FRED C. TENOVER,* ROBERT D. ARBEIT, RICHARD V. GOERING, PATRICIA A. MICKELSEN, BARBARA E. MURRAY, DAVID H. PERSING, AND BALA SWAMINATHAN National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333; Veterans Affairs Medical Center, Boston, Massachusetts 02130; Creighton University, Omaha, Nebraska 68178; Stanford University Medical Center, Stanford, California 94305; University of Texas Medical School, Houston, Texas 77030; and Mayo Clinic, Rochester, Minnesota 55905

https://courses.washington.edu/pabio568/files/tenover.pdf

Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing.

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of ≈470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

https://www.pnas.org/content/pnas/95/6/3140.full.pdf

Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms

1Department of Genetics, University of Georgia, Athens, Georgia 30602; 2NMFS/ CZES, Genetics, 2725 Montlake Boulevard East, Seattle, Washington 98112; 3Savannah River Ecology Laboratory, Drawer E, Aiken, South Carolina 29801; ~Department of Microbiology and Immunology, School of Medicine, University of California, Los Angeles, California 90024; -SSchool f Veterinary Medicine, Virginia Tech University, Blacksburg, Virginia 24046

/pdf/intraspecific-phylogeography-the-mitochondrial-dna-bridge-5e2au5n1qt.pdf

Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics

A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.

/pdf/the-codon-adaptation-index-a-measure-of-directional-3xwgbhuu5p.pdf

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.

http://webpages.icav.up.pt/PTDC/BIA-BEC/099915/2008/4.Hewitt%202004%20PhilTransRSocLondB.pdf

Genetic consequences of climatic oscillations in the Quaternary.

Methodes d'extraction d'enzymes, d'electrophorese en gel et de coloration specifique des enzymes utilisees pour etudier la variation genetique chez Escherichia coli et d'autres bacteries. Les procedures decrites peuvent s'appliquer, avec quelques modifications mineures, a toute espece de bacterie

Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics

A set of 72 reference strains of Escherichia coli isolated from a variety of hosts and geographical locations has been established for use in studies of variation and genetic structure in natural populations. The strains, which have been characterized by multilocus enzyme electrophoresis, are representative of the range of genotypic variation in the species as a whole.

Standard reference strains of Escherichia coli from natural populations.

Biochemical Polymorphism and Systematics in the Genus Peromyscus. V. Insular and Mainland Species of the Subgenus Haplomylomys

A survey of electrophoretic variation in 20 enzymes from 109 clones of escherichia coli from natural populations yielded an estimate of mean genetic diversity approximately twice that reported in an earlier study and four to five times larger than estimates fro most eukaryotic species. Despite this extensive variability, the number of distinctive genotypes apparently is rather limited. Identical clones were obtained from unassociated hosts, and a clone that is electrophoretically indistinguishable from the laboratory strain Escherichia coli K-12 was isolated from a human infant. The results suggest that rates of genetic recombination in natural populations of Escherichia coli are low. These findings have implications for our understanding of the genetic structure of Escherichia coli populations and the factors determining the amount of neutral gene variability in this bacterial species.

https://science.sciencemag.org/content/sci/210/4469/545.full.pdf

Genetic diversity and structure in Escherichia coli populations.

One hundred and seventy-five isolates of the pathogenic bacterium Listeria monocytogenes recovered from human clinical (blood and cerebrospinal fluid), animal, and environmental sources in Europe, North America, and elsewhere were analyzed electrophoretically for allelic variation at 16 genetic loci encoding metabolic enzymes Forty-five distinctive allele profiles (electrophoretic types, ETs) were distinguished, among which mean genetic diversity per locus (H) was 0424 Cluster analysis of a matrix of genetic distances between paired ETs revealed two primary phylogenetic divisions of the species separated at a distance of 054 ETs in division I were presented by strains of serotypes 4b, 1/2b, and 4a, whereas strains of ETs in division II were of serotypes 1/2a and 1/2c Human and animal isolates did not represent distinctive subsets of ETs The occurrence of linkage disequilibrium between enzyme loci and the widespread distribution of certain ETs indicate that the genetic structure of L monocytogenes is clonal One clone, marked by ET1, caused major epidemics of human disease in western Switzerland in the period 1983-1987 and in Los Angeles County, California, in 1985, both of which were attributed to contamination of soft cheese ET 1 is closely related to the clone (ET7) that caused two large outbreaks of listeriosis in Massachusetts in 1979 and 1983

https://www.pnas.org/content/pnas/86/10/3818.full.pdf

Robert K. Selander

Papers

Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics

Standard reference strains of Escherichia coli from natural populations.

Biochemical Polymorphism and Systematics in the Genus Peromyscus. V. Insular and Mainland Species of the Subgenus Haplomylomys

Genetic diversity and structure in Escherichia coli populations.

Genetic characterization of clones of the bacterium Listeria monocytogenes causing epidemic disease.