https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)63192-X/pdf

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM) and 237 Vietnamese adults with uncomplicated pulmonary tuberculosis. The host genotype of tuberculosis cases was also compared with the genotype of 392 cord blood controls from the same population. Isolates of M. tuberculosis were genotyped by large sequence polymorphisms. The hosts were defined by polymorphisms in genes encoding Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP) and Toll-like receptor-2 (TLR-2). We found a significant protective association between the Euro-American lineage of M. tuberculosis and pulmonary rather than meningeal tuberculosis (Odds ratio (OR) for causing TBM 0.395, 95% confidence intervals (C.I.) 0.193-0.806, P = 0.009), suggesting these strains are less capable of extra-pulmonary dissemination than others in the study population. We also found that individuals with the C allele of TLR-2 T597C allele were more likely to have tuberculosis caused by the East-Asian/Beijing genotype (OR = 1.57 [95% C.I. 1.15-2.15]) than other individuals. The study provides evidence that M. tuberculosis genotype influences clinical disease phenotype and demonstrates, for the first time, a significant interaction between host and bacterial genotypes and the development of tuberculosis.

/pdf/the-influence-of-host-and-bacterial-genotype-on-the-kyc7nu3uyq.pdf

The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis

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.

https://jcm.asm.org/content/jcm/42/2/792.full.pdf

spa Typing Method for Discriminating among Staphylococcus aureus Isolates: Implications for Use of A Single Marker to Detect Genetic Micro- and Macrovariation

A majority of the Mycobacterium species, called the nontuberculous mycobacteria (NTM), are natural inhabitants of natural waters, engineered water systems, and soils. As a consequence of their ubiquitous distribution, humans are surrounded by these opportunistic pathogens. A cardinal feature of mycobacterial cells is the presence of a hydrophobic, lipid-rich outer membrane. The hydrophobicity of NTM is a major determinant of aerosolization, surface adherence, biofilm-formation, and disinfectant- and antibiotic resistance. The NTM are oligotrophs, able to grow at low carbon levels [>50 microg assimilable organic carbon (AOC) l(-1)], making them effective competitors in low nutrient, and disinfected environments (drinking water). Biofilm formation and oligotrophy lead to survival, persistence, and growth in drinking water distribution systems. In addition to their role as human and animal pathogens, the widespread distribution of NTM in the environment, coupled with their ability to degrade and metabolize a variety of complex hydrocarbons including pollutants, suggests that NTM may be agents of nutrient cycling.

/pdf/surrounded-by-mycobacteria-nontuberculous-mycobacteria-in-1505wi12y3.pdf

Surrounded by mycobacteria: nontuberculous mycobacteria in the human environment.

We describe here a method for determining confidence intervals for a commonly used index of diversity. This approach facilitates the comparison of the genetic population structure of microorganisms isolated from different environments and improves the objective assessment of the discriminatory power of typing techniques.

https://jcm.asm.org/content/jcm/39/11/4190.full.pdf

Determining Confidence Intervals When Measuring Genetic Diversity and the Discriminatory Abilities of Typing Methods for Microorganisms

An index of discrimination for typing methods is described, based on the probability of two unrelated strains being characterized as the same type. This index may be used to compare typing methods and select the most discriminatory system.

Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity.

To simplify the selection of tests for bacteriological typing methods, such as bacteriophage, bacteriocin, and biotyping, a computerised method was assessed. This uses a numerical index of discrimination (D) to facilitate the selection of an efficient typing set. The computer programs take the most discriminatory test as the initial test in the partial typing set, and then select the next test by combining each of the remaining candidates with the partial set and choosing the test which maximises D. This cycle is repeated until the remaining candidates do not increase the discriminatory power of the typing set. Options are provided for the investigator to pre-select certain tests for inclusion or exclusion from the typing set. It is concluded that the numerical index D is a simple means of test selection, but it must be emphasised that it is important to combine its use with data on the incidence of reaction in each test, on reproducibility, and on the similarity among tests.

https://jcp.bmj.com/content/jclinpath/42/7/763.full.pdf

M A Gaston

Papers

Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity.

Efficient selection of tests for bacteriological typing schemes.