Many human pathogens produce phenotypic variants as a means to circumvent the host immune system and enhance survival and, as a potential consequence, exhibit increased virulence. For example, it has been known for almost 90 y that clinical isolates of the human bacterial pathogen group A streptococci (GAS) have extensive phenotypic heterogeneity linked to variation in virulence. However, the complete underlying molecular mechanism(s) have not been defined. Expression microarray analysis of nine clinical isolates identified two fundamentally different transcriptomes, designated pharyngeal transcriptome profile (PTP) and invasive transcriptome profile (ITP). PTP and ITP GAS differed in approximately 10% of the transcriptome, including at least 23 proven or putative virulence factor genes. ITP organisms were recovered from skin lesions of mice infected subcutaneously with PTP GAS and were significantly more able to survive phagocytosis and killing by human polymorphonuclear leukocytes. Complete genome resequencing of a mouse-derived ITP GAS revealed that the organism differed from its precursor by only a 7-bp frameshift mutation in the gene (covS) encoding the sensor kinase component of a two-component signal transduction system implicated in virulence. Genetic complementation, and sequence analysis of covR/S in 42 GAS isolates confirmed the central role of covR/S in transcriptome, exoproteome, and virulence modulation. Genome-wide analysis provides a heretofore unattained understanding of phenotypic variation and disease specificity in microbial pathogens, resulting in new avenues for vaccine and therapeutics research.

IRIS is common among HIV-infected persons coinfected with M. tuberculosis, M. avium complex, or C. neoformans. Antiretroviral drug-naive patients who start HAART in close proximity to the diagnosis of an opportunistic infection and have a rapid decline in HIV-1 RNA level should be monitored for development of this disorder.

Strain typing of microbial pathogens has two major aims: (i) to index genetic microvariation for use in outbreak investigations and (ii) to index genetic macrovariation for use in phylogenetic and population-based analyses. Until now, there has been no clear indication that one genetic marker can efficiently be used for both purposes. Previously, we had shown that DNA sequence analysis of the protein A gene variable repeat region (spa typing) provides a rapid and accurate method to discriminate Staphylococcus aureus outbreak isolates from those deemed epidemiologically unrelated. Here, using the hypothesis that the genetic macrovariation within a low-level recombinogenic species would accurately be characterized by a single-locus marker, we tested whether spa typing could congruently index the extensive genetic variation detected by a whole-genome DNA microarray in a collection of 36 isolates, which was recovered from 10 countries on four continents over a period of four decades, that is representative of the breadth of diversity within S. aureus. Using spa and coa typing, pulsed-field gel electrophoresis (PFGE), and microarray and multilocus enzyme electrophoresis (MLEE) data in molecular epidemiologic and evolutionary analyses, we determined that S. aureus likely has a primarily clonal population structure and that spa typing can singly index genetic variation with 88% direct concordance with the microarray and can correctly assign isolates to phylogenetic lineages. spa typing performed better than MLEE, PFGE, and coa typing in discriminatory power and in the degree of agreement with the microarray at various phylogenetic depths. This study showed that genetic analysis of the repeat region of protein A comprehensively characterizes both micro-and macrovariation in the primarily clonal population structure of S. aureus.Staphylococcus aureus is the leading cause of nosocomial infections (21) and is responsible for a wide range of human diseases, including endocarditis, food poisoning, toxic shock syndrome, septicemia, skin infections, soft tissue infections, and bone infections, as well as bovine and ovine mastitis. The recent emergence of community-associated methicillin-resistant S. aureus (MRSA) strains (23) and the movement of the vanA operon from Enterococcus faecalis into MRSA, establishing strains with high-level vancomycin resistance (3), further heighten the public health concerns. Thus, understanding and controlling the spread of S. aureus, in both the hospital and community settings, is now of paramount importance.S. aureus is a heterogenous (polymorphic) species (13) that was recently found to have a clonal population structure (11). Therefore, it is believed that S. aureus does not undergo extensive recombination, diversifies largely by nucleotide mutations, and shows a high degree of linkage disequilibrium (nonrandom associations between genetic loci). In order to distinguish strains within a heterogenous species for local epidemiologic or outbreak investigation purposes, a highly discriminating ge...

To examine trends in the incidence and epidemiology of cryptococcosis, active, population-based surveillance was conducted during 1992-2000 in 2 areas of the United States (the Atlanta, Georgia, and Houston, Texas, metropolitan areas; combined population, 7.4 million). A total of 1491 incident cases were detected, of which 1322 (89%) occurred in HIV-infected persons. The annual incidence of cryptococcosis per 1000 persons with AIDS decreased significantly during the study period, from 66 in 1992 to 7 in 2000 in the Atlanta area, and from 24 in 1993 to 2 in 1994 in the Houston area. Poisson regression analysis revealed that African American persons with AIDS were more likely than white persons with AIDS to develop disease. Less than one-third of all HIV-infected persons with cryptococcosis were receiving antiretroviral therapy before diagnosis. Our findings suggest that HIV-infected persons who continue to develop cryptococcosis in the era of highly active antiretroviral therapy (HAART) in the United States are those with limited access to health care. More efforts are needed to expand the availability of HAART and routine HIV care services to these persons.

Isoniazid (INH) is one of the primary chemotherapeutic and prophylactic drugs used against Mycobacterium tuberculosis, the causative agent of tuberculosis, which remains the leading single cause of death due to an infectious agent throughout the world. Recent studies indicate that the median rate of primary resistance to INH is 7.3% (range, 1.5 to 32%) and that the rates of acquired resistance range from 5.3 to 70% globally (9, 45). The overall rate of resistance to INH is 8.4% in the United States and has remained relatively stable in the last decade (23). Global reports of clusters of tuberculosis cases caused by drug-resistant strains together with the emergence and dissemination of multidrug-resistant tuberculosis have underscored the need for research into the mechanisms of drug resistance and the design of more effective antituberculous agents. Despite the use of INH for several decades, the molecular basis for its bactericidal action and the mechanisms by which INH resistance evolves in M. tuberculosis are only beginning to be understood.INH has a simple chemical structure consisting of a hydrazide group attached to a pyridine ring, but its mode of action is very complex (8). It is proposed that INH enters M. tuberculosis as a prodrug by passive diffusion and is activated by catalase-peroxidase, encoded by katG, to generate free radicals, which then attack multiple targets in the cells (6). Recent studies have shown that an NADH-dependent enoyl acyl carrier protein (ACP) reductase, encoded by inhA, and a ␤-ketoacyl ACP synthase, encoded by kasA, are two potential intracellular enzymatic targets for activated INH; and both of these enzymes are involved in the biosynthesis of mycolic acids (4,19,20). Resistance-associated amino acid substitutions have been identified in the katG, inhA, and kasA genes of INHresistant clinical isolates of M. tuberculosis (7,20,24,26,29). In addition, mutations in the oxyR-ahpC intergenic region have been identified in INH-resistant isolates (36). Additional genetic and biochemical studies have shown that certain promoter mutations of alkylhydroperoxide reductase, encoded by ahpC, in INH-resistant isolates result in overexpression of ahpC as a compensatory mechanism for the loss of catalase activity due to katG mutations (15, 32). Recently, missense mutations were identified in ndh, a gene encoding NADH dehydrogenase, which is an essential respiratory chain enzyme that regulates the NADH/NAD ϩ ratio in cells (18,22). The molecular mechanism by which mutations in ndh confer INH resistance in M. tuberculosis is poorly understood. In addition, low-level INH resistance in mycobacteria has been shown to be