Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.

We studied genetic variability of 100 isolates of Claviceps purpurea by using randomly amplified polymorphic DNA (RAPD), an EcoRI restriction site polymorphism in the 5.8S ribosomal DNA (rDNA), the alkaloids produced, and conidial morphology. We identified three groups: (i) group G1 from fields and open meadows (57 isolates), (ii) group G2 from shady or wet habitats (41 isolates), and (iii) group G3 from Spartina anglica from salt marshes (2 isolates). The sclerotia of G1 isolates contained ergotamines and ergotoxines; G2 isolates produced ergosine and ergocristine along with small amounts of ergocryptine; and G3 isolates produced ergocristine and ergocryptine. The conidia of G1 isolates were 5 to 8 m long, the conidia of G2 isolates were 7 to 10 m long, and the conidia of G3 isolates were 10 to 12 m long. Sclerotia of the G2 and G3 isolates floated on water. In the 5.8S rDNA analysis, an EcoRI site was found in G1 and G3 isolates but not in G2 isolates. The host preferences of the groups were not absolute, and there were host genera that were common to both G1 and G2; the presence of members of different groups in the same locality was rare. Without the use of RAPD or rDNA polymorphism, it was not possible to distinguish the three groups solely on the basis of phenotype, host, or habitat. In general, populations of C. purpurea are not host specialized, as previously assumed, but they are habitat specialized, and collecting strategies and toxin risk assessments should be changed to reflect this paradigm shift.Claviceps purpurea is an ergot fungus with a wide host range that includes the entire subfamily Pooideae, many members of the Arundinoideae, and some species belonging to the chloridoid and panicoid groups (4, 15). Its distribution is basically Holarctic, but it has been recorded in Arctic regions (14) and also occurs in southern temperate and subtropical regions. Due to movement with cereal and grass seeds by migrants, the center of origin of this species is not known.C. purpurea is morphologically quite variable. Sclerotial length ranges from 2 to 50 mm, and the color of the stromata varies over a wide range of red shades from wine to purple (25) and even to orange (31). Conidial size and shape also are polymorphic; the conidia range from oval spores that are 5 m long to cylindric or elongated spores that are up to 13 m long (15,25,31). The sclerotia contain peptide alkaloids that belong to three basic groups, the ergotamines (with alanine as the first amino acid entering the cyclopeptide moiety), the ergotoxines (with valine), and the rarely found ergoxines (with 2-aminoisobutyric acid) (for reviews see references 7 and 33).For the last 100 years, researchers have tried to use this variation to establish varieties, special forms, or races (1), and the primary focus has been on detection of host-specific groups. Stäger introduced four special forms: secalis, lolii (later joined with secalis) (2), milii (on Milium and Brachypodium only), and glyceriae (suspected to be Claviceps wilsonii) for C. purpurea se...

The Campylobacter species strains (n = 42; isolated from clinical samples and deposited in Czech National Collection of Type Cultures, Prague) originally phenotypically (and biochemically) identified as Campylobacter jejuni were re-classified using molecular biological and mass spectrometric methods. Whole-cell MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) separated the isolates into two genetically related strains--C. jejuni (n = 26) and C. coli (n = 16) and, moreover, distinguished the intimate details in the group of tested strains. It also made it possible to create the MALDI-TOF MS dendrogram; similarly, the spectral characteristics were used for the 3D cluster analysis. Polymerase chain reaction (PCR) confirmed the results obtained by mass spectrometry. Both methods (PCR and MALDI-TOF MS) gave the same results which supports their suitability in the rapid and accurate Campylobacter-species determination.

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