Prevention through immunization: new opportunities or end of the road?
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Animals↗
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Results for “bacterial evolution”
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Assessment of the fitness impacts on Escherichia coli of acquisition of antibiotic resistance genes encoded by different types of genetic element.
OBJECTIVES: Little is known of the fitness cost that antibiotic resistance exerts on wild-type bacteria, especially in their natural environments. We therefore examined the fitness costs that several antibiotic resistance elements imposed on a wild-type Escherichia coli isolate, both in the laboratory and in a pig gut colonization model. METHODS: Plasmid R46, Tn1 and Tn7 and a K42R RpsL substitution were separately introduced into E. coli 345-2 RifC, a rifampicin-resistant derivative of a recent porcine isolate. The insertion site of Tn1 was determined by DNA sequencing. The fitness cost of each resistance element was assessed in vitro by pairwise growth competition and in vivo by regularly monitoring the recovery of strains from faeces for 21 days following oral inoculation of organic piglets. Each derivative of 345-2 RifC carrying a resistance element was grown in antibiotic-free broth for 200 generations and the experiments to assess fitness were repeated. RESULTS: RpsL K42R was found to impose a small fitness cost on E. coli 345-2 RifC in vitro but did not compromise survival in vivo. R46 imposed a cost both before and after laboratory passage in vitro, but only the pre-passage strain was at a disadvantage in vivo. The post-passage isolate had an advantage in pigs. Acquisition of Tn7 had no impact on the fitness of E. coli 345-2 RifC. Two derivatives containing Tn1 were isolated and, in both cases, the transposon inserted into the same cryptic chromosomal sequence. Acquisition of Tn1 improved fitness of E. coli 345-2 RifC in vitro and in vivo in the case of the first derivative, but in the case of a second, independent derivative, Tn1 had a neutral effect on fitness. CONCLUSIONS: The fitness impact imposed on E. coli 345-2 RifC by carriage of antibiotic resistance elements was generally low or non-existent, suggesting that once established, resistance may be difficult to eliminate through reduction in prescribing alone.
Animals↗
Bacterial [Cu,Zn]-superoxide dismutase: phylogenetically distinct from the eukaryotic enzyme, and not so rare after all!
Copper- and zinc-containing superoxide dismutases ([Cu,Zn]-SODs) are generally considered almost exclusively eukaryotic enzymes, protecting the cytosol and extracellular compartments of higher organisms from damage by oxygen free-radicals. The recent description of a few examples of bacterial forms of the enzyme, located in the periplasm of different Gram-negative micro-organisms, prompted a re-evaluation of this general perception. A PCR-based approach has been developed and used successfully to identify bacterial genes encoding [Cu,Zn]-SOD in a wide range of important human and animal pathogens-members of the Haemophilus, Actinobacillus and Pasteurella (HAP) group, and Neisseria meningitidis. Comparison of [Cu,Zn]-SOD peptide sequences found in Haemophilus ducreyi, Actinobacillus pleuropneumoniae, Actinobacillus actinomycetemcomitans, Pasteurella multocida, and N. meningitidis with previously described bacterial proteins and examples of eukaryotic [Cu,Zn]-SOD has shown that the bacterial proteins constitute a distinct family apparently widely separated in evolutionary terms from the eukaryotic examples. The widespread occurrence of [Cu,Zn]-SOD in the periplasm of bacterial pathogens, appropriately located to dismute exogenously derived superoxide radical anions, suggests that this enzyme may play a role in the interactive biology of organisms with their hosts and so contribute to their capacity to cause disease.
Actinobacillus↗
Microevolution within a clonal population of pathogenic bacteria: recombination, gene duplication and horizontal genetic exchange in the opa gene family of Neisseria meningitidis.
Opacity (Opa) proteins are a family of antigenically variable outer-membrane proteins of Neisseria meningitidis. Even among clonally related epidemic meningococcal isolates, there is greater variation of Opa protein expression than can be accounted for by the opa gene repertoire of any individual strain. We characterized the opa genes of eight closely related isolates of serogroup A N. meningitidis (subgroup IV-1) from a recent meningitis epidemic in West Africa. DNA sequence analysis and Southern blot experiments indicated that changes occurred in the opa genes of these bacteria as they spread through the human population, over a relatively short period of time. Such changes in one or a few loci within a clonal population are referred to as microevolution. The distribution of sequences present in hypervariable (HV) regions of the opa genes suggests that duplication of all or part of opa genes into other opa loci changed the repertoire of Opa proteins that could be expressed. Additional variability in this gene family appears to have been introduced by horizontal exchange of opa sequences from other meningococcal strains and from Neisseria gonorrhoeae. These results indicate that processes of recombination and genetic exchange contributed to variability in major surface antigens of this clonal population of pathogenic bacteria.
Antibodies, Bacterial↗
Evidence for frequent OspC gene transfer between Borrelia valaisiana sp. nov. and other Lyme disease spirochetes.
Molecular polymorphism of the ospC gene has been reported in Borrelia burgdorferi sensu stricto, Borrelia garinii and Borrelia afzelii, the spirochetes causing human Lyme borreliosis. To assess the genetic relationship between ospC genes from the recently described Borrelia valaisiana sp. nov. and other B. burgdorferi sensu lato species, the ospC genes from eight B. valaisiana isolates were amplified by PCR, cloned and sequenced. The ospC genes of three B. valaisiana isolates were identical, but clearly distinct from ospC genes from other Borrelia species. Four B. valaisiana isolates possessed ospC genes more related to those of B. garinii, and fell into a cluster representing B. garinii species in the phylogenetic tree. One isolate had an ospC gene encoding a protein identical to that of B. afzelii strain. Since five of the eight (62.5%) B. valaisiana isolates contained a gene highly homologous or even identical to ospC genes found among B. garinii and B. afzelii strains, our findings indicate that ospC gene transfer occurs between B. valaisiana and other Lyme disease spirochetes.
Amino Acid Sequence↗
Evidence for a clonal origin of methicillin resistance in Staphylococcus aureus.
Soon after methicillin was introduced into clinical practice in the early 1960s, resistant strains of Staphylococcus aureus (MRSA) appeared, bearing a newly acquired resistance gene, mecA, that encodes a penicillin binding protein, PBP2a. MRSA have spread throughout the world, and an investigation of the clonality of 472 isolates by DNA hybridization was performed. All 472 isolates could be divided into six temporally ordered mecA hybridization patterns, and three of these were subdivided by the chromomosomal transposon Tn554. Each Tn554 pattern occurred in association with one and only one mecA pattern, suggesting that mecA divergence preceded the acquisition of Tn554 in all cases and therefore that mecA may have been acquired just once by S. aureus.
Bacterial Proteins↗
Prevalence and distribution of the hmw and hia genes and the HMW and Hia adhesins among genetically diverse strains of nontypeable Haemophilus influenzae.
Nontypeable Haemophilus influenzae is a common cause of human disease and initiates infection by colonizing the upper respiratory tract. In previous work we identified high-molecular-weight adhesins referred to as HMW1 and HMW2, expressed by nontypeable strain 12, and determined that most strains of nontypeable H. influenzae express one or two antigenically related proteins. More recently, we determined that some strains lack HMW1- and HMW2-like proteins and instead express an adhesin called Hia. In the present study, we determined the prevalence and distribution of the hmw and hia genes in a collection of 59 nontypeable strains previously characterized in terms of genetic relatedness. Based on Southern analysis, 47 strains contained sequences homologous to the hmw1 and hmw2 genes and nine strains contained homologs to hia. No strain harbored both hmw and hia, and three strains harbored neither. Although the hmw and hia genes failed to define distinct genetic divisions, the hmw-deficient strains formed small clusters or lineages within the larger population structure. Additional analysis established that the IS1016 insertion element was uniformly absent from strains containing hmw sequences but was present in two-thirds of the hmw-deficient strains. As IS1016 is associated with the capsule locus (cap) in most encapsulated strains of H. influenzae, we speculate that hmw-deficient nontypeable strains evolved more recently from an encapsulated ancestor.
Adhesins, Bacterial↗
Lineage-specific gene duplication and loss in human and great ape evolution.
Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
Animals↗
The function and organization of plasmids.
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Antitoxins↗
Problems posed by natural environments for monitoring microorganisms.
Microorganisms in natural environments have evolved to withstand fluctuations in physical and chemical conditions. This means that they often manifest very different biochemical and morphological features compared with those seen during laboratory culture. A major limitation in natural ecosystems is nutrient limitation under which microorganisms are exposed to starvation conditions and grow slowly or not at all. This review identifies the role of inimical processes on microbial properties such as the responses to starvation that may result in the adoption of viable but nonculturable (VBNC) states, discusses the problems that altered physiological states pose for detection and identification and highlights novel methods that have been developed to circumvent these difficulties. These factors dictate that to survive and respond to environmental stimuli, a cell must have evolved sophisticated programs of gene expression. These include the sigma factor rpoS that directs RNA polymerase to transcribe genes whose expression aids survival during severe nutrient limitation or cell-cell communication systems that promote a concerted population response termed quorum sensing.
Adaptation, Physiological↗
Evolution of conjugate vaccines.
Conjugate vaccines--bacterial polysaccharides conjugated to proteins to improve their immunizing properties--have been a success story since their introduction less than 20 years ago. The Haemophilus influenzae type b conjugate vaccine has nearly eliminated invasive Haemophilus influenzae type b disease in large parts of the world. The key reasons for its success are its ability to induce immunologic memory and reduce asymptomatic carriage, hence the spread of infection. The first pneumococcal conjugate vaccine was licensed in 2000 and is already in wide demand in the USA. The first meningococcal conjugate vaccine was introduced in a nationwide program in the UK in 1999. Current discussion focuses on the efficacy of the conjugate vaccines for different end-points and the cost-effectiveness of their use globally.
Adult↗
The evolution of function: a new method to assess the phylogenetic value of ribosomal sensitivity to antibiotics.
Thirty-five archaeal, bacterial and eukaryotic translational systems have been proved against forty different protein synthesis inhibitors with diverse domain and functional specificities. The inhibition curves generated in every ribosome-antibiotic combination had previously shown interesting similarities among organisms belonging to the same phylogenetic group. This opened the possibility of using such functional information for developing evolutionary studies. A new mathematical method based on the main data components analysis has been developed to extract most of the information contained in the inhibition curves. The phenograms obtained closely resemble those generated by the small ribosomal subunit rRNA sequence comparison and such functional clustering is also congruent when a particular subset of organisms and/or antibiotics is used. These results prove the phylogenetic value of our functional analysis and suggest that the ribosome represents an interesting intersection between genotypic and phenotypic (functional) information stored in organisms.
Animals↗
Regulatory relationship of two-component and ABC transport systems and clustering of their genes in the Bacillus/Clostridium group, suggest a functional link between them.
On the Bacillus subtilis chromosome there are five examples of genes encoding two-component systems with response regulators of the OmpR family adjacent to genes encoding sub-family 9 ABC transport systems. Three of these (yts, yvc, yxd) are very similar in gene organization and in sequence. We demonstrate that the TCS and ABC transporter genes do not belong to the same transcriptional unit. The ABC transport and TCS systems are functionally linked, each response regulator controlling the expression of its cognate ABC transporter genes but not its own. Analysis of 48 bacterial genomes revealed that such family clusters only exist in the Bacillus/Clostridium group. Evolutionary analyses indicated that almost all clustered OmpR response regulators constitute two groups ("GI" and "GIIl") whereas almost all clustered sub-family 9 nucleotide-binding domains belong to two other groups ("9A" and "9B"). Interestingly, there is a mutually exclusive clustering between genes encoding "GI" or a "GII" response regulators and genes encoding "9A" or a "9B" nucleotide binding proteins. We propose that a two-component system and its cognate ABC transporter genes have evolved as a unit in Bacillus/Clostridium, both systems participating in a common physiological process.
ATP-Binding Cassette Transporters↗
Plasmid fingerprinting. A tool for bacterial strain identification and surveillance of nosocomial and community-acquired infections.
Plasmid fingerprinting provides a rapid and dependable means of identifying bacterial isolates of the same strain. The stability, wide distribution, and diverse nature and size of extrachromosomal elements make it suitable for virtually all bacterial genera. There are many different procedures available for plasmid screening, and the one chosen depends primarily on the types of organisms to be analyzed. Some procedures are better suited to gram-positive organisms; others are better for visualizing the very large plasmids often seen in Pseudomonas and Rhizobium species. The key to the plasmid fingerprinting technique is agarose gel electrophoresis. In this step of the technique, it is important to differentiate open circular from closed circular forms of plasmids and to recognize the "smile effect." Plasmid fingerprinting can be utilized for epidemiologic studies of both nosocomial and community-acquired infections. The use of restriction endonuclease analysis can greatly enhance the ability of the investigator to differentiate strains that harbor only a single plasmid. Plasmid fingerprinting often provides the only differential characteristic for strains involved in epidemics.
Bacteria↗
Secondary metabolism, inventive evolution and biochemical diversity--a review.
Evidence now being obtained through nucleotide (nt) sequence analysis supports the concept that secondary metabolism has arisen by modification of existing primary metabolic reactions. Although amino acid sequence identity deduced from nt sequences of genes encoding proteins from related primary and secondary metabolic pathways is sufficient to indicate a common ancestry, the match is often better when genes in different rather than in the same species are compared. The information so far available suggests that gene transfer between organisms has been an important factor in the evolution of secondary metabolism. Many secondary pathways may be of relatively ancient origin and they may have arisen only infrequently. Much subsequent elaboration of the pathways has probably taken place after their acquisition by other species and so has been influenced by a variety of selective conditions. The characteristic diversity of secondary metabolites and their functions can be accounted for by the random manner in which the pathways initially evolved and have subsequently been exploited.
Anti-Bacterial Agents↗
RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains.
The RAPD (random amplified polymorphic DNA) fingerprinting method, which utilizes low stringency PCR amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments, was calibrated relative to the widely used, protein-based multilocus enzyme electrophoretic (MLEE) typing method. RAPD fingerprinting was carried out on five isolates from each of 15 major groups of Escherichia coli strains that cause diarrheal disease worldwide (75 isolates in all). Each group consisted of isolates that were not distinguishable from one another by MLEE typing using 20 diagnostic enzyme markers. In our RAPD tests, three or more distinct subgroups in each MLEE group were distinguished with each of five primers, and 74 of the 75 isolates were distinguished when data obtained with five primers were combined. Thus, RAPD typing is far more sensitive than MLEE typing for discriminating among related strains of a species. Despite their different sensitivities, the same general relationships among strains were inferred from MLEE and RAPD data. Thus, our results recommend use of the RAPD method for studies of bacterial population genetic structure and evolution, as well as for epidemiology.
Bacteria↗
Intracellular survival strategies of mutualistic and parasitic prokaryotes.
Endosymbiotic bacteria closely related to mammalian pathogens are widespread in invertebrates. Mutualistic and parasitic bacteria-host interactions on the various evolutionary levels apparently involve similar factors, indicating that relevant genetic information developed early in evolution. The detailed characterization of symbiotic interactions of bacteria with non-mammalian hosts should provide profound insights into the basic mechanisms of bacteria-host interactions and their evolution.
Animals↗
Molecular evolution of pathogenic Escherichia coli.
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Animals↗