Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics

16S rRNA gene sequencing has been widely used for probing the species structure of a variety of environmental bacterial communities. Alternatively, 16S rRNA gene fragments can be retrieved from shotgun metagenomic sequences (metagenomes) and used for species profiling. Both approaches have their limitations-16S rRNA sequencing may be biased because of unequal amplification of species' 16S rRNA genes, whereas shotgun metagenomic sequencing may not be deep enough to detect the 16S rRNA genes of rare species in a community. However, previous studies showed that these two approaches give largely similar species profiles for a few bacterial communities. To investigate this problem in greater detail, we conducted a systematic comparison of these two approaches. We developed PHYLOSHOP, a pipeline that predicts 16S rRNA gene fragments in metagenomes, reports the taxonomic assignment of these fragments, and visualizes their taxonomy distribution. Using PHYLOSHOP, we analyzed 33 metagenomic datasets of human-associated bacterial communities, and compared the bacterial community structures derived from these metagenomic datasets with the community structure derived from 16S rRNA gene sequencing (71 datasets). Based on several statistical tests (including a statistical test proposed here that takes into consideration differences in sample size), we observed that these two approaches give significantly different community structures for nearly all the bacterial communities collected from different locations on and in human body, and that these differences cannot be be explained by differences in sample size and are likely to be attributed by experimental method.

A structured course teaching junior doctors invasive medical procedures results in sustained improvements in self-reported confidence

Pressure on working hours has led to a decrease in opportunities for training in invasive medical procedures for junior doctors. The effect of a structured course on immediate and medium-term changes in self-reported confidence was investigated. A one-day model-based practical course was run on two separate occasions teaching central venous line placement, lumbar puncture, Seldinger-technique chest drain insertion and knee joint aspiration. Attendees were asked to indicate their confidence in each procedure on a 10-point Likert scale before, immediately after and three months after the course. Significant improvements in self-reported confidence were seen for all procedures which were sustained at three months. Feedback was universally positive. Practical preclinical training may be a useful adjunct to patient-based training in invasive procedures. The course was particularly popular with foundation year trainees: ideally this training should be available before trainees' first exposure in the clinical setting.

Recognition and treatment of genitourinary complications in paediatric Crohn's disease using Infliximab

Although genitourinary complications of Crohn's are well recognized, available information regarding their clinical course and management is sparse especially in the paediatric population. We report a myriad of urological complications in five paediatric cases, our experience from a tertiary paediatric urological and gastroenterological centre. All children with urological complications had severe Crohn's disease which necessitated the use of immuno-suppressants including Infliximab. Three of four children healed and closed their fistulas after treatment, although failed to avoid future surgery, albeit for other reasons.

CONCLUSION

We suggest Infliximab should be considered as a treatment option but in the absence of a common consensus, treatment be tailored to individual cases.

The rise and fall of a psychiatric antenatal clinic: development of a perinatal psychiatric service linked directly to the provision of antenatal care

Usual referral pathways to psychiatric services can miss opportunities for timely intervention in maternal perinatal psychiatric ill health. Psychiatric illness leading to suicide is a significant factor in at least 10% of maternal deaths. Despite Royal College of Psychiatry and National Institute for Health and Clinical Excellence recommendations for specialist provision of perinatal mental health services, this remains sporadic and insufficient. We set out to develop a new integrated antenatal-psychiatric direct referral pathway and present a year of experience using this service model. The psychiatric service was delivered from within the antenatal clinic setting with a direct health-care professional (HCP) led referral pathway between 2003 and 2004. The service comprised one session per week of a senior psychiatric specialist registrar and provided three new patients and two follow-up appointments per week. During this period, a total of 75 referrals to the service were made with 57 individuals attending for an appointment. There was a range of diagnoses among the women who attended, with only 24% meeting eligibility criteria for referral to secondary psychiatric services. The majority diagnosis was depression. More severely ill women were not referred to this clinic by obstetric HCPs. In conclusion, this model for developing and delivering a specialist perinatal psychiatric service using direct links to antenatal medical care was not successful despite requiring minimal funding. Nevertheless, it has been used to inform development of a new perinatal service in keeping with the Royal College of Psychiatrists' recommendations and incorporating enhanced training of HCPs responsible for the referral pathway.

Inpatient treatment of diabetic patients in Asia: evidence from India, China, Thailand and Malaysia

AIMS

The prevalence of Type 2 diabetes mellitus (DM) has grown rapidly, but little is known about the drivers of inpatient spending in low- and middle-income countries. This study aims to compare the clinical presentation and expenditure on hospital admission for inpatients with a primary diagnosis of Type 2 DM in India, China, Thailand and Malaysia.

METHODS

We analysed data on adult, Type 2 DM patients admitted between 2005 and 2008 to five tertiary hospitals in the four countries, reporting expenditures relative to income per capita in 2007.

RESULTS

Hospital admission spending for diabetic inpatients with no complications ranged from 11 to 75% of per-capita income. Spending for patients with complications ranged from 6% to over 300% more than spending for patients without complications treated at the same hospital. Glycated haemoglobin was significantly higher for the uninsured patients, compared with insured patients, in India (8.6 vs. 8.1%), Hangzhou, China (9.0 vs. 8.1%), and Shandong, China (10.9 vs. 9.9%). When the hospital admission expenditures of the insured and uninsured patients were statistically different in India and China, the uninsured always spent less than the insured patients.

CONCLUSIONS

With the rising prevalence of DM, households and health systems in these countries will face greater economic burdens. The returns to investment in preventing diabetic complications appear substantial. Countries with large out-of-pocket financing burdens such as India and China are associated with the widest gaps in resource use between insured and uninsured patients. This probably reflects both overuse by the insured and underuse by the uninsured.

Two novel AIRE mutations in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) among Indians

Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a rare recessive disorder resulting from mutations in the autoimmune regulator (AIRE) gene. There is no information on AIRE mutations in Indians. In a cross-sectional study, nine patients (eight families), from four referral hospitals in India, were studied for AIRE mutations by direct sequencing. We screened for new mutations in 150 controls by allele-specific PCR. The patients had 1-7 known components of APECED. Three patients had unusual manifestations: presentation with type 1 diabetes; chronic sinusitis and otitis media; and facial dysmorphism. All patients carried homozygous, probably recessive, AIRE mutations. Two unrelated patients from a small in-bred community (Vanika Vaisya) in south India carried an unreported missense mutation, p.V80G, in the N-terminal caspase recruitment domain. Another unique mutation, p.C302X, resulting in a truncated protein with deletion of both zinc-finger domains, was detected in a patient from Gujarat. Neither mutation was detected in controls. Other mutations, previously described in Caucasians, were: 13 base pair deletion (p.C322fsX372) in 4 (38%), and Finn-major (p.R257X) and p.R139X (Sardinian) mutation in one subject each. In conclusion, in this first series of APECED in Indians, we detected AIRE mutations previously reported in Caucasians, as well as unique mutations. Of these, p.V80G is possibly an ancestral mutation in an in-bred community.

CD3(+) and/or CD14(+) depletion from cord blood mononuclear cells before ex vivo expansion culture improves total nucleated cell and CD34(+) cell yields

Cord blood (CB) is used increasingly in transplant patients lacking sibling or unrelated donors. A major hurdle in the use of CB is its low cell dose, which is largely responsible for an elevated risk of graft failure and a significantly delayed neutrophil and platelet engraftment. As a positive correlation has been shown between the total nucleated cell (TNC) and CD34(+) cell dose transplanted and time to neutrophil and platelet engraftment, strategies to increase these measures are under development. One strategy includes the ex vivo expansion of CB mononuclear cells (MNC) with MSC in a cytokine cocktail. We show that this strategy can be further improved if CD3(+) and/or CD14(+) cells are first depleted from the CB MNC before ex vivo expansion. Ready translation of this depletion strategy to improve ex vivo CB expansion in the clinic is feasible as clinical-grade devices and reagents are available. Ultimately, the aim of improving TNC and CD34(+) transplant doses is to further improve the rate of neutrophil and platelet engraftment in CB recipients.

Non-firearm-related homicide, New Mexico, 2001-3

OBJECTIVE

New Mexico (NM) has the highest rate of non-firearm-related homicide in the USA and ranks 20th in firearm-related homicides. Because non-firearm-related homicides are inadequately described in the literature, characterisation of non-firearm-related homicide victims will enhance efforts to reduce homicides.

METHODS

Homicide victims were identified through the Office of the Medical Investigator. Age-specific and age-adjusted homicide death rates were calculated for 2001-3 by sex and race/ethnicity, and associations between covariates and non-firearm-related homicide were measured.

RESULTS

Non-firearm-related homicides comprised 33% of US homicide victims, 47% of NM homicide victims, and 74% of NM American Indian (AI) homicide victims. Of 212 NM non-firearm-related homicide victims, 37% had been beaten, 32% had been stabbed, and 12% had been strangled. Females comprised 30% of non-firearm-related homicide victims and 18% of firearm-related homicide victims. A blood alcohol concentration (BAC) >or=0.08 mg/dl was detected among 43% of non-firearm-related (61% of AI) and 33% of firearm-related (50% of AI) homicide victims. Non-firearm-related homicide rates were highest among AI men aged 25-34 years (31/100,000). Non-firearm-related homicide victims were more likely than firearm-related victims to be AI (adjusted odds ratio (AOR) 4.20; 95% CI 2.16 to 8.16) and female (AOR 2.05; 95% CI 1.27 to 3.31), and to have had a BAC >or=0.08 mg/dl (AOR 1.65; 95% CI 1.08 to 2.52).

CONCLUSIONS

Homicide-prevention efforts among AIs in NM should focus on non-firearm-related homicides. The association between excessive drinking and non-firearm-related homicide should be further characterised. Continued surveillance for non-firearm-related homicides will assist these efforts.

Risk assessment of isolated aripiprazole exposures and toxicities: a retrospective study

STUDY OBJECTIVE

To characterize the clinical effects of acute isolated aripiprazole poisonings and to assess the toxic dose of this drug.

METHODS

All isolated acute aripiprazole exposures reported to a poison control system from January 2002 through September 2006 were retrospectively reviewed. Patients with incomplete information or those lost to follow-up were excluded.

RESULTS

A total of 286 cases were identified. Mean age was 18.9 years (SD 15.7), with a range of 6 months-70 years. Seventy-seven patients (27%) were <or=6 years, 80 patients (28%) were 7-17 years, and 129 patients (45%) were >or=18 years. Doses were known in 255 patients (89%). Symptoms occurred in 158 patients (55%): somnolence 89 (56%), tachycardia 32 (20%, heart rate 102-186), nausea/vomiting 29 (18%), dystonic reactions 21 (13%), tremor 9 (6%), agitation 3 (2%), dizziness 3 (2%), paresthesia 2 (1%), headache 2 (1%), dysphagia 1 (<1%), syncope 1 (<1%), minor facial swelling 1 (<1%), and hypotension 1 (<1%). None of the patients required intubation, and there were no deaths or EKG abnormalities. Median dose for symptomatic and asymptomatic groups were 25 and 15 mg, respectively, for <or=6 years (p = 0.02); 60 and 30 mg for 7-17 years (p = 0.01); and 100 and 75 mg for >or=18 (p = 0.25). In comparison of drug groups (Group 1, <or=20 mg; Group 2, 21-90 mg; Group 3, >or=91 mg), symptoms were more likely to occur in Group 2 versus Group 1 (OR 2.29, 95% CI 0.79-6.61) in patients <or=6 years; in Group 3 versus Group 1 (OR 3.39, 95% CI 1.07-10.73) followed by Group 2 versus Group 1 (OR 1.14, 95% CI 0.36-3.56) in patients 7-17 years; and in Group 3 versus Group 1 (OR 1.36, 95% CI 0.54-3.42) but not any more likely in Group 2 versus Group 1 (OR 0.92, 95% CI 0.33-2.52) in patients >or=18 years.

CONCLUSIONS

Acute aripiprazole poisonings most commonly result in sedation, sinus tachycardia, nausea/vomiting, or dystonic reactions. Symptoms are more likely with doses above 90 mg, although pediatric patients can be affected at a lower dose.

Complicated crown fractures - management and treatment options

AIM

Complicated crown fractures involve enamel, dentine and the pulp. The incidence of complicated crown fractures ranges from 2% to 13% of all dental injuries and the most commonly involved tooth is the maxillary central incisor. Various treatment modalities are available depending upon the clinical, physiological and radiographic status of the involved tooth. The aim of this article was to discuss techniques for the management of complicated crown fractures.

SUMMARY

Management of complicated crown fractures depends upon several factors with the result that various clinical modalities have been suggested. Seven case reports of complicated crown fractures are presented and risks/benefits of the treatment plans are discussed.

KEY LEARNING POINTS

Proper diagnosis, treatment planning and follow-up care are important factors in the prognosis of complicated crown fractures. Thorough understanding of the available treatment modalities and their specific indications is critical. The risks and benefits of each treatment option should be carefully evaluated during the treatment planning process.

Role of autologous stem cell transplant after induction therapy with bortezomib-lenolidomide or bortezomib-thalidomide in newly diagnosed multiple myeloma patients

8596

Background: The introduction of novel therapeutic options with bortezomib and immunomodulatory agents in the up-front management of multiple myeloma (MM) has significantly improved induction response rates. However, the role of high dose chemotherapy and autologous stem cell transplant (ASCT) after induction with these highly active agents is not known, especially in patients with only a partial response to induction therapy. Methods: We conducted a retrospective review of 95 newly diagnosed MM patients treated with induction bortezomib-lenolidomide-dexamethasone (BLD) or bortezomib-thalidomide-dexamethasone (BTD) prior to ASCT. Responses were graded according to IMWG criteria. Results: 19 patients received BLD and 76 patients received BTD. All patients were conditioned with a melphalan-based regimen. Of the 19 patients who underwent induction with BLD, complete response (CR), very good partial response (VGPR) and partial response (PR) were achieved in 2 (11%), 8 (42%) and 9 (47%) respectively for an overall response rate (ORR) of 19/19 (100%). After ASCT, CR, VGPR and PR were achieved in 9 (47%), 5 (26%) and 5 (26%) respectively for a continued ORR of 21/21 (100%). Notably, 4/8 (50%) of patients with a VGPR after induction therapy with BLD improved to a CR after ASCT. 3/9 (33%) of patients with an initial PR to BLD improved to a CR and 1/9 (11%) with a PR improved to VGPR after ASCT. Of the 76 patients who underwent induction with BTD, CR, VGPR and PR were achieved in 6 (8%), 37 (49%) and 31(41%) respectively for an ORR of 74/76 (97%). 1 patient had stable disease and 1 patient had progressive disease. After ASCT, 27/76 (36%) achieved a CR, 30/76 (39%) a VGPR and 18/76 (24%) a PR for an ORR of 75/76 (99%). Of the patients who initially had a VGPR to BTD 16/37 (43%) improved to a CR while 5/32(16%)of PR patients improved to a CR and 9/32 (28%) of PR patients improved to a VGPR. Conclusions: Of the 40 patients who only achieved a PR after induction therapy with BLD or BTD, 16 (40%) had further improvement to a CR or VGPR after ASCT. Thus there is a significant benefit of ASCT in these patients who initially demonstrate relative resistance to induction therapy with highly active regimens.

[Table: see text]