Transposition and the evolution of antibiotic resistance.
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Anti-Bacterial Agents↗
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The impact of "ancient pathogen" studies on the practice of public health.
A new field of "ancient pathogens" is making an impact on our concepts of the evolution of infectious diseases, and it will eventually alter the practice of public health in their control. It has begun to answer important questions regarding past epidemics of influenza and tuberculosis by recovering the genetic sequences of the ancient causative agents. Vaccination strategics will have to study these microbial variants in order to develop tomorrow's vaccines. It may also be possible to examine the role of past and present reservoirs in the dynamics of emerging diseases. In unraveling the evolution of pathogens, insights into the mechanisms of drug and antibiotic resistance are possible. As "genome projects" of more and more pathogens are being completed. Targets for chemotherapy are being revealed which are totally different from the metabolic processes of the mammalian host. Signal molecules are being identified which alter the virulence of the microbe. Focussing on these mechanisms without attempting to kill the pathogen may in some cases drive it into a benign state. These and other aspects of the evolution of pathogens are discussed which may lead to innovative approaches to the control of infectious diseases.
Biological Evolution↗
[Evolution of the concept of genes].
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Animals↗
Metagenomics: genomic analysis of microbial communities.
Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.
Archaea↗
Evaluation of some biological tests as parameters for microbial activities in soils. II. Field investigations.
Investigations were designed to study the effect of certain factors on the microbial activities in soil. The parameters, used as an index of the microbial activities, were total bacterial counts, dehydrogenase activity, oxidation of organic carbon, and CO2 evolved/7 days. Bahteem Farm clay soil was examined for determining the effects of depth, type of fertilization, and crop rotation on the microbial activities. It appears that the microbial activities, as indicated by the tested parameters, were more pronounced in the surface 15 cm-layer than in the subsurface layer (15-30 cm). Results of all the parameters tested showed markedly higher increases with farmyard manure than with nitrogenous fertilizer and in the control, without significant differences between the latter two. Moreover, the time of sampling had no effect on the results obtained for all parameters. Different types of rotations did not exert significant variation in total bacterial counts, though more than one crop per year increased the organic carbon content of soil and mostly the dehydrogenase activity, whereas the evolution of CO2 tended to decrease. At Gabal el-Asfar Farm, the effect of irrigation with sewage effluent, for long periods, on the microbial activities of sandy soil was investigated. Sewage water stimulated the total bacteria, raised the dehydrogenase activity, the organic carbon, and the production of CO2. In North El Tahreer and Mariut Sectors, the effect of both the type and age of cultivation on the microbial activities in the calcareous soils were examined. Cultivation raised the figures of all the tested parameters progressively with time of cultivation. It was also noticed that crops exerted more beneficial effects on microbial activities than orchards, and the dehydrogenase test was the most reliable parameter to reveal this fact.
Bacteria↗
Transposon-based strategies for microbial functional genomics and proteomics.
Transposons are mobile genetic elements that can relocate from one genomic location to another. As well as modulating gene expression and contributing to genome plasticity and evolution, transposons are remarkably diverse molecular tools for both whole-genome and single-gene studies in bacteria, yeast, and other microorganisms. Efficient but simple in vitro transposition reactions now allow the mutational analysis of previously recalcitrant microorganisms. Transposon-based signature-tagged mutagenesis and genetic footprinting strategies have pinpointed essential genes and genes that are crucial for the infectivity of a variety of human and other pathogens. Individual proteins and protein complexes can be dissected by transposon-mediated scanning linker mutagenesis. These and other transposon-based approaches have reaffirmed the usefulness of these elements as simple yet highly effective mutagens for both functional genomic and proteomic studies of microorganisms.
Artificial Gene Fusion↗
New approaches to analyzing microbial biodiversity data.
Modern molecular techniques have revealed an extraordinary diversity of microorganisms, most of which are as yet uncharacterized. This poses a major challenge to microbial ecologists: how can one compare the microbial diversity of different environments when the vast majority of microbial taxa are usually unknown? Three statistical approaches developed by ecologists and evolutionary biologists--parametric estimation, nonparametric estimation and community phylogenetics--are proving to be promising tools to meet this challenge. The combination of these tools with molecular biology techniques allow the rigorous estimation and comparison of microbial diversity in different environments.
Bacteria↗
Editing at the crossroad of innate and adaptive immunity.
Genetic information can be altered through the enzymatic modification of nucleotide sequences. This process, known as editing, was originally identified in the mitochondrial RNA of trypanosomes and later found to condition events as diverse as neurotransmission and lipid metabolism in mammals. Recent evidence reveals that editing enzymes may fulfill one of their most essential roles in the defense against infectious agents: first, as the mediators of antibody diversification, a step crucial for building adaptive immunity, and second, as potent intracellular poisons for the replication of viruses. Exciting questions are raised, which take us to the depth of the intimate relations between vertebrates and the microbial underworld.
Animals↗
Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens.
The protocatechuate branch of the beta-ketoadipate pathway comprises the last six enzymatic steps in the catabolism of diverse phenolic compounds to citric acid cycle intermediates. In this paper, the regulation and tight supraoperonic clustering of the protocatechuate (pca) genes from Agrobacterium tumefaciens A348 are elucidated. A previous study found that the pcaD gene is controlled by an adjacent regulatory gene, pcaQ, which encodes an activator. The activator responded to beta-carboxy-cis,cis-muconate and was shown to control the synthesis of at least three genes (pcaD and pcaHG). In this work, eight genes required for the catabolism of protocatechuate were localized within a 13.5-kb SalI region of DNA. Isolation and characterization of transposon Tn5 mutant strains facilitated the localization of pca genes. Five structural genes were found to respond to the tricarboxylic acid and to be contiguous in an operon transcribed in the order pcaDCHGB. These genes encode enzymes beta-ketoadipate enol-lactone hydrolase, gamma-carboxymuconolactone decarboxylase, protocatechuate 3,4-dioxygenase (pcaHG), and beta-carboxy-cis,cis-muconate lactonizing enzyme, respectively. Approximately 4 kb from the pcaD gene are the pcaIJ genes, which encode beta-ketoadipate succinyl-coenzyme A transferase for the next-to-last step of the pathway. The pcaIJ genes are transcribed divergently from the pcaDCHGB operon and are expressed in response to beta-ketoadipate. The pattern of induction of pca genes by beta-carboxy-cis,cis-muconate and beta-ketoadipate in A. tumefaciens is similar to that observed in Rhizobium leguminosarum bv. trifolii and is distinct from induction patterns for the genes from other microbial groups.
Adipates↗
Thirteen-year evolution of azole resistance in yeast isolates and prevalence of resistant strains carried by cancer patients at a large medical center.
Drug resistance is emerging in many important microbial pathogens, including Candida albicans. We performed fungal susceptibility tests with archived isolates obtained from 1984 through 1993 and fresh clinical isolates obtained from 1994 through 1997 by testing their susceptibilities to fluconazole, ketoconazole, and miconazole and compared the results to the rate of fluconazole use. All isolates recovered prior to 1993 were susceptible to fluconazole. Within 3 years of widespread azole use, we detected resistance to all agents in this class. In order to assess the current prevalence of resistant isolates in our hematologic malignancy and transplant patients, we obtained rectal swabs from hospitalized, non-AIDS, immunocompromised patients between June 1995 and January 1996. The swabs were inoculated onto sheep's blood agar plates containing 10 microg of vancomycin and 20 microg of gentamicin/ml of agar. One hundred one yeasts were recovered from 97 patients and were tested for their susceptibilities to amphotericin B, fluconazole, flucytosine, ketoconazole, and miconazole. The susceptibility pattern was then compared to those for all clinical isolates obtained throughout the medical center. The antifungal drug histories for each patient were also assessed. The yeasts from this surveillance study were at least as susceptible as the overall hospital strains. There did not appear to be a direct linkage between prior receipt of antifungal agent therapy and carriage of a new, drug-resistant isolate. Increased resistance to newer antifungal agents has occurred at our medical center, but it is not focal to any high-risk patient population that we studied. Monitoring of susceptibility to antifungal agents appears to be necessary for optimizing clinical therapeutic decision making.
Antifungal Agents↗
Gene cassette-associated sequences from phosphorus and non-phosphorus removing microbial communities in aerobic:anaerobic sequencing batch reactors.
Mobile gene elements associated with integrons, including as gene cassettes, have been proposed to play an important role in bacterial evolution by providing an extensive genetic resource. This study hypothesized that critical genes for enzymes involved in EBPR systems, including those involved in polyphosphate, PHA and glycogen synthesis, may be present in mobile gene cassettes. Although no such genes were identified in any of the functional and deteriorated enhanced biological phosphorus removal (EBPR) laboratory-scale SBR systems examined here, many of the open reading frames (ORFs) remained unidentified because of the incompleteness of publicly available databases. An ORF of unknown function (SBR6-2) was encountered in deteriorated EBPR system with an unexpectedly high frequency, comprising 35% of the gene cassette-associated sequences for that system.
Aerobiosis↗
Microbial antagonism: a neglected avenue of natural products research.
Competition amongst microbes for space and nutrients in the marine environment is a powerful selective force which has led to the evolution of a variety of effective strategies for colonising and growing on surfaces. We are particularly interested in the chemical ecology of marine epibiotic bacteria which live on the surfaces of marine algae or invertebrates. Over 400 strains of surface-associated bacteria from various species of seaweed and invertebrate from Scottish coastal waters were isolated and 35% of them shown to produce antimicrobial compounds. This is a much higher proportion than free living marine isolates or soil bacteria. In addition, many strains which did not normally produce antibiotics could be induced to do so by exposing them to small amounts of live cells, supernatants from other bacterial cultures or other chemicals. Thus the number of strains able to produce antibiotics appears to be much higher than previously thought. Induction of antibiotic production was elicited by other marine epibionts and also by terrestrial human pathogens such as Bacillus subtilis, Escherichia coli and Pseudomonas aeruginosa. An understanding of this type of chemical induction and the factors regulating non-constitutive secretion of antimicrobial compounds will allow more effective strategies for searching for new chemotherapeutic antibiotics to be designed.
Acinetobacter↗
Control of microbial contamination in the use of laboratory rodents.
Historically, laboratory rodents have been used in preference to other animal species for biomedical research. Study disruptions and invalidations often have occurred due to microbial contaminants inherent to laboratory rodents. Today, many commercial suppliers and research institutions are controlling a variety of infectious diseases among laboratory rodents by careful design of animal facilities, by adaptation of managerial techniques employing precise operational policies coupled with careful supervision and attention to detail and the use of various diagnostic programs. The continued evolution of epidemiological practices, environment control systems, sophistication of barrier-sustained operations, preventative medicine and sanitation techniques, complemented by an improvement in veterinary diagnostic programs for disease surveillance further minimize microbial contamination of laboratory rodents. Such measures contribute to the fulfillment of various legislative requirements concerned with the quality of animals for biomedical research.
Animal Feed↗
Repeated pulmonary infection by Nocardia asteroides complex in a patient with bronchiectasis.
A rare case of pulmonary nocardiosis was presented in a nonimmunocompromised patient who had chronic airway obstruction and bronchiectasis without corticoid treatment. The microbial diagnosis was established after isolating Nocardia in bronchial aspirate and sputum samples. An in vitro study showed sensitivity only to imipenem, netilmicine, amikacin and ofloxacin. The evolution was chronic, with multiple clinical recurrences in spite of prolonged antibiotic treatment. Finally, the eradication of Nocardia was achieved with the combination of imipenem and amikacin.
Amikacin↗
Degradation of natural and Kraft lignins by the microflora of soil and water.
The comparative rates of microbial degradation of 14C-lignin-labeled lignocelluloses and 14C-Kraft lignins were investigated using selected soil and water samples as sources of microorganisms. Natural lignocelluloses containing 14C primarily in their lignin components were prepared by feeding plants uniformly labeled L-[14C]phenylalanine through their cut stems. 14C-Kraft lignins were prepared by pulping lignin-labeled lignocelluloses. Rates of lignin biodegradation were determined by monitoring 14CO2 evolution from incubation mixtures over incubation periods of up to 1000 h. Observed rates of lignin degradation were slow in all cases. Kraft lignins appeared more resistant to microbial attack than natural lignins, even though they were decomposed more rapidly during the first 100-200 h of incubation. Similar degradation patterns were observed in both soil and water. Individual samples, however, varied greatly in their overall rates of degradation of either lignin type. A Kraft-lignin preparation was separated into a variety of molecular weight fractions by column chromatography on LH-20 Sephadex and the biodegradability of the different molecular weight fractions determined. The lower molecular weight fractions of the Kraft lignin were decomposed at a significantly faster rate by the microflora of soil than were the fractions of higher molecular weight.
Bacteria↗
Only six kingdoms of life.
There are many more phyla of microbes than of macro-organisms, but microbial biodiversity is poorly understood because most microbes are uncultured. Phylogenetic analysis of rDNA sequences cloned after PCR amplification of DNA extracted directly from environmental samples is a powerful way of exploring our degree of ignorance of major groups. As there are only five eukaryotic kingdoms, two claims using such methods for numerous novel 'kingdom-level' lineages among anaerobic eukaryotes would be remarkable, if true. By reanalysing those data with 167 known species (not merely 8-37), I identified relatives for all 8-10 'mysterious' lineages. All probably belong to one of five already recognized phyla (Amoebozoa, Cercozoa, Apusozoa, Myzozoa, Loukozoa) within the basal kingdom Protozoa, mostly in known classes, sometimes even in known orders, families or genera. This strengthens the idea that the ancestral eukaryote was a mitochondrial aerobe. Analogous claims of novel bacterial divisions or kingdoms may reflect the weak resolution and grossly non-clock-like evolution of ribosomal rRNA, not genuine phylum-level biological disparity. Critical interpretation of environmental DNA sequences suggests that our overall picture of microbial biodiversity at phylum or division level is already rather good and comprehensive and that there are no uncharacterized kingdoms of life. However, immense lower-level diversity remains to be mapped, as does the root of the tree of life.
Animals↗
Hagfish intestinal antimicrobial peptides are ancient cathelicidins.
Three potent broad-spectrum antimicrobial peptides (HFIAP-1, -2, and -3) isolated from intestinal tissues of Myxine glutinosa (Atlantic hagfish) are identified as ancient members of the cathelicidin family of antimicrobial peptides, hitherto known only from mammals. In situ hybridization reveals that HFIAPs are produced in nests of myeloid cells within the loose connective tissue of the gut wall, a tissue reminiscent of both gut-associated lymphoid tissue (GALT) and vertebrate spleen. We suggest that this tissue organization provides local defense of the hagfish gastrointestinal tract via innate immunity and possibly served as the architectural plan upon which the adaptive immune system evolved.
Amino Acid Sequence↗