Gundlapally Sathyanarayana Reddy

Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher oasis, Antarctica

Two pure cultures of bacteria isolated from soil samples collected in Schirmacher Oasis, Antarctica, conformed to the definition of the genus Sphingobacterium. They differed from all of the known species of Sphingobacterium in being psychrotrophic. The G+C contents of the DNA of the two strains were found to be 39.3 and 40.3 mol%, and DNA-DNA hybridization studies indicated 7% homology with S. multivorum and S. spiritivorum. The name Sphingobacterium antarcticus sp. nov. is proposed for the two Antarctic strains. The type strain is 4BY (MTCC 675), and it has been deposited with the Microbial Type Culture Collection, Institute of Microbial Technology, Chandigarh, India.

Antibiotic Resistance of Bacteria

Antibiotic resistance of bacteria and other microorganisms is one of the most serious and grievous challenges of the twenty-first century. The life-saving drugs, which held a great deal of promises during the 1940s to eradicate all the infectious life-threatening diseases in the world, have ceased to work, because of the increasing emergence of microbial strains invulnerable to them. Many of the previously efficacious antibiotics are no longer usable because of widespread occurrence of multiresistant microbial strains. Lately, discovery of new antibiotics is failing to keep pace with the emergence of (multi)resistance of pathogenic and also environmental bacterial strains. Consequently, the prospect of chemotherapy looks bleak. The trepidation that we might be pushed back to a situation analogous to the preantibiotic era, when no chemotherapeutic agent was available to contain and combat deadly bacterial infections, does not appear to be an overblown imagination. n nBased on this backdrop, this special issue appears to be an aptly undertaken and well-timed endeavour to address this global problem. The articles contributed by investigators from various research laboratories with different scientific backgrounds have not only portrayed the width of the problem but also displayed some silver lining in the management of the looming crisis. Rapid detection of the profile of resistance is essential for timely application of the right antibiotic to a patient. H. Frickmann et al. summarize the efficacy and limitations of various molecular and mass spectrometric methods for the detection of resistance. The omnipresent nature of the resistant organisms is revealed in a number of articles. F. B. Atique and Md. M. R. Khalil report on the occurrence of antibiotic resistance among bacteria (predominantly skin commensal coagulase-negative staphylococci) isolated from allogenic bone samples for grafting, collected from different hospitals of Bangladesh. Food materials are believed to serve as a vehicle for transmission of resistance. This issue is addressed by F. S. Dehkordi et al. who report on the genotype and resistance-profile of Helicobacter pylori isolated from vegetables and salad samples, picked up from groceries and supermarket in a province of Iran. The high similarity in the genotype pattern of the isolates obtained from vegetables and humans indicates transmission. A. B. Florez et al. reveal tetracycline and erythromycin-resistant bacteria and genes conferring resistance to these antibiotics in 10 Spanish and 10 Italian samples of commercial cheese. P. Krupa et al. report on the population structure (based on spa typing) of oxacillin-resistant Staphylococcus aureus isolated from nasal swabs of pigs, collected from two slaughter houses of Poland. Some meat samples bought from the shops were also included into their studies. D. De Vito et al. characterize multidrug-resistant clinical isolates of Salmonella typhimurium for resistance genes in an area of southern Italy by pulsotyping and phage typing. C. Zhang et al. report on the resistant phenotype and genotype of Streptococcus suis serotype 2, isolated from 62 clinically healthy sows and 34 diseased pigs reared in different farms of China. Antibiotic resistance in the nosocomial isolates is a matter of serious concern. F. Lombardi et al. look into the molecular epidemiology of carbapenemase-producing strains of Klebsiella pneumoniae isolated from the surgery unit at a cardiovascular centre of Italy. D. Ojdana et al. demonstrate the ability of an E. coli strain obtained from a hospital of Poland to produce carbapenemase enzymes and also the presence of genes responsible for the production of carbapenemases and other β-lactamases. Extended-spectrum-β-lactamase (ESBL) is a bacterial enzyme having the ability to hydrolyse even the third-generation cephalosporins and aztreonam. Besides Klebsiella pneumoniae some strains of Escherichia coli are also known to produce this enzyme. This is indicated by M. S. Rezai et al. who performed genotyping of ESBL-producing strains of E. coli, obtained from a paediatric hospital of north Iran. The authors also show the association of ESBL-positive E. coli strains with resistance to various other antimicrobials. Occurrence of ESBL-producing Enterobacteriaceae in iceberg lettuce obtained from the retail market of Rochester (US) is described by N. Bhutani et al. A wide spectrum of diseases is caused by the virulent strains of ESBL-positive isolates of E. coli. Regional difference in the prevalence of virulence genes in 432 phenotypically ESBL-positive patient-isolates of E. coli (obtained from the Baltic Sea region) is shown by J. Lillo et al. Keeping in mind the tremendous challenge posed by drug-resistant tuberculosis, a number of relevant articles are included in this collection. The susceptibility profile of M. tuberculosis isolates to various antitubercular antibiotics varies significantly depending on the test system as revealed by Z. Mei et al. They have also shown that changes in bacterial susceptibility are further caused by mixed infection with particular genotypes of M. tuberculosis strains. Resistance-profile of 100 strains of M. tuberculosis, isolated from patients in northeast Iran, is reported by A. T. Sani et al. Occurrence of nontuberculosis Mycobacterium, in 25 out of 125 patients (20%) surveyed, underscores the need of proper diagnosis before the onset of chemotherapy. n nDiscovery of new drugs and strategies to circumvent antibiotic resistance is the need of the hour to contain the problem. N. Jafari et al. report on the isolation of an antibiotic-producing strain of a soil Actinomycetes belonging to the genus Pseudonocardia. The antibacterial compound produced by it is effective against Staphylococcus aureus. They have also purified and partially characterized this compound. R. D. Wojtyczka et al. demonstrate high antibacterial activity of two new quinoline derivatives of a structure of 3-thioacyl 1-methyl 4-arylaminoquinolinium salts against some nosocomial strains of staphylococci in both planktonic and biofilm form. In view of the widespread nature of the problem caused by inefficacy of the antibiotics produced by fermentation and chemical synthesis, it is necessary to tap alternative sources (e.g., plant kingdom) for novel antibiotics. P. Del Serrone et al. demonstrate antibacterial activity of Neem seed oil (Azadirachta indica A. Juss.) against enteropathogenic strains of E. coli and indicate that some of the ciprofloxacin-resistant isolates lost their virulence following treatment with Neem seed oil. Antimicrobial peptides are considered potential candidates for the management of multidrug-resistant infections. M. Singh and K. Mukhopadhyay evaluate the antimicrobial potential of an anti-inflammatory neuropeptide whereas C. Chen et al. report on the efficacy of recombinant lysostaphin against methicillin-resistant S. aureus (MRSA) in a mouse model. Widespread use of carbapenems is associated with emergence of resistance. The polymyxin antibiotic colistin is not used at present because of its nephrotoxicity. H.-J. Tang et al., however, demonstrate the efficacy of a combination of colistin and imipenem against carbapenem-resistant Klebsiella pneumoniae. Bacteriophages could be suitable alternatives for antibiotics, which currently have lost efficacy because of the emergence of resistant strains. N. Shivshetty et al. demonstrate the potential of a bacteriophage isolated from sewage to protect diabetic mice against Pseudomonas aeruginosa-induced bacteremia. Reversal of bacterial resistance to antibiotics is essential to restore the efficacy of the existing antimicrobials. C. Santiago et al. claim to achieve an increase in susceptibility of a MRSA strain to ampicillin when it was combined with a plant extract. A number of computerized models have been developed during the recent past to assist the physicians with the necessary information to enable prescription of the right antibiotic in the right moment. M. Rodriguez-Maresca et al. report on the efficacy of a new electronic device based on laboratory data on the most probable susceptibility profile of pathogens responsible for infections and also on local epidemiology.

Isolation and identification ofMicrococcus roseus andPlanococcus sp. from schirmacher oasis, antarctica

Five cultures isolated from soil samples collected in Schirmacher oasis, Antarctica, have been identified as members of the familyMicrococcaceae, with 3 belonging to the genusMicrococcus and two toPlanococcus. The 3Micrococcus isolates (37R, 45R and 49R) were red-pigmented and h a d ∼ 75 mol% G + C in their DNA; they were identified asMicrococcus roseus. The twoPlanococcus isolates (30Y and Lz3OR) were yellow and orange in colour, and had 43.5 and 40.9 mol % G + C in their DNA respectively; they were identified asPlanococcus sp.

Description of Thalassospira lohafexi sp. nov., isolated from Southern Ocean, Antarctica

A gram-negative, aerobic, obligatory halophilic, curved-to-spiral rod-shaped, uni- or bi-polar flagellated motile bacterium 139Z-12T was isolated from water samples collected from Southern Ocean surrounding Antarctica as part of the Indo-German iron fertilization experiment “LOHAFEX.” The bacterium was positive for catalase, oxidase, and gelatinase, with C18:1ω7c (20.1xa0%), C16:0 (7.3xa0%), C16:1ω7c (28.9xa0%), and C12:0 (19.0xa0%) as the predominant fatty acids, phosphatidylglycerol, and phosphatidylethanolamine as major lipids and Q-10 as the major respiratory quinone. DNA Gxa0+xa0C content (mol%) of strain 139Z-12T was 53.0. Both BLAST and EzTaxon identified strain 139Z-12T as affiliated species of the genus Thalassospira with 16S rRNA gene sequence similarities ranging from 97.9 to 99.9xa0%. Based on above characteristics, strain 139Z-12T was assigned to the genus Thalassospira. Since strain 139Z-12T shared a DNA–DNA similarity of <70.0xa0% with members of the genus Thalassospira, 139Z-12T was identified as a novel species of the genus and named as Thalassospira lohafexi sp. nov. In addition to this, strain 139Z-12T, based on REP-PCR, delineated at a similarity coefficient of <0.67 from other species of the genus Thalassospira and also exhibited a MLSA distance of <95.5xa0%, a value less than the interspecies distance determined previously for the genus Thalassospira, further supporting the species status. In addition, species rank was further confirmed by other polyphasic characteristics. The type strain of Thalassospira lohafexi sp. nov. is 139Z-12T (KCTC 32347Txa0=xa0LMG 27449Txa0=xa0MCC 2233Txa0=xa0NBRC 110402T).

Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm

BackgroundEscherichia coli, the gastrointestinal commensal, is also known to cause ocular infections such as conjunctivitis, keratitis and endophthalmitis. These infections are normally resolved by topical application of an appropriate antibiotic. But, at times these E. coli are resistant to the antibiotic and this could be due to formation of a biofilm. In this study ocular E. coli from patients with conjunctivitis, keratitis or endophthalmitis were screened for their antibiotic susceptibility and biofilm formation potential. In addition DNA-microarray analysis was done to identify genes that are involved in biofilm formation and antibiotic resistance.ResultsOut of 12 ocular E. coli isolated from patients ten isolates were resistant to one or more of the nine antibiotics tested and majority of the isolates were positive for biofilm formation. In E. coli L-1216/2010, the best biofilm forming isolate, biofilm formation was confirmed by scanning electron microscopy. Confocal laser scanning microscopic studies indicated that the thickness of the biofilm increased up to 72xa0h of growth. Further, in the biofilm phase, E. coli L-1216/2010 was 100 times more resistant to the eight antibiotics tested compared to planktonic phase. DNA microarray analysis indicated that in biofilm forming E. coli L-1216/2010 genes encoding biofilm formation such as cell adhesion genes, LPS production genes, genes required for biofilm architecture and extracellular matrix remodeling and genes encoding for proteins that are integral to the cell membrane and those that influence antigen presentation are up regulated during biofilm formation. In addition genes that confer antimicrobial resistance such as genes encoding antimicrobial efflux (mdtM and cycA), virulence (insQ, yjgK), toxin production (sat, yjgK, chpS, chpB and ygjN), transport of amino-acids and other metabolites (cbrB, cbrC, hisI and mglB) are also up regulated. These genes could serve as potential targets for developing strategies for hacking biofilms and overcoming antibiotic resistance.ConclusionsThis is the first study on global gene expression in antibiotic resistant ocular E. coli with a potential to form biofilm. Using native ocular isolates for antibiotic susceptibility testing, for biofilm formation and global gene expression is relevant and more acceptable than using type strains or non clinical strains which do not necessarily mimic the native isolate.

Draft Genome Sequence of a Psychrophilic Bacterium, Sphingomonas antarcticum, Isolated from the Soils of Schirmacher Oasis, Antarctica

ABSTRACT We report the 4.5-Mbp genome sequences of Sphingobacterium antarcticum 4BY, a psychrophilic bacterium isolated from the soils of Schirmacher Oasis, Antarctica. The draft genome of S. antarcticum strain 4BY consists of 4,566,318 bp with 40.4% G+C content, 4,234 protein coding genes, and 52 RNAs.

Draft Genome Sequence of Cryobacterium roopkundensis Strain RuGl7, Isolated from a Soil Sample in the Vicinity of Roopkund Lake, Himalayas, India

ABSTRACT We report the 4.36-Mb genome of Cryobacterium roopkundensis strain RuGl7, isolated from a soil sample collected in the periphery of Roopkund Lake, Himalayas, India. The draft genome consists of 4,356,863 bp, 4,048 protein-coding sequences, and 50 RNAs, with 65.3% G+C DNA content.

Biodiversity, Adaptation and Biotechnological Importance of Bacteria Occurring in Cold Climates

This review deals with the biodiversity of cold-tolerant bacteria, also known as psychrophiles, from Antarctica, Arctic and Himalayas, strategies used by them to survive and grow at low temperature and their biotechnological potential. Bacterial abundance (5.2 × 104 to 30.7 × 108 cfu/g soil) is highest in soil (Himalayas > Antarctica > Arctic) followed by that in sediment and water. Studies involving cultivation independent methods revealed the occurrence of all major groups viz, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria and Verrucomicrobia in three locations, albeit with different frequencies. Firmicutes and Acidobacterium were the dominant communities in the Himalayan soils, whereas Alphaproteobacteria and Deltaproteobacteria were found to be predominant in the Antarctic and Arctic samples. Use of cultivation-dependent methods confirmed the presence of the aforementioned groups of bacteria and led to the discovery of many new species of bacteria in the Antarctic, Arctic and Himalayan habitats. Investigations based on functional genes in conjunction with phylogenetic analysis indicate diversity in the functional genes in the bacterial taxa. The ability of psychrophilic bacteria to survive and divide at low temperature can be attributed to strategies unique to these microorganism such as the ability to catalyse reactions and continue metabolism with cold-tolerant enzymes; ability to maintain optimum membrane fluidity at low temperature; occurrence of specific genes required for survival at low temperatures; alteration in the RNA degradosome; presence of antifreeze–activity; increase in intracellular levels of ATP and alterations in DNA replication. The recently reported genome sequences of a number of novel cold-tolerant isolates are likely to provide some more insights into the mechanism of bacterial cryotolerance.

COST-EFFECTIVE AND EFFICIENT APPARATUS FOR ELECTROELUTION OF MICRO- AND MACROGRAM QUANTITIES OF PROTEINS FROM POLYACRYLAMIDE GELS

Protein recovery from gel electrophoresis plays a significant role in functional genomics and proteomics. To assist in this, a simple, cost-effective, and efficient apparatus for electroelution of proteins has been designed. The performance of the apparatus was demonstrated using the proteins bovine serum albumin (BSA), phosphorylase, ovalbumin, pepsin, and trypsinogen. In all the cases the yield of elution was found to be consistently greater than 85% and the proteins could be eluted without degradation in less than 15 min. The utility of this method can be extended to protein elution from denatured and native polyacrylamide gels, DNA purification from agarose gels, and oligomeric primers purification from polyacrylamide gels. In addition to this, the method offers an effortless purification and characterization of microbial extracellular proteins. The eluted proteins can be directly used in N-terminal amino acid sequencing, and in amino acid and proteomics analyses.

Draft Genome Sequence of Lutibaculum baratangense Strain AMV1T, Isolated from a Mud Volcano in Andamans, India

ABSTRACT The 4.3-Mb genome of Lutibaculum baratangense strain AMV1T, isolated from a soil sample collected from a mud volcano in Andamans, India, is reported. The draft genome of strain Lutibaculum baratangense AMV1T consists of 4,300,776 bp with a G+C content of 66.93 mol% and 4,198 predicted coding regions, including 56 RNAs.