The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Antibiotics have always been considered one of the wonder discoveries of the 20th century. This is true, but the real wonder is the rise of antibiotic resistance in hospitals, communities, and the environment concomitant with their use. The extraordinary genetic capacities of microbes have benefitted from man's overuse of antibiotics to exploit every source of resistance genes and every means of horizontal gene transmission to develop multiple mechanisms of resistance for each and every antibiotic introduced into practice clinically, agriculturally, or otherwise. This review presents the salient aspects of antibiotic resistance development over the past half-century, with the oft-restated conclusion that it is time to act. To achieve complete restitution of therapeutic applications of antibiotics, there is a need for more information on the role of environmental microbiomes in the rise of antibiotic resistance. In particular, creative approaches to the discovery of novel antibiotics and their expedited and controlled introduction to therapy are obligatory.

Origins and Evolution of Antibiotic Resistance

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.

Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance

The optimism of the early period of antimicrobial discovery has been tempered by the emergence of bacterial strains with resistance to these therapeutics. Today, clinically important bacteria are characterized not only by single drug resistance but also by multiple antibiotic resistance--the legacy of past decades of antimicrobial use and misuse. Drug resistance presents an ever-increasing global public health threat that involves all major microbial pathogens and antimicrobial drugs.

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Antibacterial resistance worldwide: causes, challenges and responses.

Chronic obstructive pulmonary disease (COPD) is a common problem in the elderly. The disease is characterised by intermittent worsening of symptoms and these episodes are called acute exacerbations. The best estimate, based on several lines of evidence, is that approximately half of all exacerbations are caused by bacteria. These lines of evidence include studies of lower respiratory tract bacteriology during exacerbations, correlation of airways’ inflammation with results of sputum cultures during exacerbations, analysis of immune responses to bacterial pathogens, and the observation in randomised, prospective, placebo-controlled trials that antibacterial therapy is of benefit. The most important bacterial causes of exacerbations of COPD are nontypeable Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumoniae and Chlamydia pneumoniae.

/pdf/chronic-obstructive-pulmonary-disease-4ipss13czj.pdf

Chronic obstructive pulmonary disease

vaginalis.diagnosis of Trichomonas Development of a polymerase chain

spp.,andVeilonella parvula. Amongthe Peptostreptococcus spp.,79%oftheisolates hybridized with one(64%) or more (36%)oftheprobes forTetK (27%), TetL (30%), TetM (75%)andTet0 (13%). Oftheviridans group streptococci, 82%ofthestrains hybridized with one(34%) ormore (66%)ofthefourprobes. Thedistribution ofthefourdeterminants inthis group was asfollows: TetK,36%;TetL,31%;TetM,43%;Tet0, 61%.Twenty-nine percent ofthe enterococci andforty-six percent ofthegroupBstreptococci hybridized withtheprobes; however, theTetK, TetL,andTet0 determinants were foundinonly afewstrains, while theTetM determinant predominated. Atotal of29%oftheF.nucleatum isolates, 55%oftheG.vaginalis isolates, and26%oftheV.parvula isolates hybridized withtheTetM determinant. Incontrast, 43%oftheLactobacillus spp.hybridized withtheTet0 determinant. Thedataindicate thattetracycline resistance determinants are common tomany ofthe microorganisms isolated fromtheurogenital tract.

Genetic BasisofTetracycline Resistance inUrogenital Bacteria

To assess the activities of two glycylcyclines, N,N-dimethylglycylamido (DMG) derivatives of minocycline (MINO) and 6-demethyl-6-deoxytetracycline (DMDOT), 203 gonococcal isolates recovered at six sexually transmitted disease clinics in the western United States were evaluated. Antimicrobial susceptibilities to tetracycline HCl, doxycycline, MINO, DMG-DMDOT, and DMG-MINO were determined by agar dilution tests. DMG-DMDOT and DMG-MINO were more active than tetracycline HCl, doxycycline, or MINO regardless of the presence of Tet M or of chromosomal mutations mediating tetracycline resistance (P< 0.001). Resistance to tetracyclines (Tc r )i nNeisseria gonorrhoeae is duetochromosomalmutationsortothepresenceoftheTetM determinant on conjugal plasmids (5). Resistance mediated by the Tet M determinant results in organisms with antimicrobial susceptibilities of $16 mg of tetracycline per ml and in treatment failure in virtually 100% of patients treated with tetracycline alone (2). Tet M-containing gonococci are resistant to other tetracyclines including doxycycline and minocycline. The identification of Tet M in N. gonorrhoeae resulted in discontinuation of the tetracyclines as therapies for gonococcal infection recommended by the Centers for Disease Control and Prevention (1). The recently developed glycylcyclines (8) may havegreateractivityagainstgonococcalorganismsthatcontain the Tet M determinant as well as against organisms whose tetracycline resistance is due to chromosomal mutations. We evaluated the activities of two glycylcyclines, N,N-dimethylglycylamido derivatives of minocycline (DMG-MINO) and 6-demethyl-6-deoxytetracycline (DMG-DMDOT) (American CyanamidCo.,PearlRiver,N.Y.),againstacollectionofgonococci isolated at six sexually transmitted disease clinics in the western United States. Two groups of isolates were studied. First, recent clinical isolates (n 5 172) were collected at sexually transmitted disease treatment facilities in San Francisco, Calif., Portland, Oreg., Seattle, Wash., Anchorage, Alaska, Honolulu, Hawaii, and Ft. Lewis, Wash., during January and February 1993 as part of the Gonococcal Isolate Surveillance System, sponsored by Centers for Disease Control and Prevention (6). Secondly, previously characterized Tc r isolates (n 5 31) were included. Organisms were identified by established methods (4). Antimicrobial susceptibilities to penicillin G, tetracycline HCl, doxycycline (Sigma), minocycline, DMG-MINO, and DMGDMDOT were determined by agar dilution tests (3). b-Lactamaseproductionwasdetectedbyachromogeniccephalosporin assay (4).

Susceptibilities ofNeisseria gonorrhoeaeto the Glycylcyclines

Response to letter titled “Methicillin-resistant Staphylococcus aureus infection transmission in dental health care setting: Myths and facts”

High-level resistance to tetracycline (MIC 16 to 64 µg/ml) in Neisseria gonorrhoeae was due to acquisition of the tetM determinant, a transposon-borne determinant intially described in the genus Streptococcus. In all strains of N. gonorrhoeae tested to date, the tetM determinant was located on a 25.2 Mdal plasmid which arose from the insertion of tetM into the 24.5 Mdal gonococcal conjugative plasmid. The tetM determinant was transferred to suitable recipient strains of N. gonorrhoeae by both genetic transformation and conjugation. The 25.2 Mdal plasmid represent the first description of a self-transmissible R-factor in N. gonorrhoeae.

Marilyn C. Roberts

Papers

vaginalis.diagnosis of Trichomonas Development of a polymerase chain

Genetic BasisofTetracycline Resistance inUrogenital Bacteria

Susceptibilities ofNeisseria gonorrhoeaeto the Glycylcyclines

Response to letter titled “Methicillin-resistant Staphylococcus aureus infection transmission in dental health care setting: Myths and facts”

Acquisition of the streptococcal tetMdeterminant by Neisseria gonorrhoeae