Streptococcus agalactiae
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Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome †
- Authors: Jack T. H. Wang*, Joshua N. Daly, Dana L. Willner, Jayee Patil, Roy A. Hall, Mark A. Schembri, Gene W. Tyson, Philip Hugenholtz
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Citation: Wang J, Daly J, Willner D, Patil J, Hall R, Schembri M, Tyson G, Hugenholtz P. 2015. Do you kiss your mother with that mouth? an authentic large-scale undergraduate research experience in mapping the human oral microbiome † . 16(1):50-60 doi:10.1128/jmbe.v16i1.816
- DOI 10.1128/jmbe.v16i1.816
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Abstract:
Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE). The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity—the oral microbiome—by analyzing hundreds of samples obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR) and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012–2013) revealed significantly higher student confidence in laboratory skills following the completion of the ALURE (p < 0.05 using the Mann-Whitney U-test). Learning objectives on effective scientific communication were also met through effective student performance in laboratory reports describing the research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students.
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Susceptibility Testing Instrumentation and Computerized Expert Systems for Data Analysis and Interpretation
- Authors: Sandra S. Richter, Mary Jane Ferraro
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Source: Manual of Clinical Microbiology, 10th Edition , pp 1144-1154
Publication Date :
January 2011
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Abstract:
Commercial antimicrobial susceptibility testing (AST) systems were introduced into clinical microbiology laboratories during the 1980s and have been used in the majority of laboratories since the 1990s. Manual and semiautomated broth microdilution systems are utilized for small volumes of susceptibility testing, while larger laboratories often choose an automated broth microdilution system. The AST systems include data management software that may be interfaced with a laboratory information system (LIS) and offer various levels of expert system and epidemiological analyses. This chapter focuses primarily on commercial susceptibility testing systems currently available in the United States. It discusses advantages and disadvantages of automated systems. Reports of AST performance for detecting problematic resistance phenotypes are also discussed. Expert systems to assist in the critical review of AST results are available for all commercial susceptibility systems currently marketed in the United States. Most expert systems use a rules-based approach focusing on AST results for one drug at a time without considering results for other agents tested simultaneously. Factors to consider when selecting an AST system include cost, performance, work flow, data management capabilities, and manufacturer technical support. Future advances in the development of AST systems may increase their clinical impact with the incorporation of molecular techniques that dramatically shorten the time required for results.
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Applications of Fluorescence In Situ Hybridization in Diagnostic Microbiology
- Authors: Stefan Juretschko, Thomas R. Fritsche
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Source: Molecular Microbiology , pp 3-19
Publication Date :
January 2011
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Abstract:
The presence of a sufficient number of target molecules is critical in detecting conferred fluorescence of probe-target hybrids and permits direct visualization of intact organisms by epifluorescence microscopy. This direct approach to visualization of organisms using fluorescence in situ hybridization (FISH) simultaneously provides information on phylogenetic relationships of organisms, their spatial distribution in the sample matrix, their relative abundance, and their relative physiologic activity. An incubator, a water bath, and an epifluorescence microscope are essential, with the microscope being most critical for successful FISH performance. The main goal in designing specific probes is to find a suitable and unique region within the 16S or 23S rRNA that permits discrimination of target from nontarget organisms. Once a probe has been designed and confirmed to be specific for the motif desired by using the appropriate databases, it must be evaluated against a series of reference organisms. In case of a low number of ribosomes, the simultaneous application of two fluorescence-monolabeled probes targeting two different regions of rRNA with the same specificity would theoretically result in a twofold amplification of signal intensity when applied to the test samples. The chapter talks about expanded techniques combined with FISH. FISH, based upon either DNA or PNA oligonucleotide probes, is a rapid diagnostic method capable of challenging traditional culture techniques for the direct and accurate identification not only of nonfastidious pathogens but also of fastidious, slow-growing, and difficult-to-cultivate organisms.
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DNA Probes for Culture Confirmation and Direct Detection of Bacterial and Fungal Infections: a Review of Current Technologies and Assays
- Authors: Julie Kingery, Karen C. Carroll
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Source: Molecular Microbiology , pp 21-30
Publication Date :
January 2011
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Abstract:
This chapter focuses on nonamplified nucleic acid probes and their current uses in the clinical laboratory. DNA probes are pieces of nucleic acid that are labeled in some way and are designed to seek out and bind to stretches of DNA or RNA that have sequences that are complementary to the probe. In hybridization reactions, a double-stranded DNA molecule is denatured to single strands. Several formats for the hybridization reactions exist: solid phase; in solution (liquid phase); in situ; or by use of a Southern hybridization procedure after gel electrophoresis. In sandwich hybridization assays, one probe is attached to a solid support such as a nitrocellulose filter in single-stranded form and ‘‘captures’’ homologous nucleic acids in liquid samples; a second probe, which recognizes a contiguous area of the nucleic acid, carries the reporter molecule such as a radioisotope or biotin. The target and probe nucleic acids are free to move in solution, maximizing chances that complementary sequences will bind. Southern hybridization involves using purified DNA that is cleaved with restriction endonucleases. There are numerous methods for detecting the binding of probe to target nucleic acid. Commercially available DNA probes used for culture confirmation of bacteria, mycobacteria, and fungi are discussed in the chapter. Of the assays discussed in the chapter, probes for the detection of mycobacteria have had the greatest clinical impact. The chapter describes the utility of nonamplified probes for the diagnosis of sexually transmitted diseases, vaginal infections, and streptococcal pharyngitis.
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Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory
- Authors: Rosemary C. She, Keith E. Simmon, Cathy A. Petti
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Source: Molecular Microbiology , pp 479-489
Publication Date :
January 2011
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Abstract:
Nucleic acid sequencing of various bacterial genes and other DNA targets has been used for determining the phylogeny of bacteria and for their identification. A brief overview of nucleic acid sequencing is shown in this chapter. DNA targets have conserved regions flanking variable regions that can be used to differentiate closely related bacterial species. The routine use of sequencing can greatly enhance the ability of the clinical microbiology laboratory to identify bacteria on many levels. Of consideration in the routine use of DNA target sequencing is the need for technical expertise and its cost. The chapter addresses preparation of DNA from pure culture. Certain conventional methods such as latex agglutination assays are quicker, simpler, and less expensive than DNA target sequencing for the identification of beta-hemolytic streptococci. Basic conventional methods perform well in identifying common isolates, such as Bacteroides fragilis group, Peptostreptococcus spp., and most Clostridium spp. DNA target sequencing can provide more accurate identifications, especially since databases from conventional methods often are not current and do not reflect the tremendous genetic diversity within anaerobic taxa. For agents of bioterrorism, i.e., Bacillus anthracis, Brucella spp., Clostridium botulinum, Francisella tularensis, and Yersinia pestis, 16S rRNA sequencing has varying utility. Molecular studies have enhanced our knowledge about the taxonomical diversity among bacteria and allowed better definition of the epidemiology of bacterial infections.
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Index
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Source: Molecular Microbiology
Publication Date :
January 2011
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No descriptions available.
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Cell-Cell Contact-Induced Gene Regulation in Streptococcus gordonii-Actinomyces oris Communities
- Author: Nicholas S. Jakubovics
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Source: Oral Microbial Communities , pp 283-296
Publication Date :
January 2011
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Abstract:
Microbial interactions involve sensing and responding to chemical signals or cues that are released from cells. In the early stages of plaque accumulation on freshly cleaned teeth, most interactions occur between the initial colonizers such as Streptococcus spp., Actinomyces spp., and Veillonella spp. However, mature dental plaque biofilms may contain up to 200 different phylotypes of bacteria, resulting potentially in almost 20,000 different pairwise interactions. This chapter focuses on just one of these interactions: that between two initial colonizers of oral biofilms, Streptococcus gordonii and Actinomyces oris. Interbacterial binding between oral bacteria has been investigated extensively in vitro using coaggregation assays. In these experiments, pure cultures of genetically distinct bacteria are mixed in test tubes and interactions are scored based on the extent of clumping (coaggregation). Coaggregation is used to model biofilm communities containing S. gordonii and A. oris and investigate gene regulation in mixed-species cultures. A powerful application of postgenomic technologies is the analysis of gene expression using DNA microarrays. The first genome-level analysis of S. gordonii-A. oris interactions employed microarrays to identify genes in S. gordonii that were regulated in response to coaggregation with A. oris. This study demonstrated that S. gordonii specifically activates a set of genes in response to cell-cell contact (coaggregation) with A. oris. In theory, microarrays and other genome-based expression technologies can be used to investigate cell-cell contact-induced gene regulation in any bacterial species for which the genome sequence is known.
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INDEX
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Source: Oral Microbial Communities
Publication Date :
January 2011
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No descriptions available.
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Index
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Source: Pathogens and Toxins in Foods
Publication Date :
January 2010
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No descriptions available.
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INDEX
- Publication Date : January 2009
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No descriptions available.
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INDEX
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Source: Bacterial Pathogenomics
Publication Date :
January 2007
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No descriptions available.
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Epidemiology of Resistance to Antibacterial Agents
- Author: A. Bryskier
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Source: Antimicrobial Agents , pp 39-92
Publication Date :
January 2005
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Abstract:
All bacterial species and phyla are involved in the phenomenon of resistance to antibacterial agents, sometimes posing genuine therapeutic problems. The strategy of Enterobacteriaceae faced with the aggression represented by the oxyimino cephalosporins was the production of conventional enzymes commonly known as extendedbroad-spectrum β-lactamases (ESBLs). The prevalence of nosocomial infections varied from 5 to 17% for patients admitted to ICUs in the hospital setting. In a survey conducted in central Europe, all of the strains of Staphylococcus aureus were susceptible to mupirocin, except in the case of Italy, where 1.5% of methicillin-resistant S. aureus (MRSA) strains were resistant. In S. aureus, the main mechanism of resistance of quinupristin-dalfopristin is methylation of the 23S rRNA with cross-resistance with macrolides, lincosamides, and streptogramin B. In the inducible type of resistance, quinupristin remains active because it is not an inducer of methylase; if constitutive, quinuprisitin is inactive and the combination become bacteriostatic due to alteration of quinupristin-dalfopristin activity in vitro and in vivo. S. pneumoniae is one of the major pathogenic agents of community-acquired or nosocomial parenchymatous respiratory tract infections (RTIs). The frequency of mutation of Mycobacterium tuberculosis varies according to the different antituberculosis agents. Antibiotic resistance in M. tuberculosis has long been known, particularly with streptomycin and isoniazid. Primary resistance of M. tuberculosis to isoniazid is greater than 10% in some countries.
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Cephems for Parenteral Use
- Authors: A. Bryskier, J. Aszodi
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Source: Antimicrobial Agents , pp 163-221
Publication Date :
January 2005
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Abstract:
Due to the importance of the cephems, it is essential to classify them so as to allow their optimal use. The cephems are characterized by an azetidinone ring, to which is attached an unsaturated hexacycle. Five classes of cephems may be distinguished in terms of the nature of the moiety: cephalosporins, cephamycins and cephabacins, oxa-1-cephems, carba-1-cephems, and miscellaneous. The dosage and dosing frequency of a cephalosporin are the result of a balance between its antibacterial activity and its pharmacokinetic profile. The molecules all have the same antibacterial spectrum, which principally includes gram-negative bacilli and gram-negative and gram-positive cocci, except for S. aureus. The carbacephem-type molecules are asymmetrical, and the substituents on the β-lactam moiety are in the cis position; the cis stereochemistry of the carbacephems is less stable thermodynamically than the trans stereochemistry. The antibacterial activity RWJ-54428 was designed to overcome methicillin resistance in methicillin-resistant S. aureus (MRSA) strains and ampicillin resistance in E. faecium by penicillin-binding proteins (PBP) alterations. In all species, total clearance was slower and the apparent elimination half-life was longer than that of RWJ- 54428. The antistaphylococcal activities of RWJ-333442 in comparison with RWJ-54428, vancomycin, and quinupristindalfopristin against S. aureus Smith were investigated in a sepsis model (Swiss-Webster mice) and were also investigated for S. aureus 076, a methicillin-resistant strain. A synergistic activity was shown to be species dependent in combination with streptomycin against E. faecalis.
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DNA Gyrase Inhibitors Other Than Fluoroquinolones
- Author: A. Bryskier
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Source: Antimicrobial Agents , pp 789-797
Publication Date :
January 2005
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Abstract:
Conventional DNA gyrase inhibitors belong to two major families of antibacterial agents, the fluoroquinolones and the coumarin derivatives. A number of other antibacterial agents possess DNA gyrase-inhibitory activity, directed against either the A subunit or the B subunit of DNA gyrase. These are principally cinodine, coumadin, the pyrimido [1,6-α] benzimidazoles, cyclothialidine, clerocidin, or 2-pyridinecarboxyl derivatives. The potential point of interest of these molecules is that they have a mode of action similar to that of the fluoroquinolones or coumarin derivatives, but the molecular target is different, suggesting partial cross-resistance. The cinodines differ from one another by the structure of the pentose attached to the terminal part of the trisaccharide. A number of derivatives of coumadins, including molecule A, possess in vitro activity against certain bacterial genera, and they possess activity similar to that of clindamycin against anaerobes. The β-keto group of the fluoroquinolones is attached by hydrogen bonds to the purine and pyrimidine bases of DNA, with the exception of the cytosine. Clerocidin was isolated from Oidiodendron truncatum and Fusidium viride. Clerocidin exhibits cross-resistance with the fluoroquinolones against gram-negative bacilli, but this is only partial against Staphylococcus aureus. If the culture medium contains 9 mM Mg2+, the MICs and minimum bactericidal concentrations increase 2 to 4-fold, whereas those of the fluoroquinolones increase 16-fold. The products of the mcbB to -D genes allow the conversion of the glycyl-cysteine and glycyl-serine residues to 2-aminomethylthiazolyl-4-carboxylic acid and 2-amino-methyloxazolyl-4-carboxylic acid, respectively, which are essential for the activity of microcin B17.
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Mupirocin
- Author: A. Bryskier
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Source: Antimicrobial Agents , pp 964-971
Publication Date :
January 2005
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Mupirocin is active against gram-positive cocci: it has moderate activity against gram-positive bacilli such as Listeria monocytogenes and Erysipelothrix rhusiopathiae; it is inactive against corynebacteria and Bacillus anthracis. It is inactive against Chlamydia spp. It is active against Staphylococcus aureus, whether the strains are susceptible or resistant to penicillin G, tetracyclines, erythromycin A, fusidic acid, lincomycin, chloramphenicol, or methicillin. Mupirocin has good activity against human and animal mycoplasmas. As mupirocin is highly serum protein bound, the in vitro activity is reduced in the presence of human serum. Mupirocin alters protein synthesis by blocking the incorporation of isoleucine into the peptide during synthesis. Since 1985, when mupirocin was introduced into clinical practice, two types of resistant strains have been described: those for which the MICs are between 8 and 256 µg/ml and those for which the MICs are 512 µg/ml. Extensive use of mupirocin has resulted in the emergence of resistant strains of S. aureus in the United Kingdom. Local application of mupirocin yields in situ concentrations of 20,000 mg/kg. Skin and skin structure infections are very common, but the use of topical antibiotics or other antibacterial agents is limited by a number of factors: the complexity of the anatomy of the skin, the bacterial ecology of the skin, and the nature of the microorganisms involved in these infections. Mupirocin eradicates methicillin-resistant strains of S. aureus colonizing the skin and produces an improvement in the healing of skin wounds.
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Orthosomycins
- Author: A. Bryskier
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Source: Antimicrobial Agents , pp 983-990
Publication Date :
January 2005
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Abstract:
The family of orthosomycins includes the everninomicins, which are oligosaccharide antibiotics containing two orthodiester bonds and a dichloroeverninic acid residue. The everninomicins are original antibiotics that belong structurally to the oligosaccharide antibacterial agents. They are characterized by an oligosaccharide structure with the presence of one or more orthodiester-type bonds. This type of bond is unusual in nature but has been described for a series of molecules grouped together in a family known as orthosomycins. Avilamycin is an orthosomycin complex extracted from Streptomyces viridochromogenes Tü 57 in 1965. An approach to the structure and activity of everninomicins has been undertaken by means of chemical modifications, particularly of evernimicin. The configuration of the two orthoester bonds at C-49 and C-16 is important for the antibacterial activity. Mechanisms of resistance to evernimicin are complex phenomena which include mainly mutations, methylation, and efflux. Recently it was shown that avilamycin A and evernimicin share common mechanisms of resistance. The rplP gene mutations have been also reported for enterococcal isolates resistant to avilamycin A. The steady-state apparent volume of distribution is on the order of 22 liters, indicating that evernimicin is distributed in the extravascular media. Evernimicin was thought to be an alternative in severe pneumococcal infections for which no other treatment is possible because of a multiresistant strain.
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Peptidyl Deformylase Inhibitors
- Authors: André Bryskier, John Lowther
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Source: Antimicrobial Agents , pp 991-1010
Publication Date :
January 2005
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The chapter mainly focuses on peptidyl deformylase (PDF) inhibitors. Bacterial peptidyl deformylase (PDF) belongs to subfamily 3, with at least two other members: thermolysin and matrix metalloproteases (MMPs), namely, matricins and/or metzincins. Two classes of aminopeptidases are described: MAP-1 and MAP-2. MAP-1 and MAP-2 have similar specificities, with methionine cleavage depending on the nature of the second amino acid. MAP-2 is inhibited by fumagillin and TNP-470. Bacterial PDFs are small monomers composed of about 160 to 200 amino acids with few variations in the lengths of their N- and C-terminal extremities. Deformylase inhibitors can be classified in three groups: natural compounds, hydroxamate derivatives, and miscellaneous compounds. The hydroxamic moiety is crucial for the antibacterial activity, but the pseudopeptide backbone can be altered, such as the methionine-like structure. In addition to the antibacterial activity, it has been shown that actinonin inhibits several aminopeptidases, such as human seminal alanyl aminopeptidase, as well as tumor growth. A series of β-sulfonyl and β-sulfinyl hydroxamic acid derivatives has been shown to be potent PDF inhibitors with in vitro antibacterial activity. A macrocyclic deformylase peptide inhibitor was reported. The improved affinity for PDF is probably due to the rigidity introduced by cyclization. Some compounds exhibited good activity against Bacillus subtilis, Haemophilus influenzae, and Moraxella catarrhalis but weak activity against Streptococcus pneumoniae; they were inactive against Staphylococcus aureus.
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Mutilins
- Author: A. Bryskier
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Source: Antimicrobial Agents , pp 1239-1241
Publication Date :
January 2005
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Abstract:
Some mutilins, such as tiamulin and valnemulin, were introduced into veterinary medicine for the treatment of swine infections with Brachyspira hyodysenteriae (diarrhea) and Mycoplasma hyopneumoniae (pneumonia). Mutilins are semisynthetic derivatives having a tricyclic diterpenoid structure. They differ in their side chains. It was shown that the C-14 side chain is essential for antibacterial activity. The tricyclic diol mutilin did not inhibit protein synthesis. Pleuromutilins are mainly active against gram-positive bacteria and display moderate activity against fastidious gram-negative bacilli. Tiamulin MICs of >32, 4.0, and 0.06 to 0.5 µg/ml are observed for Bordetella bronchiseptica, Leptospira spp., and Mycoplasma spp., respectively. Tiamulin and valnemulin interact with adenines 2058 and 2059 and uracils 2506, 2584, and 2585. A new series of semisynthetic pleuromutilins was presented and one compound was selected for a preclinical investigation, SB264128. In pneumococcal infections, the burden reduction obtained with SB 264128 was significant (2.7 ± 1.0 log10 CFU/lung [mean plus/minus standard deviation]). In Haemophilus influenzae H 128 infection, bacterial counts in untreated rats were 5.3 plus/minus 0.7 log10 CFU/lung. SB 264128 exhibited a higher clearing activity (1.8 ± 0.2 log10 CFU/lung) than co-amoxiclav (3.5 ± 1.2 log10 CFU/lung).
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Contents
- Publication Date : January 2004
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No descriptions available.
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INDEX
- Publication Date : January 2003
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No descriptions available.