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PubMed2001

Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation.

Nested haplotype networks for three loci in a haploid, fungal plant pathogen, Sclerotinia sclerotiorum, in two natural, Norwegian populations of the woodland buttercup, Ranunculus ficaria, were extended with DNA fingerprints to determine fine-scale population divergence. To preserve the cladistic structure in the network for both nonrecombinant and postrecombinant haplotypes in highly recombinant clades, recombinant events were not removed ('peeled off'), but instead were examined in alternative (marginal) networks. Fungi from both sampling locations share a common origin with subsequent genetic divergence, consistent with expectations for metapopulation structure. Evidence for divergence includes (i) lack of shared fingerprints between the two locations, (ii) evolution of new fingerprints, via transposition and recombination, within 2 years on a fine spatial scale within one sampling location, and (iii) increase in the size of the intergenic spacer (IGS) in both sampling locations. Sites of microsatellite repeat expansion and of an insertion were consistent with the boundaries of two recombination blocks in the IGS. Both alternative networks based on the recombination blocks were essential to finding all associations of DNA fingerprints with IGS size, sampling site, sampling year and mycelial compatibility group. Variation in the elongation factor 1alpha and calmodulin loci supported the topologies and the recurrent, ongoing polarity of change in fingerprints and IGS size inferred from the IGS.

Ascomycota↗
PubMed2000

Molecular fingerprinting of Mycobacterium tuberculosis strains isolated in Vietnam using IS6110 as probe.

SETTING: Northern and Southern areas of Vietnam. OBJECTIVE: To study the correlation between DNA fingerprinting of 168 Mycobacterium tuberculosis strains isolated from patients with a particular historical past (political separation of Vietnam for 20 years) and data about geographical origin, drug susceptibility, HIV infection and BCG vaccination status. METHODS: Comparison of restriction fragment length polymorphism (RFLP) patterns produced by Southern hybridization of Pvull-digested chromosomal DNA. RESULTS: The number of IS6110 copies for the 168 strains ranges from 0 to 23. Strains originating from the North or the South differ strongly with respect to the number of copies of IS6110. Indeed, the strains originating from the north have predominantly from 3 to 14 IS6110 copies while the southern strains have predominantly from 15 to 23 IS6110 copies. Furthermore, strains isolated in the North are dispersed into 6 groups whereas 80% of the strains isolated in the South form a single group. Moreover, the prevalence of drug resistance is higher in strains isolated in the South than in the North. No noticeable correlation is observed between RFLP patterns, drug susceptibility, or HIV infection. CONCLUSION: The IS6110 fingerprints of 168 M. tuberculosis strains isolated in Vietnam showed a high range of polymorphism. Only a few strains have been found with no IS6110 (1.8%). The differences between the strains from the North and South, having more than six IS6110, suggests that they derived from ancestral strains that would be distinguishable by the number of IS6110 and their transposition sites throughout the genome. The genomic structure of the population of strains from South Vietnam resembles that of the Beijing strain population. This could account for a similar evolution of M. tuberculosis due to a selection by BCG-induced immunity in the two populations.

BCG Vaccine↗
PubMed2001

DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes.

DNA microarrays constructed with full length ORFs from Shewanella oneidensis, MR-1, were hybridized with genomic DNA from nine other Shewanella species and Escherichia coli K-12. This approach enabled visualization of relationships between organisms by comparing individual ORF hybridizations to 164 genes and is further amenable to high-density high-throughput analyses of complete microbial genomes. Conserved genes (arcA and ATP synthase) were identified among all species investigated. The mtr operon, which is involved in iron reduction, was poorly conserved among other known metal-reducing Shewanella species. Results were most informative for closely related organisms with small subunit rRNA sequence similarities greater than 93% and gyrB sequence similarities greater than 80%. At this level of relatedness, the similarity between hybridization profiles was strongly correlated with sequence divergence in the gyrB gene. Results revealed that two strains of S. oneidensis (MR-1 and DLM7) were nearly identical, with only 3% of the ORFs hybridizing poorly, in contrast to hybridizations with Shewanella putrefaciens, formerly considered to be the same species as MR-1, in which 63% of the ORFs hybridized poorly (log ratios below -0.75). Genomic hybridizations showed that genes in operons had consistent levels of hybridization across an operon in comparison to a randomly sampled data set, suggesting that similar applications will be informative for identification of horizontally acquired genes. The full value of microbial genomic hybridizations lies in providing the ability to understand and display specific differences between closely related organisms providing a window into understanding microheterogeneity, bacterial speciation, and taxonomic relationships.

Bacterial Proteins↗
PubMed2005

Analysis of Pneumocystis jirovecii DHPS alleles implicated in sulfamethoxazole resistance using an Escherichia coli model system.

Pneumocystis jirovecii is a major opportunistic pathogen that causes Pneumocystis pneumonia (PCP). Drug treatment failure has been associated epidemiologically with point mutations in the gene for dihydropteroate synthase which is part of a gene that encodes three covalently linked enzymes involved in folic acid synthesis (FAS). The evaluation of whether mutations found in P. jirovecii FAS lead to sulfa drug resistance is hampered by the lack of a culture system for P. jirovecii as well as the failure of P. jirovecii FAS to complement in a heterologous system. Therefore, we chose to model the P. jirovecii mutations in the Saccharomyces cerevisiae FAS protein (encoded by FOL1) via its expression in Escherichia coli. An optimized drug diffusion assay was used to evaluate the FAS mutants against 15 sulfa drugs. It was established that the single amino acid substitution, P599S, in the (DHPS) domain of FAS led to sulfa drug resistance, whereas the T597A substitution led to increased sensitivity. The presence of both mutations (T597A and P599S) was cooperative and led to increased sulfa drug resistance. Analysis of a novel double mutant, (T597V P599S) was found to have significantly higher sulfa drug resistance than the T597A P599S mutant. These data suggest that further amino acid substitutions may lead to the evolution of higher sulfa drug resistance. Two sulfa drugs (sulfachloropyridazine and sulfathiazole) were identified that had higher inhibitory potential than sulfamethoxazole, which is currently the preferred treatment for PCP.

Amino Acid Substitution↗
PubMed2006

Evolutionary history of Salmonella typhi.

For microbial pathogens, phylogeographic differentiation seems to be relatively common. However, the neutral population structure of Salmonella enterica serovar Typhi reflects the continued existence of ubiquitous haplotypes over millennia. In contrast, clinical use of fluoroquinolones has yielded at least 15 independent gyrA mutations within a decade and stimulated clonal expansion of haplotype H58 in Asia and Africa. Yet, antibiotic-sensitive strains and haplotypes other than H58 still persist despite selection for antibiotic resistance. Neutral evolution in Typhi appears to reflect the asymptomatic carrier state, and adaptive evolution depends on the rapid transmission of phenotypic changes through acute infections.

Adaptation, Physiological↗
PubMed2004

Ecological sources of zoonotic diseases.

Although of zoonotic origin, pathogens or infections posing a global threat to human health such as human immunodeficiency virus, severe acute respiratory syndrome or emerging influenza type A viruses may actually have little in common with known, established zoonotic agents, as these new agents merely underwent a transient zoonotic stage before adapting to humans. Evolution towards person-to-person transmission depends on the biological features of the pathogen, but may well be triggered or facilitated by external factors such as changes in human exposure. Disease emergence may thus be depicted as an evolutionary response to changes in the environment, including anthropogenic factors such as new agricultural practices, urbanisation, or globalisation, as well as climate change. Here the authors argue that in the case of zoonotic diseases emerging in livestock, change in agricultural practices has become the dominant factor determining the conditions in which zoonotic pathogens evolve, spread, and eventually enter the human population. Livestock pathogens are subjected to pressures resulting from the production, processing and retail environment which together alter host contact rate, population size and/or microbial traffic flows in the food chain. This process is illustrated by two study cases: a) livestock development in the 'Eurasian ruminant street' (the area extending from central Asia to the eastern Mediterranean basin) and the adjacent Arabian peninsula b) poultry production in Southeast Asia. In both scenarios, environmental factors relating to demography, land pressure and imbalances in production intensification have led to an unstable epidemiological situation, as evidenced by the highly pathogenic avian influenza upsurge early in 2004, when the main outbreaks were located in areas which had both large scale, peri-urban commercial holdings and a high density of smallholder poultry units.

Adaptation, Physiological↗
PubMed2003

RNA, the first macromolecular catalyst: the ribosome is a ribozyme.

Recently, the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with substrates have been determined. These have provided exciting new insights into the principles of RNA structure, the mechanism of the peptidyl-transferase reaction and early events in the evolution of this RNA-protein complex assembly that is essential in all cells. The structures of the large subunit bound to a variety of antibiotics explain the effects of antibiotic resistance mutations and provide promise for the development of new antibiotics.

Drug Resistance, Microbial↗
PubMed2000

Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit.

The record of Archaean microfossils is sparse. Of the few bona fide fossil assemblages, most are from shallow-water settings, and they are typically associated with laminated, stromatolitic sedimentary rocks. Microfossils from deep-sea hydrothermal systems have not been reported in Precambrian rocks (> 544 million years old), although thermophilic microbes are ubiquitous in modern sea-floor hydrothermal settings, and apparently have the most ancient lineages. Here, I report the discovery of pyritic filaments, the probable fossil remains of thread-like microorganisms, in a 3,235-million-year-old deep-sea volcanogenic massive sulphide deposit from the Pilbara Craton of Australia. From their mode of occurrence, the micro-organisms were probably thermophilic chemotropic prokaryotes, which inhabited sub-sea-floor hydrothermal environments. They represent the first fossil evidence for microbial life in a Precambrian submarine thermal spring system, and extend the known range of submarine hydrothermal biota by more than 2,700 million years. Such environments may have hosted the first living systems on Earth, consistent with proposals for a thermophilic origin of life.

Archaea↗
PubMed2006

Detection of a novel variant bla(CTX-M-3) extended spectrum beta-lactamase gene in a community-acquired Escherichia coli isolate.

A highly cefotaxime- and cefepime-resistant but ceftazidime-sensitive Escherichia coli isolate was recovered from a community-acquired urinary infection of a Greek patient. Susceptibility testing, transfer assays, plasmid analysis as well as PCR and sequencing techniques were used to investigate the underlying mechanism of resistance. The isolate carried a new variant of the bla(CTX-M-3) gene that possessed a T instead of A at nt position 663. Cefotaxime resistance was transferable and carried on a 60 kb plasmid. The bla(CTX-M-3) variant was located downstream of an ISEcp1B element. The emergence of this new derivative indicates further evolution of the worldwide-distributed bla(CTX-M-3) gene.

Anti-Bacterial Agents↗
PubMed1999

How microbial ancient DNA, found in association with human remains, can be interpreted.

The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies.

Animals↗
PubMed2003

Evolutionary implications of microbial genome tetranucleotide frequency biases.

We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA.

Chromosome Mapping↗
PubMed1998

In vitro susceptibility of Plasmodium falciparum to four antimalarial drugs in the Central Province of Papua New Guinea.

The susceptibility of Plasmodium falciparum to chloroquine, quinine, mefloquine and halofantrine was investigated in the Central Province of Papua New Guinea between March 1995 and September 1996, when chloroquine resistance was widely present in the country. The standard World Health Organization in vitro microtest methodology was used in the study. Of the 30 isolates tested for chloroquine susceptibility all were resistant to chloroquine with median IC50 of 1.15 mumol/l (range 0.54 to 4.24), indicating a high prevalence and degree of resistance. Three isolates each for quinine (3/31) and halofantrine (3/28) showed resistance at concentrations of 51.2 mumol/l and 10 nM respectively, while all 31 isolates tested for mefloquine were fully susceptible. The comparative analysis of median IC50 values between isolates resistant and susceptible to chloroquine showed chloroquine-resistant isolates to be less susceptible to quinine and halofantrine while fully susceptible to mefloquine. It seems that the evolution of chloroquine resistance together with increased use of quinine treatment of P. falciparum malaria may increase the risk of emergence of quinine resistance and possibly of halofantrine resistance as well. The development of mefloquine resistance, however, is independent of chloroquine resistance.

Animals↗
PubMed1998

[Comparative evaluation of microorganisms biological characteristics isolated in the orbital complex "Mir" on different phases of its operation].

Colonizing and bio-destructive activities and pathogenetic potential of microorganisms isolated from the MIR environment at different phases of its operations were tested and evaluated in comparison with standard "museum" cultures of analogous species. Comparison of bacterial and fungal species revealed certain cultural, biochemical, and morphological distinctions of the "flight" strains. However, to assess the character and the risk associated with peculiar evolution of microflora in long-term space missions, more careful investigations should be followed with the use of the strain genetic labeling and other modern techniques.

Air Microbiology↗
PubMed1996

Microbial respiratory activity in the euphotic zone of the Mediterranean Sea.

Microplankton respiration in the euphotic zone in the Central Mediterranean Sea was calculated by ETS activity measurements. Distribution of ETSa in the studied area appeared homogeneous and comparable with previous data measured in the Mediterranean Sea. A typical ETSa value for euphotic Mediterranean waters of 0.14 meq O2 h-1 m-3 was calculated. The investigated area supports a metabolic CO2 production of 70 g C m-2 y-1. When compared with regional productivity, the respiration budget in the euphotic zone accounted for 22% of carbon fixed. ETSa appeared a useful assay for the study of evolutive history of the water masses in the Mediterranean Sea.

Animals↗
PubMed2026

Ten millennia of purifying selection on HLA-B27 reveals an ancient epidemic-scale burden of spondyloarthritis in West Eurasia.

HLA-B27 exemplifies an evolutionary trade-off between protection against infection and susceptibility to inflammatory disease. To investigate its long-term population history, this study examined three HLA-B27-tagging variants-rs116488202, rs4349859, and rs116666910-in present-day populations from UK biobank and 1000 Genomes Project, and in 15,836 ancient West Eurasian individuals. The estimated frequency of HLA-B27 reached 49.0% approximately 8500 years before present, then declined progressively to 3.9% in the present-day reference population. Comparison with genome-wide association study (GWAS) data for ankylosing spondylitis (AS) showed that HLA-B27-linked alleles conferring increased disease risk had negative selection coefficients, indicating sustained selection against HLA-B27 over the past 10,000 years. The decline coincided with major Holocene changes in settlement and subsistence patterns, microbial exposure, and enteric infection, which may have increased the inflammatory costs of HLA-B27. Because previous paleopathological studies have largely been limited to identifying advanced skeletal manifestations of AS, this ancient genetic study may provide currently the most sensitive population-level record of an otherwise largely undetectable, epidemic-scale disease burden in antiquity. These findings support the hypothesis that HLA-B27-associated spondyloarthritis was sufficiently prevalent and severe to influence human evolution in prehistoric West Eurasia.

Humans↗
PubMed2006

[Dermatosis-arthritis syndrome associated with Crohn's disease in a teenager].

INTRODUCTION: Pustulosis, erythema nodosum, arthritis and systemic manifestations are associated in the dermatosis-arthritis syndrome. It is a well recognized complication of the bowel ileo-jejunal bypass but it is also associated with inflammatory bowel diseases. EXEGESE: We report the case of an adolescent who presented with a dermatosis-arthritis syndrome associated to a Crohn's disease during a referring for pustulosis, erythema nodosum and fever. The evolution is complicated by proctorragia. Colonoscopy and intestinal biopsy found a Crohn's disease. Cutaneous and intestinal symptoms quickly improved with systemic corticosteroids. CONCLUSION: The dermatosis-arthritis syndrome can be associated with bowel bypass and with inflammatory bowel disease, more frequently with ulcerative colitis than with Crohn's disease. It consists in a vesiculo-pustular eruption, erythema nodosum, fever, arthritis and ocular manifestations. Histopathology bears a strong resemblance with Sweet's syndrome. Physiopathology implicates microbial proliferation, formation of immune complex against skin and activation and migration of neutrophils and increasing factors. The treatment is based on corticosteroids and non steroid anti-inflammatory drugs or dapsone.

Adolescent↗
PubMed1998

T cell receptor repertoire in rheumatoid arthritis.

CD4+ T cells are a major component of the inflammatory infiltrate in rheumatoid synovitis. Within synovial lesions, clonal CD4+ T cell populations are detectable, supporting the notion of an antigen specific recognition even in the joint. In general, the clonal size of individual T cell clones is small and does not lead to a marked distortion of the synovial T cell receptor (TCR) repertoire. Comparison of TCR sequences derived from different patients has not provided evidence for common sequences. Either multiple antigens are recognized or the TCR repertoire is sufficiently plastic with a multitude of different TCR structures responding to the same antigen(s). However, within one individual, the repertoire of clonal T cell populations is restricted. Identical T cell clones can be identified in different joints and at different timepoints of the disease, emphasizing that the spectrum of antigens recognized is conserved over time and that the T cell response pattern is not subject to evolution. Characterization of antigens involved in the latter stages of the disease may thus provide critical information on disease-initiating events. Recent data have led to the new concept that the role of T cells in rheumatoid arthritis (RA) is not limited to synovial inflammation. Evidence has been provided that the premorbid TCR repertoires of RA patients and normal controls can be distinguished. The T cell repertoire in RA patients is prone to recognize certain microbial products and autoantigens. The selection of this response pattern can only partially be attributed to the disease associated HLA-DRB1 alleles. Additional factors common in RA patients but not in HLA-DR matched control individuals seem to be important in shaping the TCR repertoire. Furthermore, the repertoire of mature T cells in RA patients is characterized by oligoclonality which involves T cells in the peripheral blood compartment. Possibly, these clonal T cell populations react to widespread autoantigens, raising the possibility that RA patients have a defect in controlling peripheral tolerance and an anomaly of lymphoproliferation. In contrast to joint residing CD4+ T cells, expanded clonotypes isolated from the blood of different patients have been described to share TCR beta chain structures. How these characteristic features of the global TCR repertoire in RA patients translate into mechanisms of disease remains to be elucidated.

Arthritis, Rheumatoid↗