16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria.

AIMS: Test the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer. METHODS AND RESULTS: Nine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1-V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline. Lastly, 16S rRNA gene sequencing mixtures of four species through a six log range of dilution showed species were identifiable even when present as 0·1% of the mixture. CONCLUSIONS: Sequencing the V1-V2 16S rRNA gene region, made possible by the increased read length Ion Torrent PGM sequencer's 400 base pair chemistry, may be a better choice over other commonly used regions for identifying clinically important bacteria. In addition, the SequenceMatch algorithm, freely available from the Ribosomal Database Project, is a good choice for matching filtered reads to organisms. Lastly, 16S rRNA gene sequencing's sensitivity to the presence of a bacterial species at 0·1% of a mixture suggests it has sufficient sensitivity for samples in which important bacteria may be rare. SIGNIFICANCE AND IMPACT OF THE STUDY: We have validated 16S rRNA gene sequencing on a benchtop sequencer including simple mixtures of organisms; however, our results highlight deficits for clinical application in place of current identification methods.

Prevalence of subscapularis tears and accuracy of shoulder ultrasound in pre-operative diagnosis.

PURPOSE: Subscapularis tears can be difficult to diagnose and their treatment requires advanced arthroscopic skills. The objective of this study was to find the prevalence of subscapularis tears on arthroscopic examination of shoulders with rotator cuff pathology and to determine the accuracy of pre-operative ultrasound in diagnosing these tears. METHOD: Ultrasound and intra-operative reports of 236 patients who underwent shoulder arthroscopy for rotator cuff pathology by the senior author at his institution were compared. Prevalence of subscapularis tear was noted and classified using Lafosse classification system. Ultrasound reports and intra-operative findings were compared to determine the accuracy, sensitivity and specificity of ultrasound in detecting subscapularis tears. RESULTS: The prevalence of subscapularis tears in patients needing rotator cuff repair was found to be 31.4 %. A total of 6.4 % of patients needing a rotator cuff repair had an isolated subscapularis tear. The sensitivity of ultrasound was 39.5 % and specificity 93.1 % in detection of these tears. The overall accuracy of ultrasound was 75.8 %. Sensitivity of ultrasound was low (42.8 %) for smaller (type 1 and 2) tears and higher (79 %) for larger (types 3, 4, 5) tears. The overall positive predictive value of USS was 73.1 % and negative predictive value 76.4 %. CONCLUSION: The shoulder surgeon should be skilled in diagnosing and repairing subscapularis tendon tears arthroscopically and cannot completely rely on pre-operative ultrasound scans in ruling out smaller tears as its sensitivity in diagnosing smaller tears is quite low. Unsettling anterior shoulder pain with a normal ultrasound may need further arthroscopic evaluation to rule out missed subscapularis tears.

Non-response to the intensive phase of anti-tuberculosis treatment in children: evaluation and outcome [Short Communication].

The present study evaluates the causes for the persistence of symptoms and radiological signs after at least 2 months of intensive anti-tuberculosis treatment in children. In this prospective observational study, 26 paediatric patients with partial or no response to anti-tuberculosis treatment after the 2-month intensive phase were enrolled. After a detailed history and workup, it was found that 9 (34.6%) patients had a wrong initial diagnosis, while 12 (46.2%) had either received inadequate treatment or had complications requiring prolonged treatment; 5 (19.2%) failed to respond. Failure to respond to anti-tuberculosis treatment in paediatric tuberculosis seems to be over-diagnosed.

Retapamulin: a newer topical antibiotic.

Impetigo is a common childhood skin infection. There are reports of increasing drug resistance to the currently used topical antibiotics including fusidic acid and mupirocin. Retapamulin is a newer topical agent of pleuromutilin class approved by the Food and Drug Administration for treatment of impetigo in children and has been recently made available in the Indian market. It has been demonstrated to have low potential for the development of antibacterial resistance and a high degree of potency against poly drug resistant Gram-positive bacteria found in skin infections including Staphylococcus aureus strains. The drug is safe owing to low systemic absorption and has only minimal side-effect of local irritation at the site of application.

Evidences for the Involvement of Monoaminergic and GABAergic Systems in Antidepressant-like Activity of Tinospora cordifolia in Mice.

The present study was taken up to investigate the effect of petroleum ether extract of Tinospora cordifolia (Wild.) Miers, on depression in mice. The extract (50, 100 and 200 mg/kg, p.o.) was administered for 14 successive days to Swiss young albino mice (either sex) and evaluated for antidepressant-like activity using tail suspension test and forced swim test. Petroleum ether extract at all three doses produced significant antidepressant-like effect in tail suspension test as well as in forced swim test and their efficacies were found to be comparable to imipramine (15 mg/kg, p.o.) and sertraline (20 mg/kg, p.o.). The extract at a dose of 50 mg/kg showed most potent effect and did not show any significant change in locomotor functions of mice as compared to control. The antidepressant-like effect of the extract was significantly reversed by pretreatment of animals with prazosin (a α(1)-adrenoceptor antagonist), sulpiride (a selective dopamine D(2)-receptor antagonist), p-CPA (a serotonin synthesis inhibitor) and baclofen (GABA-B agonist), when tested in tail suspension test. Moreover, petroleum ether extract also reduced the mouse whole brain monoamine oxidase (MAO-A and MAO-B) activities as compared to control, resulting in increase in the levels of brain monoamines. Therefore, the extract may have potential therapeutic value for the management of depressive disorders.

The effect of cooling on the blood composition and seminal characteristics of crossbred bulls.

In 8 healthy cattle bulls (6 Holstein Friesian X Red Dane X Sahiwal and 2 Holstein Friesian) the effect was studied of cooling on the blood and seminal parameters during the hot summer months June to September in Ludhiana, Punjab, India. Favourable effects were found only in some blood values. The seminal characteristics do not differ from those of the control group. Rectal body temperatures remained also constant, whereas the respiration rates were higher in the control group.