant as vertebrates and plants.

“We identified at least 70 new genes involved in pathogenesis,” Dr. Hiramatsu, the chairman of the Department of Bacteriology at Juntendo University, told PULMONARY REVIEWS. Among the products of these genes are “leukocidins and haemolysins, which destroy blood cells, including white blood cells, to inactivate phagocytosis, the first line of host-defense; various proteinases and DNases [deoxyribonucleases], which digest and destroy tissue; and toxic shock syndrome toxin-1, which can cause toxic shock syndrome.”

Some of the islands encode toxins of the superantigen family; gene duplication within these islands may contribute to the variety of the 25 superantigens, including 15 recently identified by Dr. Hiramatsu and colleagues. Other S aureus genes encode adhesins, which facilitate colonization by attaching to host extracellular matrices.

Several different transposons (mobile gene sequences that can insert themselves into specific regions of the bacterial genome) confer antibiotic resistance to S aureus strains. Said Dr. Hiramatsu, “Frequent acquisition of exogenous genes by S aureus makes it more versatile in surviving attacks by antibiotics and the immune system. Lateral gene transfer makes the species extremely capable of acquiring antibiotic resistance.” Transposons in both strains contained genes for resistance to spectinomycin, macrolide-lincosamide-streptogramin B antibiotics, and aminoglycosides. In addition, Mu50 had a transposon encoding tetracycline and minocycline resistance. Other resistance genes were located on separate plasmids.

However, “vancomycin resistance in S aureus is acquired by accumulation of mutations,” said Dr. Hiramatsu. “At least two sequential exposures to vancomycin are required for N315 to acquire the level of vancomycin resistance of Mu50.”

Dr. Hiramatsu added this caution: “To avoid emergence of vancomycin resistance, we should both limit methicillin-resistant strains in hospitals and restrict use of antibiotics, especially broad-spectrum antibiotics such as carbapenems and the third- and fourth-generation cephalosporins.”

WHAT’S NEXT ON THE HORIZON

Protein sequence information may help researchers develop new antimicrobial strategies and diagnostics. “People may use the data to analyze certain proteins for use in vaccines,” said Dr. Ferretti. For example, “antibodies to the strep M protein cross-react with cardiac myosin. One question is, ‘What part of the molecule triggers this immune response?’ One vaccine under development uses the M protein, but with the region that induces heart cross-reactivity cleaved away.”

Suggested Dr. Hiramatsu, “New diagnostics might take advantage of gene products specific to S aureus. Also, streptococci surface antigens may be involved in the pathogenesis of bacterial endocarditis. Antibodies neutralizing these proteins might prevent vegetation of the heart valve by S aureus.”

—Mimi Zucker, PhD

References
1. Ferretti J, McShan W, Ajdic D, et al. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A. 2001;98:4658-4663.

2. Kuroda M, Ohta T, Uchiyama I, et al. Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet. 2001;357:1225-1240.

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