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PubMed2003

Morphologies and phylogenetic classification of cellulolytic myxobacteria.

The evolutionary distances of the 16S rDNA sequences in cellulolytic myxobacteria are less than 3%, which units all the strains into a single genus, Sorangium. The size of myxospores and the shape of sporangioles, rather than fruiting body colors or swarm morphologies are consistent with the changes of the 16S rDNA sequences. It is suggested that there are at least two species in the genus Sorangium: one includes strains with small myxospores and spherical sporangioles, and the color of the fruiting bodies is normally orange or brown, though sometimes yellow or black. The second species has large myxospores, polyhedral sporangioles with many inter-cystic substrates, and normally deep brown to black color.

Cellulose↗
PubMed2000

Short therapy with amoxicillin-clavulanate and corticosteroids in acute sinusitis: results of a multicentre study in adults.

Evolution of bacterial resistance shortens antibiotic treatment in ENT infections. The efficacy and tolerance of amoxicillin-clavulanate (ACA), with and without associated short steroid therapy, was evaluated in acute sinusitis of adults at a dosage of 1.5 g/d for 5 d vs. 10 d. This multicentre, randomized, double-blind, placebo-controlled study included 433 patients, 417 of whom were suitable for intent-to-treat (ITT) analysis. The therapeutic success rate in the ITT population, assessed according to strict clinical and radiological criteria, was respectively, 80% and 85% in the 5-d and 10-d treatment groups. Due to the statistical risks that were evidenced, the 2 durations of treatment could not be considered equivalent. The analysis of medical history shows that some risk factors (recurrence of sinusitis, previous surgical sinus drainage) seem to promote therapeutic failure and that 5-d treatment is inappropriate in these patients. The persistence of therapeutic success on day 30 was not influenced by the initial duration of treatment. The efficacy and good tolerance of ACA in acute sinusitis in adults were confirmed. Further studies will be needed to define the indications of short treatments better, which seem to be indicated in the absence of specific risk factors.

Acute Disease↗
PubMed2001

Evolution, incidence, and susceptibility of bacterial bloodstream isolates from 519 bone marrow transplant patients.

Bacteria remain an important cause of infection in bone marrow transplants. To examine shifts in the etiology and susceptibility of bacterial isolates from transplants, we reviewed the incidence and susceptibility of blood isolates during a 7-year period. The infection rate fell dramatically during this time. Gram-positive organisms were isolated more often than gram-negative organisms, but the trend is reversing. Streptococci surpassed staphylococci for 5 years as the leading pathogen. Increasing resistance to penicillin, ciprofloxacin, and imipenem was noted in Streptococcus species. With the exception of type 1 beta-lactamase-producing bacteria and Pseudomonas aeruginosa, gram-negative isolates remained overall susceptible to ceftazidime. Increased antibiotic prophylaxis coincided with the reduction in percentage of infected patients and increase in resistance to beta-lactam antibiotics. Mortality attributed to bacteremia was low except for infections caused by P. aeruginosa and the Enterobacter, Serratia, Citrobacter group. There was no mortality attributable to gram-positive organisms such as Staphylococcus aureus and viridans streptococci.

Adolescent↗
PubMed2005

Genetic differentiation of methicillin-resistant Staphylococcus aureus strains from Korea and Japan.

In this study, we evaluated genetic differentiation between methicillin-resistant Staphylococcus aureus (MRSA) strains from Korea and Japan. Seventy-five MRSA strains, including 25 h VISA strains, were analyzed by molecular typing methods, including multilocus sequence typing (MLST), SCC mec typing, and spa typing. The most prevalent genotype of MRSA strains, in both Korea and Japan, was ST 5-MRSA-II with the DMGMK spa motif, characteristic of the New York/Japan MRSA clone. In spite of these common features in MRSA strains from Korea and Japan, we also observed some genotypic divergence in MRSA from the two countries. Several spa types might be differentiated from a prevalent prototype (TJMBMDMGMK) that is shared by the two countries, revealing a unique geographic distribution. SCC mec type II lacking pUB110, designated type IIA, was found more frequently in Korea than in Japan. The rate of gentamicin resistance was also dramatically different between the two countries: 87.2% (Korea) vs. 28.6% (Japan). These preliminary findings suggested that MRSA strains from Korea and Japan might have originated from a common ancestor, but then clearly differentiated according to locality. A further comprehensive study should be performed to document the hypotheses from this study.

Bacterial Typing Techniques↗
PubMed2005

Horizontal gene transfer depends on gene content of the host.

Horizontal gene transfer is a major contributor to the evolution of bacterial genomes. We examine this process through a combination of comparative genomics and in silico analysis of the Escherichia coli metabolic network. We validate our horizontal transfer estimates by confirming the predicted gradual amelioration of GC content over time. We find that the chance of acquiring a gene by horizontal transfer is up to six times higher if an enzyme that catalyses a coupled metabolite flux is already encoded in the host genome.

Base Composition↗
PubMed2006

Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen.

UNLABELLED: Genomic islands (GIs) are large chromosomal regions present in a subset of bacterial strains that increase the fitness of the organism under specific conditions. We compared the complete genome sequences of two Vibrio vulnificus strains YJ016 and CMCP6 and identified 14 regions (ranging in size from 14 to 117 kb), which had the characteristics of GIs. Bioinformatic analysis of these 14 GI regions identified the presence of phage-like integrase genes, aberrant GC content and genome signature (dinucleotide frequency) within each GI compared with the core genome indicating that these regions were acquired from an anomalous source. We examined the distribution of the nine GIs from strain YJ016 among 27 V. vulnificus isolates and found that most GIs were absent from the majority of these isolates. The chromosomal insertion sites of three GIs were adjacent to tRNA sites, which contained novel horizontally acquired DNA in all six available sequenced Vibrionaceae genomes. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Adaptation, Physiological↗
PubMed1999

Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity.

Previous studies have shown that genetic exchange in bacteria is too rare to prevent neutral sequence divergence between ecological populations. That is, despite genetic exchange, each population should diverge into its own DNA sequence-similarity cluster. In those studies, each selective sweep was limited to acting within a single ecological population. Here we postulate the existence of globally adaptive mutations, which may confer a selective advantage to all ecological populations constituting a metapopulation. Such adaptations cause global selective sweeps, which purge the divergence both within and between populations. We found that the effect of recurrent global selective sweeps on neutral sequence divergence is highly dependent on the mechanism of genetic exchange. Global selective sweeps can prevent populations from reaching high levels of neutral sequence divergence, but they cannot cause two populations to become identical in neutral sequence characters. The model supports the earlier conclusion that each ecological population of bacteria should form its own distinct DNA sequence-similarity cluster.

Adaptation, Physiological↗
PubMed2003

Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres.

We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of approximately 200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that were expanded by retrotransposon invasions. Seven centromere-specific retrotransposons of maize (CRM) were found in BAC 16H10. The CRM elements inserted randomly into either CentC monomers or other retrotransposons. Sequence comparisons of the long terminal repeats (LTRs) of individual CRM elements indicated that these elements transposed within the last 1.22 million years. We observed that all of the previously reported centromere-specific retrotransposons in rice and barley, which belong to the same family as the CRM elements, also recently transposed with the oldest element having transposed approximately 3.8 million years ago. Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family.

Base Sequence↗
PubMed2004

Reduction of the fitness burden of quinolone resistance in Pseudomonas aeruginosa.

OBJECTIVES: Quinolone resistance in the opportunistic pathogen Pseudomonas aeruginosa is commonly caused by mutations that alter the target molecules DNA gyrase/topoisomerase IV, or cause activation of various efflux systems. We have analysed the effect of quinolone resistance caused by DNA gyrase/topoisomerase IV mutations on bacterial fitness. METHODS: Norfloxacin-resistant mutants were isolated and by DNA sequencing the mutations conferring resistance were identified. Mutant fitness was determined by measuring growth rates in vitro. Mutants with reduced growth rates were serially passaged to obtain growth-compensated mutants. The level of DNA supercoiling was determined by isolating plasmid DNA from the susceptible, resistant and compensated mutants and comparing the topoisomer distribution patterns by gel electrophoresis in the presence of chloroquine. RESULTS: Low-level resistance (4-48 mg/L) was caused by single mutations in gyrA or gyrB. Among these strains, three out of eight mutants showed lower fitness, whereas high-level resistant (>256 mg/L) mutants with double mutations in gyrA and parC, parE, nfxB or unknown genes all showed a reduced fitness. Slow-growing resistant mutants with a gyrA mutation had decreased DNA supercoiling. After serial passage in laboratory medium, mutant fitness was increased by compensatory mutation(s) that restored supercoiling to normal levels. The compensatory mutation(s) was not located in any of the genes (gyrAB, topA, parCE, hupB, fis, hupN, himAD or PA5348) that were expected to affect supercoiling. CONCLUSIONS: Our results show that 'no cost' and compensatory mutations are common in quinolone-resistant P. aeruginosa.

Anti-Infective Agents↗
PubMed2006

Common regions e.g. orf513 and antibiotic resistance: IS91-like elements evolving complex class 1 integrons.

The ability of bacteria to procure, sometimes rearrange, and evince acquired DNA continues to impress us-even more so if this genetic plasticity involves the sequestering of antibiotic resistance genes. The acquisition of genes in bacteria is often facilitated by transposons, integrons and archetype insertion elements. Recently however, a new element, 'orf513', has been increasingly associated with class 1 integrons. Moreover, these 'complex' class 1 integrons can potentially mediate resistance to chloramphenicol, trimethoprim, aminoglycosides and tetracycline and may carry a range of beta-lactamase genes as well as the qnrA gene. Elements such as 'orf513' demonstrate IS91-like characteristics and will mobilize adjacent DNA via a process called rolling circle replication, and thus we have renamed them 'insertion sequence CRs' (ISCRs) to appropriately reflect their structure-function properties. In this article, we provide a brief description of these new and clinically important mobile elements, and how they are able to mobilize antibiotic resistance genes.

Anti-Bacterial Agents↗
PubMed2005

Inference and analysis of the relative stability of bacterial chromosomes.

The stability of genomes is highly variable, both in terms of gene content and gene order. Here I calibrate the loss of gene order conservation (GOC) through time by fitting a simple probabilistic model on pairwise comparisons involving 126 bacterial genomes. The model computes the probability of separation of pairs of contiguous genes per unit of time and fits the data better than previous ones while allowing a mechanistic interpretation for the loss of GOC with time. Although the information on operons is not used in the model, I observe, as expected, that most highly conserved pairs of genes are indeed within operons. However, even the other pairs are much more conserved than expected given the observed experimental rearrangement rates. After 500 Myr, about 50% of the originally contiguous orthologues remain so in the average genome. Hence, the large majority of rearrangements must be deleterious and random genome rearrangements are unlikely to provide for positively selected structural changes. I then use the deviations from the model to define an intrinsic measure of genome stability that allowed the comparison of distantly related genomes and the inference of ancestral states. This shows that clades differ in genome stability, with cyanobacteria being the least stable and gamma-proteobacteria the most stable. Without correction for phylogeny, free-living bacteria are the least stable group of genomes, followed by pathogens, and then endomutualists. However, after correction for phylogenetic inertia (or the removal of cyanobacteria from the analysis), there is no significant association between genome stability and lifestyle or genome size. Hence, although this method has allowed uncovering some of mechanisms leading to rearrangements, we still ignore the forces that differentially shape selection upon genome stability in different species.

Bacteria↗
PubMed2001

Identification and structure of the Rhizobium galegae common nodulation genes: evidence for horizontal gene transfer.

Rhizobia are soil bacteria able to fix atmospheric nitrogen in symbiosis with leguminous plants. In response to a signal cascade coded by genes of both symbiotic partners, a specific plant organ, the nodule, is formed. Rhizobial nodulation (nod) genes trigger nodule formation through the synthesis of Nod factors, a family of chitolipooligosaccharides that are specifically recognized by the host plant at the first stages of the nodulation process. Here, we present the organization and sequence of the common nod genes from Rhizobium galegae, a symbiotic member of the RHIZOBIACEAE: This species has an intriguing phylogenetic position, being symbiotic among pathogenic agrobacteria, which induce tumors instead of nodules in plant shoots or roots. This apparent incongruence raises special interest in the origin of the symbiotic apparatus of R. galegae. Our analysis of DNA sequence data indicated that the organization of the common nod gene region of R. galegae was similar to that of Sinorhizobium meliloti and Rhizobium leguminosarum, with nodIJ downstream of nodABC and the regulatory nodD gene closely linked to the common nod operon. Moreover, phylogenetic analyses of the nod gene sequences showed a close relationship especially between the common nodA sequences of R. galegae, S. meliloti, and R. leguminosarum biovars viciae and trifolii. This relationship in structure and sequence contrasts with the phylogeny based on 16S rRNA, which groups R. galegae close to agrobacteria and separate from most other rhizobia. The topology of the nodA tree was similar to that of the corresponding host plant tree. Taken together, these observations indicate that lateral nod gene transfer occurred from fast-growing rhizobia toward agrobacteria, after which the symbiotic apparatus evolved under host plant constraint.

Bacterial Proteins↗
PubMed1996

Identification and distribution of plasmid-type A replicator region in rhizobia.

Sinorhizobium meliloti strain GR4 harbors two cryptic plasmids, named pRmeGR4a and pRmeGR4b in addition to the symbiotic megaplasmids. The replicator region of plasmid pRmeGR4a has been recently cloned and sequenced. By DNA hybridization, homology to former replicator region was found on plasmid pRmeGR4b as well as on other plasmids harbored by S. meliloti and S. fredii strains. In these former bacteria, a PCR product of 362 bp was generated using pRmeGR4a-repC derived primers (C1 and C2). DNA sequence analysis showed that the amplified repC fragments were closely related being classified into two subgroups designated A(I) and A(II). Similarly, a PCR product of 482 bp was obtained when primers (C3 and C5) derived from pRmeGR4a repC-upstream non-coding DNA region (IR) were used. DNA sequence analysis of the corresponding amplified products showed that, as occurs, with repC the IRs were also conserved. In addition, we designed a set of primers (P2/P4), derived from the S. meliloti and S. fredii consensus sequence encompassing the IRs and repC loci, that are able to recognize homologous plasmid-type A replicator regions in Rhizobium. By using these primers, we determined that the former replicator region is widespread in S. meliloti indigenous populations and that its frequency within the infective isolates depends on the host plant. Furthermore, it is shown that the replicator region type A is linked to cryptic plasmids in S. meliloti and S. fredii, whereas it is located in the pSym of R. tropici strains.

Amino Acid Sequence↗
PubMed2000

The evolution of antibiotic therapy for bacterial conjunctivitis and keratitis: 1970-2000.

The editors of this Festschrift asked us to review the use of antibiotics for the treatment of bacterial conjunctivitis and keratitis over the past 25 years, a period coinciding with the life of the Castroviejo Corneal Society. We believe it is more appropriate to begin our review in the late 1960s. about the time that experimental and clinical studies and algorithms for the clinical care derived from these studies helped shape a more rigorous approach to therapy. Those years saw the introduction of antibiotics that were adapted for ophthalmic use, many of which are still being used today. We will give more weight to our review of keratitis than conjunctivitis.

Anti-Bacterial Agents↗
PubMed2001

High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes.

The causes of the variation between genomes in their guanine (G) and cytosine (C) content is one of the central issues in evolutionary genomics. The thermal adaptation hypothesis conjectures that, as G:C pairs in DNA are more thermally stable than adenonine:thymine pairs, high GC content may he a selective response to high temperature. A compilation of data on genomic GC content and optimal growth temperature for numerous prokaryotes failed to demonstrate the predicted correlation. By contrast, the GC content of Structural RNAs is higher at high temperatures. The issue that we address here is whether more freely evolving sites in exons (i.e. codonic third positions) evolve in the same manner as genomic DNA as a whole, Showing no correlated response, or like structural RNAs showing a strong correlation. The latter pattern would provide strong support for the thermal adaptation hypothesis, as the variation in GC content between orthologous genes is typically most profoundly seen at codon third sites (GC3). Simple analysis of completely sequenced prokaryotic genomes shows that GC3, but not genomic GC, is higher on average in thermophilic species. This demonstrates, if nothing else, that the results from the two measures cannot be presumed to be the same. A proper analysis, however, requires phylogenetic control. Here, therefore, we report the results of a comparative analysis of GC composition and optimal growth temperature for over 100 prokaryotes. Comparative analysis fails to show, in either Archea or Eubacteria, any hint of connection between optimal growth temperature and GC content in the genome as a whole, in protein-coding regions or, more crucially at GC. Conversely, comparable analysis confirms that GC content of structural RNA is strongly correlated with optimal temperature. Against the expectations of the thermal adaptation hypothesis, within prokaryotes GC content in protein-coding genies, even at relatively freely evolving sites, cannot be considered an adaptation to the thermal environment.

Adaptation, Physiological↗
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↗