Phylogenetic and Timescale Analysis of Barmah Forest Virus as Inferred from Genome Sequence Analysis.

Barmah Forest virus (BFV) is a medically important mosquito-borne alphavirus endemic to Australia. Symptomatic disease can be a major cause of morbidity, associated with fever, rash, and debilitating arthralgia. BFV disease is similar to that caused by Ross River virus (RRV), the other major Australian alphavirus. Currently, just four BFV whole-genome sequences are available with no genome-scale phylogeny in existence to robustly characterise genetic diversity. Thirty novel genome sequences were derived for this study, for a final 34-taxon dataset sampled over a 44 year period. Three distinct BFV genotypes were characterised (G1-3) that have circulated in Australia and Papua New Guinea (PNG). Evidence of spatio-temporal co-circulation of G2 and G3 within regions of Australia was noted, including in the South West region of Western Australia (WA) during the first reported disease outbreaks in the state's history. Compared with RRV, the BFV population appeared more stable with less frequent emergence of novel lineages. Preliminary in vitro assessment of RRV and BFV replication kinetics found that RRV replicates at a significantly faster rate and to a higher, more persistent titre compared with BFV, perhaps indicating mosquitoes may be infectious with RRV for longer than with BFV. This investigation resolved a greater diversity of BFV, and a greater understanding of the evolutionary dynamics and history was attained.

Metabolic screening in primary care for patients with schizophrenia or schizoaffective disorder and taking antipsychotic medication.

INTRODUCTION Life expectancy in patients with schizophrenia is 15-20 years less than the general population. A dominant cause of morbidity and mortality in these patients is cardiovascular disease. Adverse consequences of modifiable cardiovascular risk factors can be reduced by regular monitoring of metabolic outcomes and intervention if required. AIM To evaluate the metabolic screening in primary care for patients with schizoaffective disorders managed in primary care. To show the usefulness of combining simple practice audits in evaluating such areas of clinical practice. METHODS An audit was undertaken in eight general practices in the Waikato and Bay of Plenty regions of New Zealand. Specifically, the monitoring of patients with schizophrenia or schizoaffective disorder whose antipsychotic medication was prescribed by primary care doctors was audited. Patient monitoring was compared to the guideline recommendation of the Royal Australian and New Zealand College of Psychiatrists (RANZCP) and the Best Practice Advisory Centre (BPAC). RESULTS In total, 117 patients were included in the audit and none were fully monitored, as recommended by the RANZCP guidelines. Although two-thirds of patients had been evaluated for glycosylated haemoglobin (HbA1c), lipids, blood pressure, complete blood count and weight, <10% of patients had had prolactin, waist circumference or electrocardiogram measurements recorded. The proportion of patients having a HbA1c measured was also significantly higher in younger patients and patients who were non-Maori or enrolled with an urban practice (all P<0.05). When using the simplified BPAC guidelines, half of all patients were correctly monitored. DISCUSSION These findings show there is room for improvement in the monitoring of patients receiving antipsychotic medication in primary care. This may indicate the need for clear guidance and general practitioner education around the monitoring requirements of these patients. Alternatively, a more simplified monitoring protocol may need to be developed. This audit has also shown that there is value in several practices completing the same audit and providing a larger cohort of patients for pooled data analysis.

Detection of Neisseria gonorrhoeae and Chlamydia trachomatis from pooled rectal, pharyngeal and urine specimens in men who have sex with men.

OBJECTIVES: Screening of men who have sex with men (MSM) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) requires sampling from anorectal and pharyngeal sites in addition to urogenital sampling. Due to the cost of testing multiple anatomical sites individually testing of pooled specimens has potential merit. The Cepheid GeneXpert CT/NG assay (GeneXpert), which also has potential for point-of-care nucleic acid testing in the sexual health clinic, has not been assessed for pooled specimen testing. METHODS: We prospectively compared GeneXpert testing of pooled pharyngeal and rectal swabs with urine samples to standard of care testing of individual specimens from 107 participants using the Roche cobas 4800 CT/NG assay (cobas) for CT and NG in high-risk MSM attending an inner city sexual health clinic. RESULTS: We found testing of pooled pharyngeal, rectal and urine samples by the GeneXpert to have 100% agreement for NG and 94% overall agreement for CT when compared with individual specimen testing by cobas. For CT testing, 14 cases were detected for both tests, 4for cobas only, 2 for GeneXpert only and 89 participants were negative for both tests. CONCLUSIONS: Pooled specimen CT and NG testing by the GeneXpert was accurate when compared with single specimen testing and has potential for screening MSM for CT and NG. The role of pooled specimen testing with the GeneXpert as a point-of-care nucleic acid test in MSM requires further investigation.

Improved blood culture identification by FilmArray in cultures from regional hospitals compared with teaching hospital cultures.

Rapid identification of bacteria isolated from blood cultures by direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now in wide spread use in major centres but is not yet feasible in smaller hospital laboratories. A FilmArray multiplex PCR panel for blood culture isolate identification (BCID) provides an alternative approach to near point-of-care microbial identification in regional hospitals. We assessed the accuracy and time to identification of the BCID FilmArray in a consecutive series of 149 blood cultures from 143 patients in a teaching hospital and smaller regional hospitals, currently identified by direct MALDI-TOF and proprietary molecular methods. The BCID FilmArray contained 18 of 34 species and 20 of 23 species isolated from teaching and regional hospital, respectively. Overall, 85 % of the teaching hospital and 100 % of the regional hospital monomicrobial blood cultures were identified, compared with 60 and 68 %, respectively, for direct MALDI-TOF on the same cultures. There were no incorrect results from blood cultures containing Staphylococcus aureus, streptococci, Pseudomonas aeruginosa or Enterobacteriaceae. The three discrepant results were all in mixed cultures. The mean reduction in time to identification of blood culture isolates was 53 h, which did not include the time required to transport cultures from regional centres to a central laboratory. The overall performance of the BCID FilmArray is stronger in blood cultures from smaller regional hospitals that encounter a narrower range of bacterial species dominated by the commonest species. This approach is more suited to smaller clinical laboratories than the MALDI-TOF direct method.