A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis.

Peptidoglycan (PG), an essential structure in the cell walls of the vast majority of bacteria, is critical for division and maintaining cell shape and hydrostatic pressure. Bacteria comprising the Chlamydiales were thought to be one of the few exceptions. Chlamydia harbour genes for PG biosynthesis and exhibit susceptibility to 'anti-PG' antibiotics, yet attempts to detect PG in any chlamydial species have proven unsuccessful (the 'chlamydial anomaly'). We used a novel approach to metabolically label chlamydial PG using d-amino acid dipeptide probes and click chemistry. Replicating Chlamydia trachomatis were labelled with these probes throughout their biphasic developmental life cycle, and the results of differential probe incorporation experiments conducted in the presence of ampicillin are consistent with the presence of chlamydial PG-modifying enzymes. These findings culminate 50 years of speculation and debate concerning the chlamydial anomaly and are the strongest evidence so far that chlamydial species possess functional PG.

Coordinating development with the cell cycle in Caulobacter.

During the Caulobacter life cycle, the timing of DNA replication, cell division and development is precisely coordinated. Recent work has begun to unravel the complex regulatory networks that couple these processes. A key aspect of these regulatory networks is the dynamic localization of multiple histidine protein kinases that control a master response regulator, thus driving downstream pathways.

Global analysis of a bacterial cell cycle: tracking down necessary functions and their regulators.

New, post-genomic analyses are increasing the rate at which information about highly complex processes such as bacterial growth and development can be acquired. The recent use of DNA-microarray and proteomic analysis to study the differentiating bacterium Caulobacter crescentus has provided the first global view of the requirements of a bacterium as it progresses through its cell cycle. Potential regulators of cell cycle progression have been identified, and it has been suggested that proteolysis could have a global role in regulating the bacterial cell cycle.

Precise mapping and comparison of two evolutionarily related regions of the Escherichia coli K-12 chromosome. Evolution of valU and lysT from an ancestral tRNA operon.

Two tRNA operons have been found near the gltX gene encoding the glutamyl-tRNA synthetase of Escherichia coli K-12. The alaW operon previously undetected from genetic data and containing two identical tRNA(GGCAla) genes is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon containing genes for three identical tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN), is adjacent to gltX and is transcribed from the opposite strand. Five open reading frames were also found in this region encoding putative polypeptides of 62, 105, 130, 167 and 294 amino acid residues. ORF294 is a new member of the lysR family of bacterial transcriptional activators. The possibility that this is the xapR gene is discussed. Comparison of the physical and linkage maps of the E. coli chromosome in the 52 minute region has permitted precise mapping of most of the 18 genes in this region with the order nupC-glk- less than (alaW beta-ala W alpha)-1 kb- less than gltX-0.3 kb-(valU alpha-valU beta-valU gamma-lysV = supN) greater than xapR-xapA- less than lig-1 kb-cysK greater than -0.4 kb-ptsH greater than -0.05 kb-pstI greater than -0.05 kb-crr greater than -cysM-cysA in the clockwise order (greater than and less than indicate the direction of transcription; kb, 10(3) bases). The last two genes of valU (52 min) and lysT (16.5 min) are arranged in a similar fashion and a highly conserved region has been found in both operons. This suggests that the valU and lysT operons probably arose by a duplication of an ancestral tRNA operon. This is the first example of what may be two different tRNA operons from the same organism evolving from an ancestral tRNA gene. Comparison of the 16 and 52 minute regions of the E. coli K-12 chromosome suggests that these two regions could share a common ancestor.

Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase gene and a tRNA operon in Escherichia coli. Transcriptional and post-transcriptional regulation of gltX, valU and alaW.

The transcription of the gltX gene encoding the glutamyl-tRNA synthetase and of the adjacent valU and alaW tRNA operons of Escherichia coli K-12 has been studied. The alaW operon containing two tRNA(GGCAla) genes, is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon, containing three tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN) genes, is adjacent to gltX and is transcribed from the opposite strand. Its only promoter is upstream from the gltX promoters. The gltX gene transcript is monocistronic and its transcription initiates at three promoters, P1, P2 and P3. The transcripts from one or more of these promoters are processed by RNase E to generate two major species of gltX mRNA, which are stable and whose relative abundance varies with growth conditions. The stability of gltX mRNA decreases in an RNase E- strain and its level increases with growth rate about three times more than that of the glutamyl-tRNA synthetase. The 5' region of these mRNAs can adopt a stable secondary structure (close to the ribosome binding site) that is similar to the anticodon and part of the dihydroU stems and loops of tRNA(Glu), and which might be involved in translational regulation of GluRS synthesis. The gltX and valU promoters share the same AT-rich and bent upstream region, whose position coincides with the position of the upstream activating sequences of tRNA and rRNA promoters to which they are similar. This suggests that gltX and valU share transcriptional regulatory mechanisms.

The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system.

Modeling approaches to the dynamics of a living cell are presented that are strongly based on its underlying physical and chemical processes and its hierarchical spatio-temporal organization. Through the inclusion of a broad spectrum of processes and a rigorous analysis of the multiple scale nature of cellular dynamics, we are attempting to advance cell modeling and its applications. The presentation focuses on our cell modeling system, which integrates data archiving and quantitative physico-chemical modeling and information theory to provide a seamless approach to the modeling/data analysis endeavor. Thereby the rapidly growing mess of genomic, proteomic, metabolic, and cell physiological data can be automatically used to develop and calibrate a predictive cell model. The discussion focuses on the Karyote cell modeling system and an introduction to the CellX and VirusX models. The Karyote software system integrates three elements: (1) a model-building and data archiving module that allows one to define a cell type to be modeled through its reaction network, structure, and transport processes as well as to choose the surrounding medium and other parameters of the phenomenon to be modeled; (2) a genomic, proteomic, metabolic cell simulator that solves the equations of metabolic reaction, transcription/translation polymerization and the exchange of molecules between parts of the cell and with the surrounding medium; and (3) an information theory module (ITM) that automates model calibration and development, and integrates a variety of data types with the cell dynamic computations. In Karyote, reactions may be fast (equilibrated) or slow (finite rate), and the special effects of enzymes and other minority species yielding steady-state cycles of arbitrary complexities are accounted for. These features of the dynamics are handled via rigorous multiple scale analysis. A user interface allows for an automated generation and solution of the equations of multiple timescale, compartmented dynamics. Karyote is based on a fixed intracellular structure. However, cell response to changes in the host medium, damage, development or transformation to abnormality can involve dramatic changes in intracellular structure. As this changes the nature of the cellular dynamics, a new model, CellX, is being developed based on the spatial distribution of concentration and other variables. This allows CellX to capture the self-organizing character of cellular behavior. The self-assembly of organelles, viruses, and other subcellular bodies is being addressed in a second new model, VirusX, that integrates molecular mechanics and continuum theory. VirusX is designed to study the influence of a host medium on viral self-assembly, structural stability, infection of a single cell, and transmission of disease.

rRNA gene restriction patterns as an epidemiological marker in nosocomial outbreaks of Staphylococcus aureus infections.

rRNA gene restriction patterns (ribotyping) were compared with phage typing, serotyping, enterotoxins and exfoliatin production in the analysis of 26 Staphylococcus aureus strains isolated from two different nosocomial outbreaks. Total DNA was cleaved by EcoRI restriction endonuclease. After agarose gel electrophoresis and Southern transfer, the hybridization of the membranes was done with radiolabelled 16S rRNA gene from Bacillus subtilis inserted into a plasmid vector. Six to 13 fragments were visualized. A core of common fragments was discerned for all strains tested. A full correlation between ribotyping and conventional markers was observed in only one of the outbreaks studied. In both outbreaks, ribotyping proved helpful in characterizing otherwise untypable strains.

Distribution of Staphylococcus sciuri subspecies among human clinical specimens, and profile of antibiotic resistance.

The distribution of three subspecies comprising Staphylococcus sciuri was determined for a collection of 30 clinical isolates originating from Morocco, the United Kingdom, and France. The sources of these isolates were principally wounds, skin, and soft tissue infections. At the species level, the isolates were identified according to biochemical characteristics and at the subspecies level by the ribotyping technique. PCR analysis performed with the 16S-23S ribosomal DNA intergenic spacer was less powerful for subspecies differentiation. S. sciuri subsp. sciuri was the most frequent subspecies (21 isolates) found in the collection, whereas S. sciuri subsp. rodentium (seven isolates) and S. sciuri subsp. carnaticus (two isolates) were less common. mecA or a mecA-related gene was detected by PCR and Southern blot in all 30 S. sciuri isolates, supporting the suggestion that S. sciuri species are the natural reservoir of the mecA gene. While the linA/linA' gene coding for lincomycin resistance was present in five isolates, an uncharacterized gene for this resistance was suspected in seventeen other isolates.

Phenotypic and genotypic (pulsed-field gel electrophoresis) characteristics of enterotoxin-A-producing Staphylococcus aureus strains.

The phenotypic (antibiotype, serotype, phagetype) and genotypic (SmaI restriction patterns using pulsed-field gel electrophoresis) characters of 162 Staphylococcus aureus epidemiologically unrelated strains were studied. Eighty-two of the isolates produced enterotoxin-A (SEA+), while 80 produced none (SEA-). None of the phenotypic characters observed were characteristic of SEA+ strains. On the other hand, the electrophoretic profiles revealed a non-random distribution of the SEA+ strains (p < 0.01 in groups PI and PIII, and p < 0.03 in group PII). It can therefore reasonably be assumed that the enterotoxin-A-producing strains did not constitute a single clone, but rather, seemed to belong to strains derived from at least three clones with distinct genetic organization.

Identification of atypical strains of Staphylococcus epidermidis by use of molecular tools.

Four atypical coagulase-negative staphylococcal (CNS) isolates from clinical sources were compared with Staphylococcus epidermidis strains by ribotyping. The ribotypes of the four strains shared close rDNA restriction profiles with those of the S. epidermidis strains used. The DNA sequence encoding 16S rRNA demonstrated 99.9% homology with S. epidermidis. S1 nuclease experiments showed that these atypical strains formed a homogeneous genomic group. DNA-DNA homologies between the S. epidermidis type strain CCM 2124 and the four CNS isolates ranged from 70 to 89%. The guanine-plus-cytosine content of the deoxyribonucleic acid of the four strains ranged from 31 to 32 mol%.

Clinical isolates of Staphylococcus lugdunensis and S. schleiferi: bacteriological characteristics and susceptibility to antimicrobial agents.

The bacteriological characteristics and susceptibility to antimicrobial agents of 108 clinical isolates of Staphylococcus lugdunensis and Staphylococcus schleiferi are described. Fifty out of 108 isolates were considered to be responsible for 16 documented infections, including some severe infections (endocarditis, bacteraemia, osteitis). A number of bacteriological characteristics enabled the identification of these species in the clinical microbiology laboratory: the absence of coagulase and protein A, and the presence of a fibrinogen affinity factor and thermonuclease along with other biochemical characteristics (ornithine and arginine decarboxylases, carbohydrate acidification, novobiocin susceptibility) differentiated these new species from other staphylococci; however, they did not possess virulence markers such as toxins or haemagglutinin, but were haemolytic. In this series, almost all isolates were susceptible to 22 antibiotics and 4 antiseptics representative of the main groups of antimicrobial agents. More information is needed on the ecology and epidemiology of these new opportunistic pathogens.

Effectiveness of simple measures to control an outbreak of nosocomial methicillin-resistant Staphylococcus aureus infections in an intensive care unit.

Between June 1985 and March 1986, 14 cases of severe nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infection, including septicemia, were observed in the intensive care unit (ICU) of a 400-bed cancer reference center. Simple control measures including contact isolation of colonized patients and reinforcement of handwashing practices among personnel were followed by a sharp decrease in the rate of infection and colonization. An epidemiological investigation showed that a single serophage variant MRSA strain was involved; peak incidence of infection was 17 per 100 ICU patient discharges; the index case was identified as a patient admitted from another hospital and the epidemic strain was then transmitted from patient-to-patient in the ICU; risk factors for acquiring infection were length of prior hospitalization, invasive procedures and number of antibiotic treatments; dissemination of the strain to other wards was only anecdotal. These results stress the effectiveness of simple measures to control outbreaks of MRSA nosocomial infections even in immunocompromised cancer patients.

In vitro antitumor activity of 9-nitro-camptothecin as a single agent and in combination with other antitumor drugs.

Preclinical studies at Roswell Park Cancer Institute by Minderman, Cao, and Rustum (unpublished results) showed that a combination of SN-38 and 5-FU against HCT-8 human colon carcinoma cells in vitro was synergistic, with the best interaction occurring when the drugs were added sequentially, SN-38 first. Their in vivo studies using HCT-8 tumor xenografts implanted s.c. in nude athymic mice demonstrated superior efficacy for a sequential i.v. administration of CPT-11, 24 hr before 5-FU. On the basis of these studies, our group has begun to evaluate effects of RFS2000 (9-nitro-20(S)-camptothecin) (9-NC) in combination with a series of other antitumor agents. Using a panel of human tumor cell lines including A121 ovarian cancer, HCT-8 colon cancer, H-460 NSCLC, HT-1080 fibrosarcoma, and MCF7 mammary cancer, we found that a 2-hr exposure to 9-NC resulted in ID50 values of < 1.0 microM, whereas continuous exposure to drug resulted in ID50 values of < 1.0 nM. Tumor growth inhibitory activities of 5-FU, gemcitabine, and paclitaxel were determined for comparison. Combinations of these agents were evaluated with 9-NC using the human HCT-8 colon tumor cell line. Concurrent and sequential combinations of 9-NC with 5-FU had some regions of the concentration-effect surface with local synergy and some with local antagonism. However, sequential combination of 9NC or SN-38 followed by 5-FU, 24 hr later appeared to be highly synergistic at high dose-effect levels (i.e., ID90), suggesting that sequential drug administration may be more efficacious at high effect level and that the order of drug addition is very important. Overall, our results were similar to that found earlier by Rustum's group with CPT11 (or SN-38) and 5-FU, suggesting that sequential combination of 9-NC (or other camptothecin analogues) followed by 5-FU has potential for the treatment of cancer in man.

Instability of characteristics amongst coagulase-negative staphylococci causing endocarditis.

Variation in typing of clinically significant isolates of coagulase-negative staphylococci (CNS) was determined by five typing methods with 143 isolates obtained from 19 patients over periods from 2 days to 1 year. In only one case did all isolates give exactly the same typing pattern by all five tests. No single method, or simple combination, provided a ready means of confirming the relatedness of separate isolates. The most frequently useful tests were antibiotic susceptibility and extrachromosomal DNA banding patterns. However, the results of biotyping, serotyping and phage typing were also helpful in showing the relationship between different isolates from a given patient. In most cases a core pattern varying by the gain or loss of a small number of features, characterised a given patient's isolates. In two causes, apparently radical changes in the infecting organism were observed, and confirmed by restriction endonuclease analysis. Care should be taken when successive isolates of CNS show distinct typing differences in deciding their clinical relevance.

Clonal dissemination of epidemic methicillin-resistant Staphylococcus aureus in Belgium and neighboring countries.

OBJECTIVES: To determine the diversity of pulsed-field gel electrophoresis (PFGE) types among epidemic strains of methicillin-resistant Staphylococcus aureus (MRSA) recovered in Belgium, France, Germany and The Netherlands over the period 1981-94. METHODS: MRSA strains collected in a multicenter survey in Belgium (n = 171) and from reference laboratories in neighboring countries (n = 102) were characterized by PFGE analysis using the SmaI enzyme. RESULTS: In total, 32 PFGE types were found. Epidemic PFGE type 1, first recognized in 1984, accounted for 82% of Belgian strains (87% of hospitals) and 51% of European MRSA strains. Four other internationally epidemic PFGE types (types 8, 10, 11 and 12) were less widely disseminated and more recently detected (1991-94), each recovered from two or three countries. International spread of two PFGE types was linked to transfer of colonized patients to Dutch hospitals from another country where this type was frequently recovered. CONCLUSIONS: Genotypic analysis indicated widespread distribution of several outbreak-associated MRSA strains over large European regions, which was in some instances related to interhospital patient transfer. These findings underscore the need for standardized international surveillance and control of MRSA transmission between healthcare institutions across Europe.

Gradient separation of polymers at critical point of adsorption.

Theoretical and experimental analysis of interaction polymer chromatography revealed a new mode of polymer separation: gradient elution at the critical point of adsorption (the eluent composition where size-exclusion and adsorption interactions completely compensate each other). This mode allows for molecular-mass-independent separation by chemical composition and/or other structural differences between macromolecules. The isocratic and gradient elution of narrow polydispersity polystyrenes and poly(methylmethacrylates) on reversed- and normal-phase columns confirmed all basic theoretical assumptions and conclusions. The gradient separation of poly(alkylmethacrylate) and poly(alkylacrylate) blends, as well as styrene-butadiene copolymers provided further experimental verification of the theory.

Experimental study of antidiarrheal activity of Salicairine.

Experimental antidiarrheal activity of a traditionally used medication, Salicairine, was demonstrated in comparison to loperamide by significant inhibition of castor oil-induced diarrhea in mice (increases in hard faeces/total faeces ratio of 38 and 54 and 5 and 54% with respect to controls, at 0.5 and 1 mL/kg and 1 and 2 mg/kg, respectively) and bisacodyl-induced increase in large intestine transit in rats (125 and 280 and 210% with respect to controls, at 0.4 and 2 mL/kg Salicairine and 5 mg/kg loperamide, respectively). Salicairine was able to reduce contractions of isolated rat duodenum induced by barium chloride and acetylcholine, although not completely (that is about 60%) as seen with loperamide. Also, it did not change normal gastrointestinal transit in mice at doses of 0.5 to 1 mL/kg, conversely to loperamide which had a significant effect (decrease of 50%) at 2 mg/kg. Finally, Salicairine at 0.01 mL/mL, like loperamide at 0.2 mg/mL, significantly increased net fluid absorption in rat colon, either in basal conditions (30 and 64% respectively) or after a prostaglandin E1-induced increase in net fluid secretion (41 and 35%, respectively). The antidiarrheal activity of Salicairine is possibly related, at least in part, to an increase in colon net fluid absorption or a decrease in net fluid secretion.

Enterotoxin production by coagulase-negative staphylococci isolated from goats' milk and cheese.

An antigen related to the Enterotoxin E from Staphylococcus aureus was produced by ten of 187 coagulase-negative staphylococci (CNS) isolated from goats' milk, whey and cheese in quantities ranging from 10 to 90 ng/ml supernatant. The enterotoxin-producing strains were identified at the species level as S. simulans, S. xylosus, S. equorum, S. lentus and S. capitis. Detection of the enterotoxins was done by the VIDAS SET test (bioMérieux) and by an indirect double-sandwich ELISA technique using anti-enterotoxin monoclonal antibodies. The results obtained were further confirmed by Southern blotting, using two radioactive oligonucleotide probes that hybridized specifically with the gene of S. aureus coding for the enterotoxin E.

Identification of micrococcaceae isolated from goat's milk and cheese in the Poitou-Charentes region.

One hundred and ninety strains of coagulase-negative staphylococci were isolated from goat's milk, whey and cheese at various stages of manufacture. Sixteen different coagulase negative Staphylococci (CNS) species were recovered, 3 of which were predominant: Staphylococcus simulans, Staphylococcus epidermidis and Staphylococcus xylosus. The prevalent species were recovered at least at two different stages of cheese manufacturing, suggesting a better adaptation to the environment. After 15 days of ripening, the cheeses showed lower counts of Micrococcaceae.

Identification and ribotyping of Staphylococcus xylosus and Staphylococcus equorum strains isolated from goat milk and cheese.

Twenty-five strains of staphylococci isolated from goat milk and cheese were identified as belonging to the Staphylococcus xylosus/equorum group using the ID 32 Staph system (bioMérieux, Marcy-L'Etoile, France). This system, however, was not able to discriminate between these two species for 19 of the strains tested. Ribotyping was performed on these 25 strains, as well as on three reference strains of each of these two species. Hybridization membranes were scanned and analyzed using the Taxotron software package (Taxolab, Institut Pasteur, Paris, France). A dendrogram representation showed that ribotypes were distributed in two clear-cut clusters corresponding to S. equorum (21 strains) and S. xylosus (four strains).