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PubMed2000

Detection of emerging resistance patterns within longitudinal surveillance systems: data sensitivity and microbial susceptibility. MYSTIC Advisory Board. Meropenem Yearly Susceptibility Test Information Collection.

Communicating information from antimicrobial resistance surveillance study data to microbiologists and physicians can be challenging. Large amounts of data, commonly reaching millions of MICs or zone diameter endpoints, must be analysed and condensed to easily-read tables or figures. Furthermore, data must not be prejudged relative to susceptibility categories, because of the diverse nature of interpretive criteria available internationally. An attempt must be made to present results of all surveillance studies in a mode that can be reinterpreted for immediate use in different geographical areas, or used to compare future data with relative ease and high accuracy. Such data displays require peer-reviewed journals to permit greater numbers of more complex tables to present results. The Meropenem Yearly Susceptibility Test Information Collection (MYSTIC) study is a year-on-year global surveillance programme in medical centres where meropenem is available for use. We have developed a presentation strategy that expands the long-term clinical value of MYSTIC results. In addition to statistical parameters, tables of cumulative percentages or numbers of strains inhibited at each tested antimicrobial concentration will be presented. Alternative figures (Finland-o-grams) could also be used, but these generally lack precise extractable rates and require more journal space. Regardless of study design, promotion of this presentation philosophy enhances any surveillance study's value to each reader or user and facilitates application to locally appropriate interpretations. The widespread use of these analysis and presentation principles as benchmarks by various resistance studies and networks is strongly encouraged, particularly by investigations across international boundaries.

Anti-Bacterial Agents↗
PubMed1981

Microbial colonization of prosthetic devices. I. Microtopographical characteristics of intravenous catheters as detected by scanning electron microscopy.

Ten commercially available unused intravenous catheters were investigated by Scanning Electron Microscopy (SEM). Different types of irregularities in the external and internal surface could be detected in all catheters examined. Representative examples were demonstrated in 6 SEM-photos. The possible role of such irregularities in favouring bacterial attachment to catheter surfaces was discussed.

Bacteria↗
PubMedDate not supplied

[Study of the nature of the associated microflora in the prolonged substrateless cultivation of beet plants].

The purpose of the present investigation was to study variations in the population density of microorganisms, their qualitative and quantitative composition during substrate-free cultivation of beats. The results obtained show that the microbial number in the nutrient solution increased by the time of intensive growth of beats and decreased by the time of harvesting. The number of root microorganisms was much greater than the total number of microorganisms in the nutrient solution. Oligonitrophils and nitrogen fixing bacteria were found in the solution. This may be associated with a transient decrease of nitrogen in the solution. The number of ammonifiers and denitrifiers in the solution increased significantly by the end of plant vegetation; the amount of denitrifiers inhabiting the roots decreased during vegetation and that of ammonifiers increased. In the middle of vegetation cellulose decomposing aerobes appeared; this might occur since root hairs began to die off. By the end of vegetation an insignificant amount of fungi was also found. Nitrifying and spore-forming microorganisms were not detected. The identification of predominant microbial species showed them to be bacteria of the genera Pseudomonas and Mycobacterium. Besides, microorganisms of the genera Bacterium, Micrococcus, Mycococcus, Chromobacterium and Pseudobacterium also occurred.

Actinomycetales↗
PubMed2006

The role of indigenous bacterial and fungal soil populations in the biodegradation of crude oil in a desert soil.

The biodegradation capacity of indigenous microbial populations was examined in a desert soil contaminated with crude oil. To evaluate biodegradation, soil samples supplemented with 5, 10 or 20% (w/w) of crude oil were incubated for 90 days at 30 degrees C. The effect of augmentation of the soil with vermiculite (50% v/v) as a bulking agent providing increased surface/volume ratio and improved soil aeration was also tested. Maximal biodegradation (91%) was obtained in soil containing the highest concentration of crude oil (20%) and supplemented with vermiculite; only 74% of the oil was degraded in samples containing the same level of crude oil but lacking vermiculite. Gas chromatograms of distilled fractions of crude oil extracted from the soil before and after incubation demonstrated that most of the light and part of the intermediate weight fractions initially present in the oil extracts could not be detected after incubation. Monitoring of microbial population densities revealed an initial decline in bacterial viable counts after exposure to oil, presumably as a result of the crude oil's toxicity. This decline was followed by a steep recovery in microbial population density, then by a moderate increase that persisted until the end of incubation. By contrast, the inhibitory effect of crude oil on the fungal population was minimal. Furthermore, the overall increased growth response of the fungal population, at all three levels of contamination, was about one order of magnitude higher than that of the bacterial population.

Aluminum Silicates↗
PubMed1996

The influence of abutment surface roughness on plaque accumulation and peri-implant mucositis.

Bacterial adhesion to intra-oral, hard surfaces is firmly influenced by the surface roughness to these structures. Previous studies showed a remarkable higher subgingival bacterial load on rough surfaces when compared to smooth sites. More recently, the additional effect of a further smoothening of intra-oral hard surfaces on clinical and microbiological parameters was examined in a short-term experiment. The results indicated that a reduction in surface roughness below R(a) = 0.2 microns, the so-called "thresholds R(a)", had no further effect on the quantitative/qualitative microbiological adhesion or colonisation, neither supra- nor subgingivally. This study aims to examine the long-term effects of smoothening intra-oral hard transgingival surfaces. In 6 patients expecting an overdenture in the lower jaw, supported by endosseus titanium implants, 2 different abutments (transmucosal part of the implant): a standard machined titanium (R(a) = 0.2 microns) and one highly polished and made of a ceramic material (R(a) = 0.06 microns) were randomly installed. After 3 months of intra-oral exposure, supra- and subgingival plaque samples from both abutments were compared with each other by means of differential phase-contrast microscopy (DPCM). Clinical periodontal parameters (probing depth, gingival recession, bleeding upon probing and Periotest-value) were recorded around each abutment. After 12 months, the supra- and subgingival samples were additionally cultured in aerobic, CO2-enriched and anaerobic conditions. The same clinical parameters as at the 3-month interval were recorded after 12 months. At 3 months, spirochetes and motile organisms were only detected subgingivally around the titanium abutments. After 12 months, however, both abutment-types harboured equal proportions of spirochetes and motile organisms, both supra- and subgingivally. The microbial culturing (month 12) failed to detect large inter-abutment differences. The differences in number of colony- forming units (aerobic and anaerobic) were within one division of a logarithmic scale. The aerobic culture data showed a higher proportion of Gram-negative organisms in the subgingival flora of the rougher abutments. From the group of potentially "pathogenic" bacteria, only Prevotella intermedia and Fusobacterium nucleatum were detected for anaerobic culturing and again the inter-abutment differences were negligible. Clinically, the smoothest abutment showed a slightly higher increase in probing depth between months 3 and 12, and more bleeding on probing. The present results confirm the findings of our previous short-term study, indicating that a further reduction of the surface roughness, below a certain "threshold R(a)" (0.2 microns), has no major impact on the supra- and subgingival microbial composition.

Adult↗
PubMedDate not supplied

Clinical evaluation of an ionic tooth brush on oral hygiene status, gingival status, and microbial parameter.

It has long been recognised that the presence of dental plaque leads to gingivitis and periodontal disease, as well as dental caries. Today tooth brushing is the most widely accepted method of removing plaque. Hence this present clinical study was undertaken to evaluate the effectiveness of an ionic toothbrush on oral hygiene status. For this study, 20 dental students in the age group of 18-20 years were included. All the subjects after undergoing dental prophylaxis were then provided with ionic toothbrushes, either active (equipped with lithium battery) or inactive (without lithium battery). Plaque index and gingival bleeding index were examined at 7th, 14th, and 21st day. Microbial assessment was done for detection of colony forming units (CFU) from the plaque samples which were collected on 0 day and 21st day, both before brushing and after brushing. Results shown a significant reduction in all the parameters and the reduction was more significant in active and inactive ionic toothbrush users. It was concluded that both active and inactive ionic toothbrushes reduced the plaque index and gingival bleeding index scores significantly and active ionic tooth brushes were more effective as compared to inactive ionic toothbrushes. There was no soft tissue trauma following the use of both type of toothbrushes, which showed that ionic toothbrushes were equally safe for regular long-term use.

Adolescent↗
PubMed1998

The effect of a 1-stage full-mouth disinfection on oral malodor and microbial colonization of the tongue in periodontitis. A pilot study.

Oral malodor affects a large proportion of the population and may be the cause of a significant social and psychological handicap. This pilot study aimed to examine whether a 1-stage full-mouth disinfection in periodontitis patients (scaling and root planing of all pockets within 24 hours together with the application of chlorhexidine to all intra-oral niches followed by chlorhexidine mouth rinsing for 2 months) resulted in a significant improvement in malodor when compared to a fractionated periodontal therapy (consecutive root planings per quadrant, at a 1 to 2 week interval). The baseline and outcome data concerning oral malodor were linked to the presence of tongue coating and to its roughness (fissures). Twenty-four patients with severe periodontitis were randomly allocated to test and control groups. At baseline and after 1 and 2 months, the concentration of volatile sulfur compounds (VSC) in the mouth was measured and organoleptic ratings (expired air and total mouth air) were given. Plaque samples were collected from the dorsum of the tongue to calculate the number of colony forming units (CFU) per ml (anaerobic culturing) as well as the number of pigmented CFU/ml. Both the baseline organoleptic ratings and the VSC scores correlated well with the presence of tongue coating but not with the tongue roughness. Because a correlation between tongue coating and its microbial load could not be detected, it was hypothesized that the tongue coating per se, and not the bacteria, might be responsible for the malodor. The 1-stage full-mouth disinfection resulted in a faster and additional reduction in the organoleptic ratings of the oral malodor, even after 2 months. This might be explained by the improved periodontal outcome and/or the more significant reduction in the CFU/ml of pigmented species. In contrast to the organoleptic ratings, which were significantly reduced in both treatment groups (when compared to baseline), the VSC levels remained unchanged. This pilot study indicates that a 1-stage full-mouth disinfection has, in comparison to a standard periodontal therapy, additional beneficial effects in the treatment of oral malodor.

Adult↗
PubMed1991

The epidemiology of Neisseria gonorrhoeae isolates in Dakar, Sénégal 1982-1986: antimicrobial resistance, auxotypes and plasmid profiles.

A total of 460 Neisseria gonorrhoeae isolates from patients seen at three clinics in Dakar, Sénégal, 1982-1986, have been investigated. In this period a significant change in antimicrobial susceptibility was observed: the percentage of strains susceptible to penicillin (MIC less than or equal to 0.08 micrograms/ml) fell from 61 to 18 (p less than 0.0001) and the percentage of resistant strains (MIC greater than or equal to 1.2 micrograms/ml) increased from 18 to 46. Among penicillin-resistant strains the proportion of penicillinase-producing strains (PPNG) was fairly constant (range 35-55%). The determination of susceptibility to anti-microbial agents performed locally allowed detection of approximately all PPNG strains whereas the increase in the occurrence of strains with chromosomally determined resistance was not revealed. The study comprised 70 PPNG strains of which 19% (13/70) carried the 7.4 kb Asian plasmid and 81% (57/70) the 5.3 kb African plasmid. None of these strains possessed the 38 kb conjugative plasmid, whereas it was found in 4.5% of the 376 non-PPNG strains available for plasmid analysis; 92% (410/446) of all strains had the small 4.2 kb plasmid and 5.4% (24/446) did not contain any plasmid. Overall, auxotype zero and proline-requiring strains were predominant, accounting for 53% (244/460) and 28% (131/460), respectively. In general, PPNG strains carrying the 5.3 kb plasmid were auxotype zero (49/57 = 86%) and those carrying the 7.4 kb plasmid were proline-requiring (9/13 = 69%).

Female↗
PubMed1998

Use of pulsed field gel electrophoresis to determine the source of microbial contamination of central venous catheters.

Microorganisms detected in situ on the distal tip of central venous catheters (CVC) within 90 min of insertion were investigated using pulsed-field gel electrophoresis to analyse genomic fragments obtained with the SmaI restriction enzyme. Thirty patients received a triple lumen CVC, which was inserted directly through the skin using the Seldinger technique. In a further 30 patients a triple lumen CVC was inserted through a Swan sheath, thereby avoiding direct contact of the CVC with the skin. Staphylococci were isolated from the distal tips of the catheters in 6 patients (5 who had the CVC inserted directly through the skin and 1 who had the CVC inserted via a Swan sheath.) Twenty-three staphylococcal isolates were also isolated from the insertion equipment and the skin swabs surrounding the insertion site of these six patients. All the isolates were genotyped. In one of the patients the organisms isolated from the skin were identical to those on the CVC tip. In two further patients similar organisms were isolated from the insertion equipment and the patients' skin. These results, in addition to the reduced colonisation rates observed when catheters were introduced through a Swan sheath, support the hypothesis that microorganisms from the skin are impacted onto the CVC tip and the CVC insertion equipment at catheter insertion.

Bacteria↗
PubMed2005

Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities.

Here, we describe a three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors. In the first step, the nearly complete 16S rRNA gene was amplified using bacterial primers. Subsequently, this product was used as a template in a second PCR with group-specific SRB primers. A third round of amplification was conducted to obtain fragments suitable for DGGE. The largest number of bands was observed in DGGE patterns of products obtained with primers specific for the Desulfovibrio-Desulfomicrobium group, indicating a large diversity of these SRBs. In addition, members of other phylogenetic SRB groups, i.e., Desulfotomaculum, Desulfobulbus, and Desulfococcus-Desulfonema-Desulfosarcina, were detected. Bands corresponding to Desulfobacterium and Desulfobacter were not detected in the bioreactor samples. Comparative sequence analysis of excised DGGE bands revealed the identity of the community members. The developed three-step PCR-DGGE strategy is a welcome tool for studying the diversity of sulfate-reducing bacteria.

Base Sequence↗
PubMed1995

Detection, isolation, and stability of megaplasmid-encoded chloroaromatic herbicide-degrading genes within Pseudomonas species.

Dicamba is used as a model system for microbial degradation of chloroaromatic benzoic acids. The detection, isolation, and stability of a megaplasmid within a Pseudomonas sp. is described as the first step in optimizing the growth of this microorganism and other microorganisms similar to it. A large plasmid, pDK1, consisting of approximately 250 kb, was purified from dicamba-degrading Pseudomonas sp. PXM. This plasmid was purified by the method of Allen (personal communication, 1994), which is a modified version of several that have been attempted for the isolation of large plasmids (Lee and Rasheed, 1990). The restriction analysis of this plasmid (pDK1) from PXM. revealed many distinctive bands on agarose gel electrophoresis. Based on the preliminary restriction enzyme analysis, the estimated size of this plasmid is 250 kb, which could make it one of the largest procaryotic plasmids encoding for chloroaromatic degrading enzymes. Allen's methodology results in very high purity and reproducibility compared to the other methods used in this study. As described in this work, the method of Kado and Liu (1981) is easier to perform and results in a more reproducible plasmid preparation than the method of Casse et al. (1979). Casse's protocol requires the use of a highly alkaline SDS solution (pH 12.45) in order to eliminate the chromosomal DNA. However, only incomplete removal of the chromosomal DNA results. Compared to the Casse et al. protocol, the Kado and Liu protocol requires the use of a highly alkaline solution (pH 12.6) and a high temperature (55-65 degrees C) to eliminate the chromosomal DNA. This results in a nearly complete removal of the chromosomal DNA. The high temperature treatment also quickly eliminates the RNA. Another advantage of the protocol of Kado and Liu over the protocol of Casse et al. is that the former uses phenol-chloroform extraction while the latter uses only phenol extraction. The phenol-chloroform extraction step denatures the DNA along with the proteins. In addition to this, the phenol-chloroform mixture minimizes the formation of a brown oxidation pigment that usually occurs with phenol extraction alone. Finally, the time needed to complete the Kado and Liu protocol is much shorter (2 hr) than the time needed to complete the Casse protocol (8 hr). As described previously, a highly purified plasmid preparation with minimal chromosomal DNA was prepared by following the suggestions of L. Allen.(ABSTRACT TRUNCATED AT 400 WORDS)

Biodegradation, Environmental↗
PubMed1993

Contamination of Ammonium-Based Nutrient Solutions by Nitrifying Organisms and the Conversion of Ammonium to Nitrate.

Conversion of ammonium to nitrate and contamination by nitrifying organisms are often assumed not to be significant in ammonium-based nutrient solutions. To assess this assumption, maize (Zea mays) and pea (Pisum sativum) were grown under greenhouse conditions in aeroponic, hydroponic, and sand-culture systems containing 2 mM ammonium chloride as the sole nitrogen source and evaluated for the activity of contaminating nitrifying organisms. In all three culture systems, root colonization by nitrifying organisms was detected within 5 d, and nitrate was detected in the nutrient solution within 10 d after seedling transfer. In sand culture, solution nitrate concentration reached 0.35 mM by the end of the 17-d experiment. Consistent with the microbial ammonium oxidation sequence, nitrite was detected earlier than nitrate and remained at lower levels throughout the experiment. Nitrate was found in significant quantities in root and shoot tissues from seedlings grown in ammonium-based nutrient solutions in all of the solution culture systems. Maize seedlings grown in an ammonium-based hydroponic system contained nitrate concentrations at 40% of that found in plants grown in nitrate-based solution. Determination of nitrate (or nitrite) levels in the nutrient solution was the weakest indicator of the activity of nitrifying organisms. A bioassay for the presence of nitrifying organisms in combination with tissue analysis for nitrate was a better indicator of microbial conversion of ammonium to nitrate in nutrient solution culture. The results have implications for the use of ammonium-based nutrient solutions to obtain plants suitable for research on induction of nitrate uptake and reduction or for research using solution culture to compare ammonium versus nitrate fertilization.

Journal Article↗
PubMed1985

Detection of beta-lactamase activity with nitrocefin of multiple strains of various microbial genera.

The production or presence of beta-lactamase(s) was studied by the rapid method utilizing the chromogenic cephalosporin compound nitrocefin in cultures of multiple strains belonging to the same genus as well as groups of microorganisms. The genera were: Staphylococcus spp., Streptococcus faecalis, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, indole-positive Proteus spp., Enterobacter spp., Serratia marcescens, rare Enterobacteriaceae, Pseudomonas aeruginosa, Haemophilus influenzae and Neisseria gonorrhoeae. With this sensitive and rapid assay for beta-lactamase, it was possible to verify and separate the beta-lactamase producing cultures from the non-producers and include the useful strains to on-going research, such as beta-lactam screen, beta-lactamase inhibitory study and lytic properties of beta-lactams. The data also provide evidence for the possible role of beta-lactamase(s) in the physiology, biochemistry and pathogenicity of bacterial strains. The nitrocefin method was found a very specific and extremely useful procedure for the detection and estimation of beta-lactamase activity.

Bacteria↗
PubMed2005

Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes.

The generation of microarray probes with specificity below the species level is an ongoing challenge, not least because the high-throughput detection of microorganisms would be an efficient means of identifying environmentally relevant microbes. Here, we describe how suppression subtractive hybridization (SSH) can be applied to the production of microarray probes that are useful for microbial differentiation at the subspecies level. SSH was used to initially isolate unique genomic sequences of nine Salmonella strains, and these were validated in quadruplicate by microarray analysis. The results obtained indicate that a large group of genes subtracted by SSH could serve together, as one probe, for detecting a microbial subspecies. Similarly, the whole microbial genome (not subjected to SSH) can be used as a species-specific probe. The detailed methods described herein could be used and adapted for the estimation of any cultivable bacteria from different environments.

Bacterial Infections↗
PubMed1999

PCR-based identification of postmortem microbial contaminants--a preliminary study.

Investigation of postmortem blood can reveal the presence of significant ethanol levels. However, in some instances it cannot easily be determined if the source of ethanol is from ingestion or from postmortem endogenous fermentation by contaminating microbes. Described here is a robust polymerase chain reaction (PCR)-based method for detecting the presence of common ethanol producing microbial contaminants in human blood. A set of DNA primers were designed for use in PCR to amplify and detect the genomic DNA from humans and three test microorganisms Escherichia coli, Proteus vulgaris, and Candida albicans. A rapid and reproducible protocol was developed for isolating genomic DNA from mixed human blood-microorganism samples that yields a suitable template for PCR. The organism-specific primer pairs can detect the presence of the target microorganisms in human blood at concentrations as low as 10 colony forming units/mL. The PCR products readily can be detected after agarose gel electrophoresis. This method provides an additional means of rapidly identifying microbial contaminants in postmortem blood samples.

Candida albicans↗
PubMed2004

Isolation and identification of fungi from vaginal flora in three species of captive Leontopithecus.

The ability to reproduce in captivity is an essential component of lion tamarin (Leontopithecus) conservation programs. However, infections such as vaginitis, cervicitis, and endometritis are important diseases that may influence the reproduction of these animals. Therefore, it is important to detect continuous or occasional vaginal microbial populations, and to understand their potential role as an endogenous source of infection [Collins, 1964; Blue, 1983; Pugh et al., 1986]. Vaginal swabs were collected from 25 female tamarins of the three currently available species (L. rosalia, L. chrysopygus, and L. chrysomelas) at the Center of Primatology in Rio de Janeiro, Brazil. The swabs were processed according to standard mycological protocols, and isolates were biochemically characterized. Fungal isolates were recovered from 16 animals (64.0%). The results showed that 70.6% of the isolated microorganisms consisted of yeast, including three species of Candida (mainly C. glabrata). We suggest that this species is a resident member of the normal vaginal flora in Leontopithecus. Filamentous fungi (mainly from Trichosporon, Aspergillus, and Penicilliumgenera) constituted 29.4% of the isolates, and were considered to be transitory contaminants of the genital area. We suggest that colonization of the vaginal environment is related to the endocrine pattern associated with the reproductive status of these animals, but not to parity.

Animals↗