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PubMed2000

Status of genome projects for nonpathogenic bacteria and archaea.

Since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. Although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon Methanococcus jannaschii in 1996. The past 18 months have seen the completion of the genomes of several unusual organisms, including Thermotoga maritima, whose genome reveals extensive potential lateral transfer with archaea; Deinococcus radiodurans, the most radiation-resistant microorganism known; and Aeropyrum pernix, the first Crenarchaeota to be completely sequenced. Although the functional characterization of genomic data is still in its initial stages, it is likely that microbial genomics will have a significant impact on environmental, food, and industrial biotechnology as well as on genomic medicine.

Archaea↗

PubMed2000

Loss of antiretroviral drug susceptibility at low viral load during early virological failure in treatment-experienced patients.

BACKGROUND: Clinical studies have demonstrated a correlation between the response to second-line antiretroviral therapy and the number of drugs in the regimen to which the virus is susceptible. These studies have largely been performed in patients with viral loads over 1000 copies/ml. OBJECTIVES: To examine the evolution of resistance during early virological failure, and the potential role of susceptibility testing in patients with low viral loads (below 1000 copies/ml), in treatment-experienced patients. METHODS: Drug susceptibility and genotypes of HIV-1 from indinavir-experienced patients undergoing therapy with nelfinavir, saquinavir, abacavir and either a second nucleoside reverse transcriptase inhibitor (NRTI) or nevirapine were determined. RESULTS: Sixteen subjects were studied. Five of the ten subjects treated with nevirapine, and one of six treated with a second NRTI, achieved and maintained plasma HIV RNA < 500 copies/ml. Virus from the treatment failures lost susceptibility to one or more treatment drugs, including nelfinavir and/or saquinavir, after 4 to 36 weeks of treatment. In six of the ten failures, virus with new reductions in drug susceptibility was detected prior to failure. In five of the six failures who had at least one plasma sample with a viral load between 50 and 1000 copies/ml, reductions in susceptibility to one or more treatment drugs were detected (viral load range: 260 to 630 copies/ml). CONCLUSIONS: Drug resistance can be detected at viral loads below 1000 copies/ml which may be predictive of treatment failure. Failure of a second line regimen was typically associated with early evolution of resistance in HIV protease.

Anti-HIV Agents↗

PubMed1992

Isolation and characterization of the aadA aminoglycoside-resistance gene from Salmonella choleraesuis.

The streptomycin- and spectinomycin-resistance gene of Salmonella choleraesuis was cloned and its nucleotide sequence determined. The gene is 789 bases long, encoding a protein of a predicted size of 29,353 Da. The gene product inactivated streptomycin and spectinomycin by an adenylation modification. It is homologous (c. 40% total identity) to streptomycin adenylyltransferase, a 3'(9)-O-nucleotidyltransferase (AAD(3')(9)), which is encoded by the aadA gene in Escherichia coli, Agrobacterium tumefaciens, Klebsiella pneumonia, and Serratia marcescens. The AadA protein of S. choleraesuis differs significantly from the other AadA proteins, indicating that it may have diverged from the other members of this family earlier in evolution. Southern hybridization analysis revealed that homologous aadA sequences were also present in other streptomycin-resistant Salmonella species.

Amino Acid Sequence↗

PubMed1991

Homologous recombination of a plasmid containing the SV40 early region in rabbit cells.

The plasmid pSV3-neo that carries the SV40 early genetic region and the neor resistance gene underwent homologous recombination between SV40-duplicated sequences of the small t antigen intron and the polyadenylation site after transfection into rabbit vascular smooth muscle cells. This recombination yielded two free plasmids of 1.7 and 3.0 kb that replicated in transfected rabbit cells, while the vector plasmid did not. Replication of the two recombinant plasmids continued for several months in rabbit cells transformed by pSV3-neo, and their structure remained unchanged. Between 15 and 2,510 copies per cell of the 3.0-kb plasmid and between 370 and 1,565 copies per cell of the 1.7-kb plasmid were found in different pSV3-neo-transformed rabbit clones. Similar recombined plasmids were found 3 days after transfection of pSV3-neo onto SV40-transformed rabbit cells. By comparison, pSV3-neo was replicated in simian cells, but no recombined plasmids were detected by Southern analysis. No replication was detected after transfection of pSV3-neo into mouse cells. These results appear to reflect important differences between rabbit and simian cells in the efficiency of homologous recombination involving specific SV40 sequences and/or in the replication of the resulting recombinants. The role of the host cell in the evolution of SV40 sequences may influence the outcome of the infection with this virus.

Animals↗

PubMed2001

Treatment of mycobacterial infections.

Treatment of mycobacterial infections differs from that of other bacterial diseases due to several properties possessed by the mycobacteria and the host. A hallmark of mycobacteria is the complex lipid-rich cell envelope that protects the organism from both the host response and antimycobacterial therapy. In addition, mycobacteria are facultative intracellular parasites which generally cause a more chronic type of disease. These properties add greater constraints to efficient therapy. To be effective, drugs must be able to penetrate the host macrophage and preferably have reduced toxicity and be effective at low doses to allow prolonged therapy. The author presents the general properties of the pathogen/host relationship in mycobacterial infections, in addition to the therapeutic choices available and the mechanisms of action involved in treatment. The evolution of technology for antimycobacterial therapy is illustrated by a discussion of new strategies being developed for the treatment of mycobacterial infections.

Animals↗

PubMed2004

Analysis of a novel class of predictive microbial growth models and application to coculture growth.

In this paper, a novel class of microbial growth models is analysed. In contrast with the currently used logistic type models (e.g., the model of Baranyi and Roberts [Baranyi, J., Roberts, T.A., 1994. A dynamic approach to predicting bacterial growth in food. International Journal of Food Microbiology 23, 277-294]), the novel model class, presented in Van Impe et al. (Van Impe, J.F., Poschet, F., Geeraerd, A.H., Vereecken, K.M., 2004. Towards a novel class of predictive microbial growth models. International Journal of Food Microbiology, this issue), explicitly incorporates nutrient exhaustion and/or metabolic waste product effects inducing stationary phase behaviour. As such, these novel model types can be extended in a natural way towards microbial interactions in cocultures and microbial growth in structured foods. Two illustrative case studies of the novel model types are thoroughly analysed and compared to the widely used model of Baranyi and Roberts. In a first case study, the stationary phase is assumed to be solely resulting from toxic product inhibition and is described as a function of the pH-evolution. In the second case study, substrate exhaustion is the sole cause of the stationary phase. Finally, a more complex case study of a so-called P-model is presented, dealing with a coculture inhibition of Listeria innocua mediated by lactic acid production of Lactococcus lactis.

Coculture Techniques↗

PubMed1991

Contemporaneous N(2) Fixation and Oxygenic Photosynthesis in the Nonheterocystous Mat-Forming Cyanobacterium Lyngbya aestuarii.

The nonheterocystous filamentous cyanobacterial genus Lyngbya is a widespread and frequently dominant component of marine microbial mats. It is suspected of contributing to relatively high rates of N(2) fixation associated with mats. The ability to contemporaneously conduct O(2)-sensitive N(2) fixation and oxygenic photosynthesis was investigated in Lyngbya aestuarii isolates from a North Carolina intertidal mat. Short-term (<4-h) additions of the photosystem II (O(2) evolution) inhibitor 3(3,4-dichlorophenyl)-1,1-dimethylurea stimulated light-mediated N(2) fixation (nitrogenase activity), indicating potential inhibition of N(2) fixation by O(2) production. However, some degree of light-mediated N(2) fixation in the absence of 3(3,4-dichlorophenyl)-1,1-dimethylurea was observed. Electron microscopic immunocytochemical localization of nitrogenase, coupled to microautoradiographic studies of CO(2) fixation and cellular deposition of the tetrazolium salt 2,4,5-triphenyltetrazolium chloride, revealed that (i) nitrogenase was widely distributed throughout individual filaments during illuminated and dark periods, (ii) CO(2) fixation was most active in intercalary regions, and (iii) daylight 2,4,5-triphenyltetrazolium chloride reduction (formazan deposition) was most intense in terminal regions. Results suggest lateral partitioning of photosynthesis and N(2) fixation during illumination, with N(2) fixation being confined to terminal regions. During darkness, a larger share of the filament appears capable of N(2) fixation.

Journal Article↗

PubMed1989

Microfossils from silicified stromatolitic carbonates of the Upper Proterozoic Limestone-Dolomite 'Series', central East Greenland.

Silicified flake conglomerates and in situ stratiform stromatolites of the Upper Proterozoic (c. 700-800 Ma) Limestone-Dolomite 'Series', central East Greenland, contain well preserved microfossils. Five stratigraphic horizons within the 1200 m succession contain microbial mat assemblages, providing a broad palaeontological representation of late Proterozoic peritidal mat communities. Comparison of assemblages demonstrates that the taxonomy and diversity of mat builder, dweller, and allochthonous populations all vary considerably within and among horizons. The primary mat builder in most assemblages is Siphonophycus inornatum, a sheath-forming prokaryote of probable but not unequivocally established cyanobacterial affinities. An unusual low diversity unit in Bed 17 is dominated by a different builder, Tenuofilum septatum, while a thin cryptalgal horizon in Bed 18 is built almost exclusively by Siphonophycus kestron. Although variable taphonomic histories contribute to observed assemblage variation, most differences within and among horizons appear to reflect the differential success or failure of individual microbial populations in colonizing different tidal flat microenvironments. Twenty-two taxa are recognized, of which two are described as new: Myxococcoides stragulescens n.sp. and Scissilisphaera gradata n. sp.

Biological Evolution↗

PubMed2000

Geochemical evidence for terrestrial ecosystems 2.6 billion years ago.

Microorganisms have flourished in the oceans since at least 3.8 billion years (3.8 Gyr) ago, but it is not at present clear when they first colonized the land. Organic matter in some Au/U-rich conglomerates and ancient soils of 2.3-2.7 Gyr age has been suggested as remnants of terrestrial organisms. Some 2.7-Gyr-old stromatolites have also been suggested as structures created by terrestrial organisms. However, it has been disputed whether this organic matter is indigenous or exogenic, and whether these stromatolites formed in marine or fresh water. Consequently, the oldest undisputed remnants of terrestrial organisms are currently the 1.2-Gyr-old microfossils from Arizona, USA. Unusually carbonaceous ancient soils--palaeosols--have been found in the Mpumalanga Province (Eastern Transvaal) of South Africa. Here we report the occurrences, elemental ratios (C, H, N, P) and isotopic compositions of this organic matter and its host rocks. These data show that the organic matter very probably represents remnants of microbial mats that developed on the soil surface between 2.6 and 2.7 Gyr ago. This places the development of terrestrial biomass more than 1.4 billion years earlier than previously reported.

Biological Evolution↗

PubMed2000

The Escherichia coli aquaporin-Z water channel.

The membrane pathway of the rapid fluxes of water by which microorganisms adapt promptly to abrupt changes in environmental osmolality have begun to be understood since the discovery of the Escherichia coli aquaporin-Z water channel, AqpZ. As in animals and plants, aquaporins are variously represented among microorganisms, in which 31 homologous genes have already been identified in eubacteria, Archaea, fungi and protozoa. The AqpZ channel is selectively permeable to water, although other functions are not excluded. Consistent with a conservation over the course of evolution, AqpZ and AQP1, a human counterpart, share similar structures. The aqpZ gene is growth phase and osmotically regulated. AqpZ has a role in both the short- and the long-term osmoregulatory response and is required by rapidly growing cells. AqpZ-like proteins seem to be necessary for the virulence expressed by some pathogenic bacteria. Microbial aquaporins are also likely to be involved in spore formation and/or germination. Additional roles may still be unknown. The use of AqpZ as a model system will continue to provide insight into the understanding of the importance of aquaporins.

Aquaporins↗

PubMed1988

Molecular epidemiology of multiresistant Staphylococcus epidermidis.

Molecular epidemiology has provided several clues about the antimicrobial resistance genes of nosocomial, multiresistant coagulase-negative staphylococci. First, it has shown that a huge reservoir of resistance genes is maintained in these organisms on the bodies of both patients and the hospital personnel who care for them. In turn, extensive use of antimicrobial agents within specific sectors of the hospital probably provides selection pressure for the evolution and amplification of these genes. Secondly, indirect evidence suggests that Staphylococcus epidermidis may itself serve as a reservoir for antimicrobial resistance genes that are transferred to S. aureus.

Conjugation, Genetic↗

PubMed2005

Putative VanRS-like two-component regulatory system associated with the inducible glycopeptide resistance cluster of Paenibacillus popilliae.

Paenibacillus popilliae contains vanF encoding a putative D-Ala:D-lactate (D-Lac) ligase, VanF, as part of the vanY(F)Z(F)H(F)FX(F) cluster that is similar in structure to the enterococcal vanA and vanB clusters. Using growth curves, we demonstrated that vancomycin resistance in P. popilliae is inducible. Using degenerate oligonucleotides targeted at bacterial cell wall ligases, we identified a second ligase gene with features of a D-Ala:D-Ala ligase in both P. popilliae and the related, vancomycin-susceptible, Paenibacillus lentimorbus. The 3,380-bp region upstream of vanY(F)Z(F)H(F)FX(F) in P. popilliae ATCC 14706 was sequenced and found to contain genes encoding a putative two-component regulator, VanR(F)S(F), similar to VanRS but more closely related to a family of two-component regulators linked to VanY-like carboxypeptidases in several glycopeptide-susceptible Bacillus species. This upstream region also included a transposase similar to a transposase found in Bacillus halodurans and, in some strains, a 99-bp insertion of unknown function with 95% nucleotide identity to a portion of the Tn1546 transposase gene. Analysis of glycopeptide resistance-associated clusters from soil and/or insect-dwelling organisms may provide important clues to the molecular evolution of acquired glycopeptide resistance elements in human pathogens.

Amino Acid Sequence↗

PubMed2003

Fatal acute cellulitis due to Neisseria meningitidis.

We describe the first fatal evolution of cellulitis due to Neisseria meningitidis serogroup Y involving an 85-year-old woman. She presented with an extensive cellulitis of the left side of the face, neck, and thorax and septic shock. In spite of active antibiotic therapy, evolution was rapidly fatal.

Aged↗

PubMed1998

Effects of aerosolized interferon-alpha in patients with pulmonary tuberculosis.

Interferon-alpha (IFN-alpha) is a cytokine exerting pleiotropic activities, including antimicrobial effects, especially directed against intracellular infectious bacteria. It may be administered by aerosol to reach the lower respiratory tract without systemic side effects. The aim of the study reported here was the evaluation of aerosolized IFN-alpha treatment (3 MU/dose, given three times a week; total study dose: 72 MU/2 mo) in combination with conventional antimycobacterial therapy in patients with pulmonary tuberculosis. Two groups of 10 patients each were compared before and after 2 mo of conventional antituberculous chemotherapy with or without inhaled IFN-alpha. Several biologic (bronchoalveolar lavage fluid [BALF] cellularity, Mycobacterium tuberculosis [MT] number in sputum), biochemical (BALF concentrations of 10 cytokines, BALF IFN-alpha receptor levels), and clinical (fever, vital signs, high-resolution computed tomography [HRCT] images) measures were made in these patients at the time of their enrollment and at the end of the observation period of the study. Fever, MT number in sputum, and abnormalities in HRCT images showed significantly earlier resolution in the IFN-alpha-treated group, together with a more significant decrease in BALF interleukin-1beta (IL-1beta), IL-6, and tumor necrosis factor-alpha (TNF-alpha) concentrations and significantly greater pre- versus posttreatment variations in IL-2 and IFN-gamma. These data, taken together, suggest that IFN-alpha administration may favorably affect the evolution of pulmonary tuberculosis when combined with antimycobacterial therapy.

Administration, Inhalation↗

PubMed2001

Coevolutionary networks: a novel approach to understanding the relationships of humans with the infectious agents.

Human organism is interpenetrated by the world of microorganisms, from the conception until the death. This interpenetration involves different levels of interactions between the partners including trophic exchanges, bi-directional cell signaling and gene activation, besides genetic and epigenetic phenomena, and tends towards mutual adaptation and coevolution. Since these processes are critical for the survival of individuals and species, they rely on the existence of a complex organization of adaptive systems aiming at two apparently conflicting purposes: the maintenance of the internal coherence of each partner, and a mutually advantageous coexistence and progressive adaptation between them. Humans possess three adaptive systems: the nervous, the endocrine and the immune system, each internally organized into subsystems functionally connected by intraconnections, to maintain the internal coherence of the system. The three adaptive systems aim at the maintenance of the internal coherence of the organism and are functionally linked by interconnections, in such way that what happens to one is immediately sensed by the others. The different communities of infectious agents that live within the organism are also organized into functional networks. The members of each community are linked by intraconnections, represented by the mutual trophic, metabolic and other influences, while the different infectious communities affect each other through interconnections. Furthermore, by means of its adaptive systems, the organism influences and is influenced by the microbial communities through the existence of transconnections. It is proposed that these highly complex and dynamic networks, involving gene exchange and epigenetic phenomena, represent major coevolutionary forces for humans and microorganisms.

Adaptation, Physiological↗

PubMed2002

Antimicrobial resistance of food-related Salmonella isolates, 1999-2000.

Salmonellosis is a major foodborne infection in the United States, and strains of Salmonella that are resistant to a variety of antimicrobial agents have become a major public health concern. To estimate the incidence of antimicrobial-resistant Salmonella in our food supply, the U.S. Food and Drug Administration (FDA) has initiated screening of foodborne isolates for sensitivity to antimicrobial agents, including several antibiotics. Salmonella cultures (n = 502) isolated by FDA laboratories during fiscal year 2000 (1 October 1999 through 30 September 2000) from domestic and imported food products and related samples were tested for susceptibility to each of 12 antimicrobial agents using a disc diffusion assay. Because all isolates were resistant to rifampin (5 or 25 microg), only results with the remaining 11 antimicrobial agents are discussed in this paper. Of the 502 isolates, 247 (49.2%) were resistant to one or more antimicrobial agents, and of these 247 isolates, 170 (68.8%) were resistant to one antimicrobial agent, 33 (13.4%) to two antimicrobial agents, 25 (10.1%) to three antimicrobial agents, 7 (2.8%) to four antimicrobial agents, 8 (3.2%) to five antimicrobial agents, and 2 (0.8%) each to six and seven antimicrobial agents. No isolates were resistant to norfloxacin, whereas only seven were resistant to sulfamethoxazole/trimethoprim, six to trimethoprim, three to gentamicin, and one to ciprofloxacin. These results, for the first time, provide a baseline of data on the incidence of antimicrobial-resistant Salmonella in the U.S. food supply, which should be useful in determining the evolution of antimicrobial resistance in the future.

Anti-Bacterial Agents↗

PubMed1983

Investigation of nosocomial infections by plasmid analysis.

Molecular biological techniques, including agarose gel electrophoresis, restriction endonuclease analysis and DNA-DNA hybridization (Southern blotting and heteroduplex analysis) are being applied very successfully to the investigation of nosocomial infections. 'Plasmid fingerprinting' by electrophoresis, with or without restriction endonuclease analysis, can be used to identify epidemic strains of bacteria and 'epidemic plasmids' which have spread through several different bacterial species. This technique is rapid and inexpensive, and can be applied to drug-sensitive as well as resistant strains. This approach is especially useful for investigation of organisms for which no standard typing system is available. DNA-DNA hybridization techniques can be used to study the evolution of plasmids in the hospital environment, and to demonstrate the presence and spread of translocatable DNA sequences (transposons) carrying drug resistance determinants from plasmid to plasmid within a bacterial cell.

Cross Infection↗

PubMed1996

Drug efflux as a mechanism of resistance.

A review of efflux as a mechanism of antibiotic resistance in both bacterial and eukaryotic cells is presented. This covers membrane transport, the evolution of efflux transporters, their genetic control and classification into families, and an appreciation of the widespread distribution and occurrence of these mechanisms in nature.

Anti-Bacterial Agents↗