Species-specific PCR primers for simultaneous detection of Aspergillus fumigatus, Aspergillus terreus, Candida albicans and Candida glabrata in invasive fungal infections

A rapid and accurate diagnosis of invasive fungal infections (IFIs) has been a great challenge particularly in cases requiring prompt antifungal treatment. In this study, four primer pairs were designed for a quadruplex PCR assay, which was developed for detection of four fungal species simultaneously. DNA extraction of cultured colonies and spiked blood samples were performed using conventional (phenol-chloroform) techniques and commercial DNA extraction kit. The optimum annealing temperature for this assay was 60°C. The assay was able to amplify all four genes and showed 100% specificity. No amplification of any genes was obtained against other species (n=14), which included two bacteria species. In conclusion, this quadruplex PCR assay is specific, rapid and reliable to detect A. fumigatus, A. terreus, C. albicans and C. glabrata simultaneously.

Interactions between the lipidome and genetic and environmental factors in autism

Autism omics research has historically been reductionist and diagnosis centric, with little attention paid to common co-occurring conditions (for example, sleep and feeding disorders) and the complex interplay between molecular profiles and neurodevelopment, genetics, environmental factors and health. Here we explored the plasma lipidome (783 lipid species) in 765 children (485 diagnosed with autism spectrum disorder (ASD)) within the Australian Autism Biobank. We identified lipids associated with ASD diagnosis (n = 8), sleep disturbances (n = 20) and cognitive function (n = 8) and found that long-chain polyunsaturated fatty acids may causally contribute to sleep disturbances mediated by the FADS gene cluster. We explored the interplay of environmental factors with neurodevelopment and the lipidome, finding that sleep disturbances and unhealthy diet have a convergent lipidome profile (with potential mediation by the microbiome) that is also independently associated with poorer adaptive function. In contrast, ASD lipidome differences were accounted for by dietary differences and sleep disturbances. We identified a large chr19p13.2 copy number variant genetic deletion spanning the LDLR gene and two high-confidence ASD genes (ELAVL3 and SMARCA4) in one child with an ASD diagnosis and widespread low-density lipoprotein-related lipidome derangements. Lipidomics captures the complexity of neurodevelopment, as well as the biological effects of conditions that commonly affect quality of life among autistic people.

Autism-related dietary preferences mediate autism-gut microbiome associations

There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.

A rare and unusual cause of Vibrio cholerae non-O1, non-O139 causing spontaneous peritonitis in a patient with cirrhosis

Spontaneous bacterial peritonitis caused by Vibrio cholerae non-O1/ non-O139 is a rare phenomenon. V. cholerae is known as a common aetiology of epidemic diarrheal disease and rarely causes extra-gastrointestinal infections. In this report, a 52-year-old man presented to our hospital with a clinical scenario for chronic liver cirrhosis with low grade fever and loose stools. V. cholerae was isolated from peritoneal fluid culture, which was further confirmed as non-O1/ non-O139 strain by multiplex polymerase chain reaction. The patient was successfully treated with antimicrobial therapy and peritoneal drainage. This case represents the first isolation of V. cholerae non-O1/ non-O139 strain from peritoneal fluid.

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

BACKGROUND

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition whose biological basis is yet to be elucidated. The Australian Autism Biobank (AAB) is an initiative of the Cooperative Research Centre for Living with Autism (Autism CRC) to establish an Australian resource of biospecimens, phenotypes and genomic data for research on autism.

METHODS

Genome-wide single-nucleotide polymorphism genotypes were available for 2,477 individuals (after quality control) from 546 families (436 complete), including 886 participants aged 2 to 17 years with diagnosed (n = 871) or suspected (n = 15) ASD, 218 siblings without ASD, 1,256 parents, and 117 unrelated children without an ASD diagnosis. The genetic data were used to confirm familial relationships and assign ancestry, which was majority European (n = 1,964 European individuals). We generated polygenic scores (PGS) for ASD, IQ, chronotype and height in the subset of Europeans, and in 3,490 unrelated ancestry-matched participants from the UK Biobank. We tested for group differences for each PGS, and performed prediction analyses for related phenotypes in the AAB. We called copy-number variants (CNVs) in all participants, and intersected these with high-confidence ASD- and intellectual disability (ID)-associated CNVs and genes from the public domain.

RESULTS

The ASD (p = 6.1e-13), sibling (p = 4.9e-3) and unrelated (p = 3.0e-3) groups had significantly higher ASD PGS than UK Biobank controls, whereas this was not the case for height-a control trait. The IQ PGS was a significant predictor of measured IQ in undiagnosed children (r = 0.24, p = 2.1e-3) and parents (r = 0.17, p = 8.0e-7; 4.0% of variance), but not the ASD group. Chronotype PGS predicted sleep disturbances within the ASD group (r = 0.13, p = 1.9e-3; 1.3% of variance). In the CNV analysis, we identified 13 individuals with CNVs overlapping ASD/ID-associated CNVs, and 12 with CNVs overlapping ASD/ID/developmental delay-associated genes identified on the basis of de novo variants.

LIMITATIONS

This dataset is modest in size, and the publicly-available genome-wide-association-study (GWAS) summary statistics used to calculate PGS for ASD and other traits are relatively underpowered.

CONCLUSIONS

We report on common genetic variation and rare CNVs within the AAB. Prediction analyses using currently available GWAS summary statistics are largely consistent with expected relationships based on published studies. As the size of publicly-available GWAS summary statistics grows, the phenotypic depth of the AAB dataset will provide many opportunities for analyses of autism profiles and co-occurring conditions, including when integrated with other omics datasets generated from AAB biospecimens (blood, urine, stool, hair).

Distribution of candidemia in Malaysian tertiary care hospital revealed predominance of Candida parapsilosis

Candida parapsilosis is an important pathogen of healthcare-associated bloodstream infections (BSI) causing high mortality and morbidity in immunocompromised patients in addition to other Candida species including C. albicans, C. tropicalis, C. glabrata, and C. krusei. Knowledge on recent local species distribution and trend is essential. An increase in the proportion of C. parapsilosis candidemia has been recently observed as a result of many risk factors. The distribution of candidemia has been changing in the last three decades. To determine the proportion of different Candida species causing candidemia in a tertiary-care hospital during January 2001 - December 2018, a retrospective study performed in a 853-bedded tertiary-care hospital in north-eastern Malaysia. All cases of candidemia from January-2001 to December-2018 were included, and the review was performed based on patients' medical records and laboratory database. The frequency of different Candida species was determined. This study showed that out of 1175 patients with candidemia, C. parapsilosis was the most common species contributing to 29.2% (343/1175) of candidemia, followed by C. albicans 20.1% (236/1175), C. tropicalis 18.7% (220/1175), C. glabrata 6.0% (71/1175), C. guilliermondii 3.7% (43/1175), C. rugosa 1.9% (22/1175), C. famata 1.7% (20/1175), C. krusei 1.4% (16/1175), C. dubliniensis 0.8% (9/1175), C. lusitaniae 0.7% (8/1175), C. lipolytica 0.3% (4/1175), C. pelliculosa 0.3% (4/1175), C. haemulonii, C. kefyr, C. utilis and C. inconspicua (1/1175 each). In addition, 14.9% (175/1175) belonged to Candida spp. which were not identified to species level. In conclusion, a different scenario for the proportion of Candida species with C. parapsilosis predominates over C. albicans as a nosocomial pathogen leading to candidemia has been shown in this study.

Reduced susceptibility of Burkholderia pseudomallei following exposure to carbapenem

Reduced susceptibility in Burkholderia pseudomallei during carbapenem therapy may lead to treatment failure. We isolated a clinical strain that had developed reduced susceptibility to carbapenems while on treatment. After reviewing the patient's clinical notes, the initial isolate (BUPS01/14) was exposed to carbapenem in vitro to mimic the clinical scenario. The stability of susceptibility of the carbapenem-exposed strain (BUPS01/14R) was examined by serial subculture in antibiotic-free broth. Biochemical and morphological comparison was performed by the VITEK® system and electron microscopy. MICs increased 32-fold following carbapenem exposure and became stable in the antibiotic-free environment. On electron microscopic examination, the BUPS01/14R cells were smoother and less wrinkled compared to BUPS01/14 cells. This report highlights a potential anti-melioidosis treatment failure due to the emergence of resistance while on carbapenem monotherapy. Further study of this strain is necessary to understand the mechanism of resistance at a molecular level.

Development and validation of TaqMan real-time PCR for the detection of Burkholderia pseudomallei isolates from Malaysia

Rapid detection of Burkholderia pseudomallei, the etiologic agent of melioidosis, allows for timely initiation of appropriate treatment and better clinical outcomes. In the current gold standard, the culture method is time consuming and suffers from low sensitivity. Meanwhile, previously reported molecular assays are fast and sensitive, but their performance on isolates from Malaysia, an endemic region of melioidosis is under reported. This study designed oligonucleotides targeting orf2 of Type III secretion system (TTSS) genes cluster for the detection of Malaysian B. pseudomallei isolates and evaluated the assay on 95 local B. pseudomallei strains, 58 other microorganisms and 71 clinical specimens from patients. The developed assay exclusively detected all tested B. pseudomallei isolates with a detection limit of 20 fg per reaction (equivalent to ~2.5 copies). Subsequent testing on clinical samples showed that the assay detected all confirmed specimens with the growth of B. pseudomallei (n = 10/10). None of the negative specimens had a detectable signal of our TTSS-orf2 assay (n = 0/61). In conclusion, the present study provides crucial preliminary data for a subsequent study and should be considered as a potential alternative to current time-consuming culture method for the detection of B. pseudomallei.

Knowledge, Attitude and Practice of Bangladeshi Women towards Breast Cancer: A Cross Sectional Study

In Bangladesh incidence rate of breast cancer was about 22.5 per 100000 females. Breast cancer has been reported as the highest prevalence rate (19.3 per 100,000) among Bangladeshi women between 15 and 44 years of age. For this prevailing situation a cross-sectional study was designed to assess the knowledge, attitude and practices of community-dwelling women in Bangladesh towards breast cancer at Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from July 2013 to June 2014. All female participants attending at outpatient department of BSMMU having age more than 20 years and education at least JSC, purposively selected until the sample size achieved 500. Only applying simple cost free method like self breast examination (SBE) and clinical breast examination (CBE) one can asses her breast. Thereby awareness develops regarding her breast so any mass newly appear can be assessed by the lady herself. Early diagnosis of the breast cancer will reduce the burden of treatment cost, mortality & morbidity. Research and development strategy of the project is to enhance the awareness of the community people about breast cancer prevention. Mean age of the study population was 36.16 years. Regarding education nearly 30% (n=150) of them studied up to Junior School, 16% (n=80) respondents completed masters and above remaining in between. Regarding occupation, almost 60% (n=300) were house wife, 32% (n=160) were service holder and only 8% (n=40) of them were students. Knowledge about common female cancer 60% (n=300) were aware about the cervical cancer, 24% (n=120) mentioned breast cancer, 4% (n=20) mentioned ovarian cancer, and 12% (n=60) don't know anything regarding common women cancer. Knowledge about early symptoms of breast cancer, majority of the respondents 66% (n=330) were aware that mass in the breast is the main symptom, 2% (n=10) mentioned pain in breast, 32% (n=160) mentioned that they don't know anything regarding the early symptoms. About the cause of breast cancer 60% (n=300) mentioned that, they don't know anything regarding the cause of breast cancer, 36% (n=180) were aware that non lactation is a cause of breast cancer. About 4% (n=20) of the study population mentioned others, like due to some ones bad did cancer occur as punishment. Knowledge about risk factor of breast cancer, 65% (n=325) have no idea about the risk of breast cancer, 32% (n=160) mentioned few risk factors which have relation with breast cancer and 3% (n=15) did not mention anything. Regarding diagnosis of cancer breast 72% (n=360) mentioned they don't know anything, 16% (n=80) by doing ultra sonogram of breast, 6% (n=30) mentioned about Mammography and 6% (n=30) MRI & others. Regarding screening for prevention of breast cancer 60% (n=300) mentioned that they don't know anything regarding screening. Thirty percent (n=150) were aware that there is screening method but they are not aware specifically regarding this method and they also not aware that breast cancer is a preventable disease. 10% (n=50) were fully aware about screening method like CBE & SBE. About the cause of not seeking medical advice for prevention of Breast cancer, majority of the respondents 40% (n=200) mentioned expenditure problems, 32% (n=160) they don't have any knowledge about this type of medical advice, 8% (n=40) mentioned communication problems and 20% (n=100) others. Regarding Practice of CBE & SBE 68% (n=340) never practice CBE & SBE, 30% (n=150) occasionally practiced CBE & SBE. Only 2% (n=10) mentioned that they were regularly practicing CBE & SBE.

Symptom severity in autism spectrum disorder is related to the frequency and severity of nausea and vomiting during pregnancy: a retrospective case-control study

Background

Nausea and vomiting during pregnancy (NVP) is thought to be caused by changes in maternal hormones during pregnancy. Differences in hormone exposure during prenatal life have been implicated in the causal pathways for some cases of autism spectrum disorder (ASD). However, no study has investigated whether the presence and severity of NVP may be related to symptom severity in offspring with ASD.

Methods

A large sample of children with ASD (227 males and 60 females, aged 2 to 18 years) received a clinical assessment, during which parents completed questionnaires regarding their child’s social (Social Responsiveness Scale, SRS) and communication (Children’s Communication Checklist–2nd edition, CCC-2) symptoms. Parents also reported on a 5-point scale the frequency and severity of NVPs during the pregnancy of the child being assessed: (1) no NVP during the pregnancy, (2) occasional nausea, but no vomiting, (3) daily nausea, but no vomiting, (4) occasional vomiting, with or without nausea, and (5) daily nausea and vomiting.

Results

Impairments in social responsiveness in offspring, as indexed by SRS total score, significantly increased as a function of the frequency and severity of their mothers’ NVP, as did the level of language difficulties as indexed by the Global Communication Composite of the CCC-2.

Conclusions

The strong, positive association between increasing frequency and severity of NVP and ASD severity in offspring provides further evidence that exposure to an atypical hormonal environment during prenatal life may affect neurodevelopment and contribute to the ASD phenotype. Given that the measure of NVP symptoms in the current study was based on retrospective recall, replication of this finding is required before strong conclusions can be drawn.

Electronic supplementary material

The online version of this article (10.1186/s13229-018-0223-7) contains supplementary material, which is available to authorized users.

How to Train to Discharge a Dermatology Outpatient: A Review

BACKGROUND/AIMS

The decision to discharge is a critical and common outpatient consultation event. However, little guidance exists over how discharge decision-making can be taught. We aimed to provide educational recommendations concerning outpatient discharge decision-making.

METHODS

Recommendations were drawn from prior interviews with 40 consultant dermatologists and 56 dermatology outpatients, and from the "traffic light" design discharge information checklist, developed using the Delphi technique.

RESULTS

The key strategies to follow to appropriately manage the outpatient discharge process are: to warn patients in advance, to understand patients' agendas, to allow extra time for the discharge process, to prepare patients to self-manage, to provide a "safety net" and provide the GP with a clear management plan. Aspects to be considered include patient mobility, presence of carer, type of employment, diagnostic certainty, and use of the checklist or guidelines. Key training aspects include teaching structured thought processes when discharging, discharging according to context, developing communication and negotiation skills, avoiding decision biases and encouraging good interprofessional collaboration. Training should include the consideration of the possibility of discharge at each consultation. Novel training strategies have been developed on how to appropriately manage the outpatient discharge process, including involving and informing patients. These strategies focus on safe decision-making, being patient-centred and organizing an efficient health care service framework.

CONCLUSION

Structured outpatient discharge training for dermatologists is now possible, based on information from detailed doctor- and patient-based qualitative studies.

Chlorine inactivation of fungal spores on cereal grains

Although 0.4% chlorine for 2 min has been recommended for surface disinfection of food samples before direct plating for fungal enumeration, this procedure may not be adequate for highly contaminated products. The effectiveness of a range of chlorine solutions was investigated using barley samples artificially contaminated with four different concentrations of Aspergillus flavus. A. niger, A. ochraceus, Eurotium repens, Penicillium brevicompactum P. chrysogenum and Cladosporium cladosporioides. At initial contamination levels greater than 10(4)/g, 0.4% chlorine did not inactivate sufficient spores to produce less than 20% contamination. Of the test fungi, ascospores of E. repens were the most resistant to chlorine inactivation, whereas the conidia of C. cladosporioides were the most sensitive. Rinsing the samples with 70% ethanol improved the effectiveness of the recommended surface disinfection procedure. However, some ethanol appears to permeate into the grains and may inactivate sensitive internal fungi, although a minimal effect only was observed on wheat infected with Alternaria.