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PubMed2006

Microbial community dynamics in nutrient-pulsed chemostats.

In nature, microbes are subject to nutrient fluxes. As the periodicity of nutrient flux lengthens, different physiological traits may be selected. The competitive exclusion principle stipulates that one organism will dominate these systems; however, interspecies interactions may produce a dynamic microbial community. These issues were investigated in chemostats pulsed with gelatin. Chemostats were run over 30 days with substrate addition continuously or at intervals of 0.5, 1 or 3 days. Growth rates were similar between pulse intervals. Ectoaminopeptidase activity levels remained relatively constant within a pulse interval. Bacterial community structure was monitored using denaturing gradient gel electrophoresis of PCR products of the 16S rRNA gene. There were dynamic changes at all periodicities; however, the pace of these changes decreased over time. Final communities were not identical between different treatments. The structure of persistent vs. active microbial populations was compared by denaturing gradient gel electrophoresis of the PCR and reverse transcriptase-PCR amplicons of 16S rDNA and rRNA templates, respectively. For all the chemostats, the rRNA profiles were not identical to the rDNA profiles for a sample. These experiments demonstrate that complex community dynamics can occur under environmental heterogeneities that are modest relative to those found in natural aquatic habitats. Furthermore, the physiological functionality of these dynamic communities was stable.

Aminopeptidases↗
PubMed2006

Preparation of anti-pefloxacin antibody and development of an indirect competitive enzyme-linked immunosorbent assay for detection of pefloxacin residue in chicken liver.

Pefloxacin has been increasingly used in veterinary medicine to treat microbial infections. To avoid using a labor-intensive instrumental method to detect the residue of pefloxacin in food, a simple and convenient indirect competitive enzyme-linked immunosorbent assay method has been developed in this study. The antibody generated from immunogen cationized bovine serum albumin-pefloxacin showed high sensitivity toward pefloxacin with an IC50 value of 6.7 ppb in buffer and was suitable for a screening assay to detect the residue of pefloxacin in food products. The antibody has been assessed using rapid enzyme immunoassays to exploit its specificity. The antibody prepared shows cross-reactivity with a few other (fluoro)quinolones including fleroxacin (116%), enrofloxacin (88%), and ofloxacin (10%). The assay measured drug residue in chicken liver spiked with pefloxacin with an interassay coefficient of variation of 13.6% or less and an intra-assay coefficient of variation of 10.9% or less. The average recovery rates at 0.5, 5, 10, 50, and 100 ppb were in the range of 86-106% for interassay and in the range of 87-103% for intra-assay, respectively.

Animals↗
PubMed1990

Mechanism of imipenem resistance acquired by three Pseudomonas aeruginosa strains during imipenem therapy.

Imipenem sensitive pretherapy isolates (MICs 1-2 mg/l) and the corresponding resistant posttherapy isolates (MICs 16 mg/l) of Pseudomonas aeruginosa from three patients undergoing imipenem treatment were analyzed to establish the resistance mechanism. The identity of pyocin types, serotypes, DNA restriction endonuclease profiles and plasmid profiles strongly suggested isogenicity of pre- and posttherapy isolates. The imipenem resistant posttherapy isolates showed cross-resistance only to another carbapenem, meropenem. There were neither qualitative nor quantitative differences between pre- and posttherapy isolates in beta-lactamase production. Affinity of the penicillin-binding proteins 1A, 1B, 2, 3, 4,4' and 5 for [14C]imipenem was the same in pre- and posttherapy isolates. One-dimensional and two-dimensional gel electrophoresis of outer membrane protein preparations showed diminished expression of an outer membrane protein of about 46.5 and 47.5 kilodaltons, respectively, in the posttherapy isolates. This protein had an apparent isoelectric point of about pH 5.2 in two-dimensional gel electrophoresis. Growth in proteose peptone no. 2 broth did not reduce expression of this outer membrane protein, which spoke against its identity with the outer membrane protein D1. The permeability of the outer membrane for imipenem was reduced in the posttherapy isolates, since addition of 0.5 or 0.25 of the MIC of the permeabilizing agent ethylene-diaminetetraacetate reduced the MICs of imipenem for all isolates from each patient to the same (susceptible) level. The diminished expression of one of the outer membrane proteins might be the reason for this reduced permeability.

Bacterial Outer Membrane Proteins↗
PubMed1991

Partial sequencing and characterization of the tumor cell-derived collagenase stimulatory factor.

A tumor cell-derived, collagenase stimulatory factor (TCSF), previously isolated and purified from LX-1 human lung carcinoma cells and judged by immunoblotting and SDS-PAGE to contain a single protein of approximately 58 kDa, has been further analyzed for its biological activity and composition. Three significant new findings have been made. First, the biological activity of TCSF preparations was shown definitively to reside in the 58-kDa protein. This was achieved in two ways: (a) a polyclonal antibody was raised against the 58-kDa protein, after excision from an SDS-PAGE gel, and shown to inhibit the stimulation of fibroblast collagenase production by TCSF preparations; (b) the 58-kDa protein was eluted from a transblot of purified TCSF and shown to stimulate fibroblast collagenase production. Second, partial sequencing of the 58-kDa protein revealed no significant homologies with other known collagenase stimulatory factors. Third, purified TCSF was found, on transblotting to Immobilon, to contain a doublet of 58 kDa (TCSF1) and 54 kDa (TCSF2) proteins; the former was present in higher concentration than the latter. N-terminal amino acid sequencing of the two intact proteins and of four corresponding pairs of tryptic peptides derived from the two proteins showed identity in each case, indicating that TCSF1 and TCSF2 are very similar in composition. However, TCSF1 but not TCSF2 stimulated fibroblast collagenase production, confirming that the 58-kDa protein is the major active component of TCSF preparations.

Amino Acid Sequence↗
PubMed1989

The ketone cinnamoyl-(1-13C-Phe)-CGly-Pro-Pro is a tetrahedral transition state analog inhibitor of C. histolyticum collagenase.

The ketone cinnamoyl-(1-13C-Phe)-CGly-Pro-Pro [(4-13C-5-cinnamido-4-oxo-6-phenylhexanoyl)-Pro-Pro 2] competitively inhibits a mixture of collagenases from Clostridium histolyticum with a Ki of 40 +/- 6 nM. 13C-nmr spectroscopy of the ketone in the presence of this collagenase shows a bound 13C resonance at 102.6 ppm and the resonance of the free ketone at 212 ppm. Ketone alone shows no trace (less than 0.5%) of a resonance in the region around 100 ppm. The bound resonance is displaceable by another competitive inhibitor. This ketone is thus a transition state analog which is rehybridized from trigonal planar to tetrahedral upon binding to collagenase.

Binding Sites↗
PubMed1990

Penicillin binding proteins of Vibrio cholerae.

Eleven penicillin binding proteins (PBPs) of Vibrio cholerae have been identified using [125I] labelled p-hydroxybenzyl penicillin (PenX). These proteins are localised in the inner membrane and have molecular weights ranging from 97,000 to 22,000. Neutral hydroxylamine released the labelled PenX from the PBPs and pretreatment with cold benzyl penicillin inhibited labelling completely. The PBP 4 is the most sensitive target for cephaloridine and aztreonam. Cephaloridine also binds to three other high molecular weight PBPs, 1, 2 and 3. Aztreonam, in addition to PBP 4, has affinity for another low molecular weight PBP, PBP 7. Mecillinam has affinity for PBPs 1, 4 and 11.

Aztreonam↗
PubMed2006

Involvement of DNA mismatch repair in stationary-phase mutagenesis during prolonged starvation of Pseudomonas putida.

One of the popular ideas is that decline in methyl-directed mismatch repair (MMR) in carbon-starved bacteria might facilitate occurrence of stationary-phase mutations. We compared the frequency of accumulation of stationary-phase mutations in carbon-starved Pseudomonas putida wild-type and MMR-defective strains and found that knockout of MMR system increased significantly emergence of base substitutions in starving P. putida. At the same time, the appearance of 1-bp deletion mutations was less affected by MMR in this bacterium. The spectrum of base substitution mutations which occurred in starving populations of P. putida wild-type strain was distinct from mutation spectrum identified in MMR-defective strains. The spectrum of base substitutions differed also in this case when mutants emerged in starved populations of MutS or MutL-defective strains were comparatively analyzed. Based on our results we suppose that other mechanisms than malfunctioning of MMR system in resting cells might be considered to explain the accumulation of stationary-phase mutations in P. putida. To further characterize populations of P. putida starved on selective plates, we stained bacteria with LIVE/DEAD kit in situ on agar plates. We found that although the overall number of colony forming units (CFU) did not decline in long-term-starved populations, these populations were very heterogeneous on the plates and contained many dead cells. Our results imply that slow growth of subpopulation of cells at the expenses of dead cells on selective plates might be important for the generation of stationary-phase mutations in P. putida. Additionally, the different survival patterns of P. putida on the same selective plates hint that competitive interactions taking place under conditions of prolonged starvation of microbial populations on semi-solid surfaces might be more complicated than previously assumed.

Base Pair Mismatch↗
PubMed2005

Trace metal exposure of soil bacteria depends on their position in the soil matrix.

Micropores and biofilms of soils may protect bacteria against chemical stress, predation, and competition phenomena, explaining the great diversity and robustness of soil microbial communities and functions. We used sequential dispersion/density gradient centrifugation to separate free and loosely attached cells (FLA) from strongly attached cells (SA). The two fractions of the soils communities were investigated along a Zn and Cd pollution gradient, and the pollution-induced trace metal community tolerance (PICT) for SA and FLA was analyzed. FLA had developed a strong PICT in response to the 80 years of Zn and Cd pollution, whereas SA was virtually unaffected. It appears that the position of SA in biofilms and micropores has effectively protected them against toxic metal concentrations. The estimated free ion activity showed that the Cd activity was too low to reach toxic levels (PICT(cd) was probably caused by Zn). In contrast, the estimated Zn ion activity was close to a critical level, and could have caused the observed PICT(Zn) in FLA, at least if temporal/ spatial fluctuations of soil pH are taken into account. Such fluctuations could also explain the protection of SA as a result of diffusion constraints; which would be of little help under constant conditions because chemical equilibrium would be reached throughout.

Bacteria↗
PubMed2003

Understanding resistance to beta-lactams and beta-lactamase inhibitors in the SHV beta-lactamase: lessons from the mutagenesis of SER-130.

Bacterial resistance to beta-lactam/beta-lactamase inhibitor combinations by single amino acid mutations in class A beta-lactamases threatens our most potent clinical antibiotics. In TEM-1 and SHV-1, the common class A beta-lactamases, alterations at Ser-130 confer resistance to inactivation by the beta-lactamase inhibitors, clavulanic acid, and tazobactam. By using site-saturation mutagenesis, we sought to determine the amino acid substitutions at Ser-130 in SHV-1 beta-lactamase that result in resistance to these inhibitors. Antibiotic susceptibility testing revealed that ampicillin and ampicillin/clavulanic acid resistance was observed only for the S130G beta-lactamase expressed in Escherichia coli. Kinetic analysis of the S130G beta-lactamase demonstrated a significant elevation in apparent Km and a reduction in kcat/Km for ampicillin. Marked increases in the dissociation constant for the preacylation complex, KI, of clavulanic acid (SHV-1, 0.14 microm; S130G, 46.5 microm) and tazobactam (SHV-1, 0.07 microm; S130G, 4.2 microm) were observed. In contrast, the k(inact)s of S130G and SHV-1 differed by only 17% for clavulanic acid and 40% for tazobactam. Progressive inactivation studies showed that the inhibitor to enzyme ratios required to inactivate SHV-1 and S130G were similar. Our observations demonstrate that enzymatic activity is preserved despite amino acid substitutions that significantly alter the apparent affinity of the active site for beta-lactams and beta-lactamase inhibitors. These results underscore the mechanistic versatility of class A beta-lactamases and have implications for the design of novel beta-lactamase inhibitors.

Ampicillin↗
PubMed1991

Beta-lactam resistance mechanisms of methicillin-resistant Staphylococcus aureus.

In vitro and in vivo activity of amoxicillin and penicillin G alone or combined with a penicillinase inhibitor (clavulanate) were tested against five isogenic pairs of methicillin-resistant Staphylococcus aureus (MRSA) producing or not producing penicillinase. Loss of the penicillinase plasmid caused an eight times or greater reduction in the MICs of amoxicillin and penicillin G (from greater than or equal to 64 to 8 micrograms/ml), but not of the penicillinase-resistant drugs methicillin and cloxacillin (greater than or equal to 64 micrograms/ml). This difference in antibacterial effectiveness correlated with a more than 10 times greater penicillin-binding protein 2a affinity of amoxicillin and penicillin G than of methicillin and a greater than or equal to 90% successful amoxicillin treatment of experimental endocarditis due to penicillinase-negative MRSA compared with cloxacillin, which was totally ineffective (P less than .001). Amoxicillin was also effective against penicillinase-producing parent MRSA, provided it was combined with clavulanate. Penicillinase-sensitive beta-lactam antibiotics plus penicillinase inhibitors might offer a rational alternative treatment for MRSA infections.

Animals↗
PubMed1999

Rhizosphere feedbacks in elevated CO(2).

Understanding rhizosphere processes in relation to increasing atmospheric CO(2) concentrations is important for predicting the response of forest ecosystems to environmental changes, because rhizosphere processes are intimately linked with nutrient cycling and soil organic matter decomposition, both of which feedback to tree growth and soil carbon storage. Plants grown in elevated CO(2) substantially increase C input to the rhizosphere. Although it is known that elevated CO(2) enhances rhizosphere respiration more than it enhances root biomass, the fate and function of this extra carbon input to the rhizosphere in response to elevated CO(2) are not clear. Depending on specific plant and soil conditions, the increased carbon input to the rhizosphere can result in an increase, a decrease, or no effect on soil organic matter decomposition and nutrient mineralization. Three mechanisms may account for these inconsistent results: (1) the "preferential substrate utilization" hypothesis; (2) the "priming effect" hypothesis; and (3) the "competition" hypothesis, i.e., competition for mineral nutrients between plants and soil microorganisms. A microbial growth model is developed that quantitatively links the increased rhizosphere input in response to elevated CO(2) with soil organic matter decomposition. The model incorporates the three proposed mechanisms, and simulates the complexity of the rhizosphere processes. The model also illustrates mechanistically the interactions among nitrogen availability, substrate quality, and microbial dynamics when the system is exposed to elevated CO(2).

Journal Article↗
PubMed1998

Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria

Are nutrients available to microbial communities in micropatches long enough to influence growth and competition? And what are the sources of such patches? To answer these questions, the swimming behavior of chemotactic bacteria in seawater samples was examined. Clusters of bacteria formed in conjunction with cell lysis and excretion by protozoa. These point sources of nutrients spread into spherical patches a few millimeters in diameter and sustained swarms of bacteria for about 10 minutes. Within that time, a large proportion of the nutrients was encountered by bacteria, chemotactic and nonchemotactic alike. Chemotaxis is advantageous for bacteria using patches over a certain size.

Journal Article↗
PubMed1981

Properties of penicillin-binding proteins in Neisseria gonorrhoeae.

The properties of penicillin-binding proteins (PBPs) of Neisseria gonorrhoeae were studied by comparing PBPs of clinical isolates of different penicillin susceptibility and by putting various beta-lactam antibiotics in competition with radioactive penicillin for PBP binding. Apparent molecular weights of the three major PBPs found were 87,000 (PBP 1), 59,000 (PBP 2), and 44,000 (PBP 3). Relative penicillin resistance was associated with decreased binding to PBP 2 and, to a lesser extent, to PBP 1. Cephaloridine and benzylpenicillin, which produced spheroplasts at minimal inhibitory concentrations, bound to all three PBPs. In contrast, antibiotics which produced a majority of enlarged but apparently intact cells bound only to PBP 2 (mecillinam) or to PBPs 2 and 3 (cephalexin) at their minimal inhibitory concentrations.

Anti-Bacterial Agents↗
PubMed1996

In vitro selection of one-step mutants of Streptococcus pneumoniae resistant to different oral beta-lactam antibiotics is associated with alterations of PBP2x.

Many oral penicillins and cephalosporins are used to treat clinical infections caused by Streptococcus pneumoniae. Therefore, using different beta-lactams as selectors, we estimated the frequencies of one-step mutations leading to resistance. Resistant mutants were obtained from penicillin-susceptible, intermediately resistant, and penicillin resistant strains. For cefixime, cefuroxime, cefpodoxime, cefotaxime, and ceftriaxone, the frequencies of mutation ranged from 10(-6) to 10(-8) when resistant mutants were selected at 2- to 8-fold the MIC, and the MICs increased 2- to 16-fold. For ampicillin, ampicillin-sulbactam, amoxicillin, amoxicillin-clavulanic acid, cefaclor, and loracarbef, the frequencies of mutation were about 10(-7) to 10(-8), and the MICs increased twofold at most. One to three resistance profiles of the resulting mutants were selected for each of the selecting antibiotics. Among those, some showed resistance to the cephalosporins associated with a 2- to 32-fold increase in susceptibility to the penicillins. Competition experiments showed a decreased affinity of PBP2x for cefpodoxime in all mutants. In some mutants that were more susceptible to amoxicillin, a decreased affinity of PBP2x for cefpodoxime was associated with an increased affinity for amoxicillin and a particular substitution of alanine for threonine at position 550 just after the KSG triad. From these results we infer (i) that among the beta-lactams tested the penicillins, cefaclor, and loracarbef selected one-step resistant mutants less frequently and that they achieved a lower level of resistance, and (ii) that mutants with different profiles may have acquired different point mutations in PBP2x.

Amino Acid Sequence↗
PubMed1997

Semiquantitation of cooperativity in binding of vancomycin-group antibiotics to vancomycin-susceptible and -resistant organisms.

The association of vancomycin group antibiotics with the growing bacterial cell wall was investigated by using the cell wall precursor analog di-N-acetyl-Lys-D-Ala-D-Ala in competition binding experiments. The affinities of the antibiotics for the -D-Ala-D-Ala-containing cell wall precursors of Bacillus subtilis ATCC 6633 (a model for vancomycin-susceptible gram-positive bacteria) and for the -D-Ala-D-Lac-containing cell wall precursors of Leuconostoc mesenteroides (a model for vancomycin-resistant strains of Enterococcus faecium and Enterococcus faecalis) were determined by a whole-cell assay. The binding of strongly dimerizing antibiotics such as eremomycin to the bacterial surface was thus shown to be enhanced by up to 2 orders of magnitude (relative to the binding in free solution) by the chelate effect, whereas weakly dimerizing antibiotics like vancomycin and antibiotics carrying lipid tails (teicoplanin) benefited less (ca. 1 order of magnitude). The affinity measured in this way correlates well with the MIC of the antibiotic, and a consequence of this is that future design of semisynthetic vancomycin-group antibiotics should attempt to incorporate chelate effect-enhancing structural features.

Anti-Bacterial Agents↗
PubMed2004

Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis.

Rifampin is a major drug used in the treatment of tuberculosis infections, and increasing rifampin resistance represents a worldwide clinical problem. Resistance to rifampin is caused by mutations in the rpoB gene, encoding the beta-subunit of RNA polymerase. We examined the effect of three different rpoB mutations on the fitness of Mycobacterium tuberculosis. Rifampin-resistant mutants were isolated from a virulent clinical isolate of M. tuberculosis (strain Harlingen) in vitro at a mutation frequency of 2.3 x 10(-8). Mutations in the rpoB gene were identified, and the growth rates of three defined mutants were measured by competition with the susceptible parent strain in laboratory medium and by single cultures in a macrophage cell line and in laboratory medium. All of the mutants showed a decreased growth rate in the three assays. The relative fitness of the mutants varied between 0.29 and 0.96 (that of the susceptible strain was set to 1.0) depending on the specific mutant and assay system. Unexpectedly, the relative fitness ranking of the mutants differed between the different assays. In conclusion, rifampin resistance is associated with a cost that is conditional.

Antibiotics, Antitubercular↗