A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses

Multilocus sequence typing (MLST) analysis for semi-routine applications is hindered by the downstream, manually intensive steps of processing the raw sequence data files. This report describes the development of an MLST pipeline that automates DNA sequence editing and analysis in order to significantly reduce the time required for processing data. Validation using a pneumococcal dataset revealed complete agreement between the results generated by manual and automated workflows. The MLST pipeline was developed for both double-strand and single-strand sequencing.     

Daily,limited access to methamphetamine self-administration during pregnancy leads to increased methamphetamine sensitivity in adult offspring

Methamphetamine use by women, even throughout pregnancy, is common. But there is limited knowledge about the effects in prenatally methamphetamine-exposed children. This study investigated how prenatal methamphetamine exposure in rats, via maternal i.v. self-administration, affected the sensitivity of adult offspring to methamphetamine in comparison with controls. The offspring were generated from dams either self-administering methamphetamine daily under limited-access conditions prior to and throughout pregnancy, or their respective saline-yoked control dams. Spontaneous and methamphetamine-induced locomotor activity was assessed in male and female offspring of both exposure groups after a range of methamphetamine doses. In a separate group of offspring, acquisition of i.v. methamphetamine self-administration, responding under fixed and progressive ratio schedules of methamphetamine reinforcement, and reinstatement of extinguished drug-seeking behavior were assessed. Methamphetamine dose-dependently increased locomotor activity in both exposure groups. However, methamphetamine-exposed males showed significantly enhanced locomotor activity compared with controls at 1 mg/kg, and methamphetamine-exposed females showed significantly enhanced locomotor activity compared with controls at 3.2 mg/kg. Methamphetamine-exposed offspring of both sexes acquired methamphetamine self-administration faster and showed overall higher levels of methamphetamine-induced reinstatement compared with controls. Taken together, these results indicate that prenatal methamphetamine exposure to relatively low levels alters methamphetamine sensitivity in male and female adult offspring.     

The low prevalence of allergic disease in Eastern Europe

Background The prevalence of allergic disease is known to be low in Eastern Europe.
Objective To assess the association of suspected risk factors, including several closely linked to the hygiene hypothesis, with allergic symptoms and atopic sensitization in young school-aged children.
Methods Observational study of 13 889 Belarusian children followed up at age 6.5 years in the Promotion of Breastfeeding Intervention Trial (PROBIT). Allergic symptoms and diseases were based on parental responses to the International Study of Asthma and Allergy in Childhood questionnaire, and prick tests to five common inhalant allergens were performed using standard methods.
Results Significantly increased risks of wheezing and hayfever symptoms in the past 12 months, and of recurrent itchy rash were observed in boys, children with a positive first-degree family atopic history, and those who had received probiotics (especially as prophylaxis with antibiotic use). Pet ownership, contact with farm animals, the presence and number of younger and (especially) older siblings, and residency in rural areas of Western Belarus were associated with reduced risks. Maternal postnatal smoking was associated with wheezing and hayfever symptoms, while the duration of exclusive breastfeeding was not protective against any of the studied outcomes. The risk factors for allergic symptoms were similar in children with positive skin-prick tests to those in the overall cohort.
Conclusion Many of the risk and protective factors we identified are consistent with those reported in Western countries and with the hygiene hypothesis. Further research on dietary and other environmental and genetic factors is necessary to understand the low prevalence of allergic disease in Belarus and other Eastern European countries.     

Development of an algorithm for surveillance of ventilator-associated pneumonia with electronic data and comparison of algorithm results with clinician diagnoses .

OBJECTIVE: Surveillance for ventilator-associated pneumonia (VAP) using standard Centers for Disease Control and Prevention (CDC) criteria is labor intensive and involves many subjective assessments. We sought to improve the efficiency and objectivity of VAP surveillance by adapting the CDC criteria to make them amenable to evaluation with electronic data. DESIGN: Prospective comparison of the accuracy of VAP surveillance by use of an algorithm with responses to prospective queries made to intensive care physicians. CDC criteria for VAP were used as a reference standard to evaluate the algorithm and clinicians' reports. SETTING: Three surgical intensive care units and 2 medical intensive care units at an academic hospital. METHODS: A total of 459 consecutive patients who received mechanical ventilation for a total of 2,540 days underwent surveillance by both methods during consecutive 3-month periods. Electronic surveillance criteria were chosen to mirror the CDC definition. Quantitative thresholds were substituted for qualitative criteria. Purely subjective criteria were eliminated. Increases in ventilator-control settings were taken to indicate worsening oxygenation. Semiquantitative Gram stain of pulmonary secretion samples was used to assess whether there was sputum purulence. RESULTS: The algorithm applied to electronic data detected 20 patients with possible VAP. All cases of VAP were confirmed in accordance with standard CDC criteria (100% positive predictive value). Prospective survey of clinicians detected 33 patients with possible VAP. Seventeen of the 33 possible cases were confirmed (52% positive predictive value). Overall, 21 cases of confirmed VAP were identified by either method. The algorithm identified 20 (95%) of 21 known cases, whereas the survey of clinicians identified 17 (81%) of 21 cases. CONCLUSIONS: Surveillance for VAP using electronic data is feasible and has high positive predictive value for cases that meet CDC criteria. Further validation of this method is warranted.     

Isolated congenital tuberculosis otitis in a preterm infant

We report an unusual case of localized congenital tuberculosis otitis in a preterm infant. Unlike disseminated congenital cases, the manifestations of localized otitis are associated with a triad of signs: (i) regional lymphadenopathy in the absence of typical systemic features of tuberculosis; (ii) delayed onset of presentation; and (iii) refractory otitis unresponsive to conventional antimicrobial agents. The need for greater diligence in looking for neonatal tuberculosis is emphasized, especially in an ethnic or socioeconomic environment where the disease is prevalent. Congenital tuberculosis, otitis, preterm
PC Ng, Department of Paediatrics, Level 6, Clinical Sciences Building, Prince of Wales Hospital, Shatin, NT, Hong Kong     

Dynamics of human chorionic gonadotropin, prolactin, and growth hormone in serum and amniotic fluid throughout normal human pregnancy

This study was performed to establish the dynamics of human chorionic gonadotropin, prolactin, and growth hormone throughout pregnancy in serum and amniotic fluid. Two hundred fifty healthy women at 8 to 42 weeks' gestation were studied. The highest serum human chorionic gonadotropin level was measured between weeks 8 to 12 (53,715 +/- 3574 mIU/ml, mean +/- SEM), with a decline to a mean plateau of 11,806 +/- 1250 mIU/ml from week 18. Amniotic fluid human chorionic gonadotropin had a similar pattern with a mean of 68,100 +/- 8422 mIU/ml at weeks 8 to 10, declining from week 18 to a plateau of 2005 +/- 260 mIU/ml. Human chorionic gonadotropin showed a significant correlation (r = 0.85, p less than 0.001) between levels of both compartments demonstrating an even distribution. Prolactin levels showed a dichotomy of patterns and levels. Serum prolactin showed a continuous rise from 45.3 +/- 14 ng/ml at week 8 to 224 +/- 20 ng/ml at week 36. In contrast, amniotic fluid prolactin remained low until week 14 (33.1 +/- 0.8 ng/ml), followed by a sharp and significant (p less than 0.001) increase to a plateau of 3750 +/- 200 ng/ml between weeks 18 to 26, declining to a second plateau of 500 +/- 50 ng/ml at week 36. Serum growth hormone increased from a mean of 3.5 +/- 1.4 ng/ml seen at weeks 8 to 10 to a mean of 14 +/- 2.0 ng/ml at weeks 28 to 30, followed by a plateau of similar levels. The pattern of growth hormone secretion in amniotic fluid demonstrated a sharp increase during the 14-16 interval with a maximum mean level of 15.5 +/- 1.5 ng/ml and a slow steady decline thereafter. In conclusion, the similar pattern and concentration of human chorionic gonadotropin throughout pregnancy in both maternal and amniotic fluid are probably the result of direct human chorionic gonadotropin diffusion from the placenta. The dissimilar pattern and concentration of prolactin are the result of two different sources of prolactin secretion during pregnancy. Serum prolactin originates from the pituitary and amniotic fluid prolactin from the decidua. Since the pattern of growth hormone secretion resembles that of prolactin, it is possible that growth hormone, like prolactin, is secreted by the same sources.