Multiple genetic variants explain measurable variance in type 2 diabetes-related traits in Pakistanis

AIMS/HYPOTHESIS

Multiple genetic variants are associated with type 2 diabetes-related traits in Europeans, but their role in South Asian populations needs further study. We hypothesised that genetic variants associated with diabetes-related traits in Europeans would explain a similar proportion of phenotypic variance in a Pakistani population and could be used in Mendelian randomisation analyses.

METHODS

We used data from 2,131 individuals from the Control of Blood Pressure and Risk Attenuation Trial (COBRA) in Karachi, Pakistan. Individuals were aged 40 years or older.

RESULTS

Combining information from multiple genetic variants showed that fasting glucose, BMI, triacylglycerol, and systolic and diastolic blood pressure variants explained 2.9%, 0.7%, 5.5%, 1.2% and 1.8% of the variance in those traits respectively. Genetic risk scores of fasting glucose, triacylglycerol, BMI, systolic blood pressure and diastolic blood pressure variants were associated with these traits, with per allele SD effects of 0.057 (95% CI 0.041, 0.074), p=3.44 × 10(-12), 0.130 (95% CI 0.105, 0.155), p=2.9 × 10(-21), 0.04 (95% CI 0.014, 0.072), p=0.004, 0.031 (95% CI 0.016, 0.047), p=7.9 × 10(-5), 0.028 (95% CI 0.015, 0.042), p = 5.5 × 10(-5), respectively. These effects are consistent with those observed in Europeans, except that the effect of triacylglycerol variants in South Asians was slightly lower. Mendelian randomisation provided evidence that genetically influenced, raised triacylglycerol levels do not causally affect type 2 diabetes risk to the extent predicted from observational data (p=0.0003 for difference between observed and instrumental variables correlations).

CONCLUSIONS/INTERPRETATION

Genetic variants identified in Europeans are associated with type 2 diabetes-related traits in Pakistanis, with comparable effect sizes. Larger studies are needed to perform adequately powered Mendelian randomisation and help dissect the relationships between type 2 diabetes-related traits in diverse South Asian subgroups.

Virulence markers of Helicobacter pylori in patients with diarrhoea-dominant irritable bowel syndrome

Recent studies suggest that irritable bowel syndrome (IBS) is associated with low-grade inflammation. This study aims to determine the distribution of Helicobacter pylori cytotoxin-associated gene A (cagA) and vacuolating cytotoxin A (vacA) alleles (e.g., s1 and s2) in patients with diarrhoea-dominant IBS (IBS-D) as the latter causes vacuolation in colonic epithelial cells in vitro. One hundred and seventy patients meeting Rome III criteria for IBS-D (mean age: 40 +/- 15 years) were enrolled. Gastric biopsy was assessed histologically and DNA extraction was performed by polymerase chain reaction (PCR) for H. pylori genus 16S ribosomal DNA (16S rDNA), cagA and vacA allele s1 and s2. There was no age- or gender-related difference in H. pylori positivity in IBS-D compared to the control group. H. pylori was positive in 116 (68%) with IBS-D compared to 88 (55%) in the control group (P=0.01). cagA was positive in 73 (63%) with IBS-D compared to 42 (48%) in the control group (P=0.03). vacA s1 was positive in 61 (53%) with IBS-D compared to 32 (36%) in the control group (P=0.02). cagA s1 was positive in 39 (34%) with IBS-D compared to 13 (15%) in the control group (P=0.002).

An FTO variant is associated with Type 2 diabetes in South Asian populations after accounting for body mass index and waist circumference

AIMS

A common variant, rs9939609, in the FTO (fat mass and obesity) gene is associated with adiposity in Europeans, explaining its relationship with diabetes. However, data are inconsistent in South Asians. Our aim was to investigate the association of the FTO rs9939609 variant with obesity, obesity-related traits and Type 2 diabetes in South Asian individuals, and to use meta-analyses to attempt to clarify to what extent BMI influences the association of FTO variants with diabetes in South Asians.

METHODS

We analysed rs9939609 in two studies of Pakistani individuals: 1666 adults aged ≥40 years from the Karachi population-based Control of Blood Pressure and Risk Attenuation (COBRA) study and 2745 individuals of Punjabi ancestry who were part of a Type 2 diabetes case-control study (UK Asian Diabetes Study/Diabetes Genetics in Pakistan; UKADS/DGP). The main outcomes were BMI, waist circumference and diabetes. Regression analyses were performed to determine associations between FTO alleles and outcomes. Summary estimates were combined in a meta-analysis of 8091 South Asian individuals (3919 patients with Type 2 diabetes and 4172 control subjects), including those from two previous studies.

RESULTS

In the 4411 Pakistani individuals from this study, the age-, sex- and diabetes-adjusted association of FTO variant rs9939609 with BMI was 0.45 (95%CI 0.24-0.67) kg/m(2) per A-allele (P=3.0 × 10(-5) ) and with waist circumference was 0.88 (95% CI 0.36-1.41) cm per A-allele (P=0.001). The A-allele (30% frequency) was also significantly associated with Type 2 diabetes [per A-allele odds ratio (95%CI) 1.18 (1.07-1.30); P=0.0009]. A meta-analysis of four South Asian studies with 8091 subjects showed that the FTO A-allele predisposes to Type 2 diabetes [1.22 (95%CI 1.14-1.31); P=1.07 × 10(-8) ] even after adjusting for BMI [1.18 (95%CI 1.10-1.27); P=1.02 × 10(-5) ] or waist circumference [1.18 (95%CI 1.10-1.27); P=3.97 × 10(-5) ].

CONCLUSIONS

The strong association between FTO genotype and BMI and waist circumference in South Asians is similar to that observed in Europeans. In contrast, the strong association of FTO genotype with diabetes is only partly accounted for by BMI.

Respiratory bacterial flora from healthy as well as respiratory symptoms' subjects

Respiratory system is the primary settlement place of opportunistic organisms and considered as chief carrier of common respiratory pathogens. The aim of the study was to know the opportunistic organisms present in the healthy subjects as well as subjects that were suffering from respiratory symptoms. The organisms were identified as per standard bacteriological protocol and pathogenicity tests of the identified organisms were performed in mouse model. Antibiotic sensitivity of the identified organisms was performed. The bacterial flora present in the throat swab of apparently healthy as well as subjects suffering from respiratory symptoms were: Staphylococcus spp. (39.44%) of which Coagulase positive Staphylococcus (21.13%) and Coagulase negative Staphylococcus (18.31%), Klebsiella spp. (19.72%), Pseudomonas spp. (15.49%), Proteus spp. (4.23%), E. coli (9.86%) and Bacillus spp. (11.27%). Among the isolates Staphylococcus, Klebsiella and Pseudomonas were the predominant species. Percentages of identified bacteria were higher in respiratory symptoms exhibiting individuals (53.52%) than apparently healthy individuals (46.48%). All coagulase positive Staphylococcus, Klebsiella spp. and Pseudomonas spp. isolated from respiratory symptoms' subjects were found to be pathogenic. The isolated bacteria were resistant to amoxicillin and ampicillin but sensitive to ciprofloxacin and norfloxacin. Isolated Pseudomonas spp. showed multidrugs resistant properties. The study provided information about the pathogenic organisms' present respiratory systems of apparently healthy as well as subjects suffering from respiratory symptoms. The pathogenic natures of the isolated organisms were determined to make aware of scientists as well as clinicians. Antibiotics sensitivity assays would provide information to the clinicians for the selection of appropriate antibiotics to treat their patients.

Recurrent synovial chondromatosis of the foot

Synovial chondromatosis rarely occurs in the foot. We have diagnosed such a case in National Institute of Cancer Research and Hospital, Mohakhali, Dhaka. The patient came to us with a swelling in the dorsum of left foot. He had a history of operation but one year later swelling reappeared in the same place. Fine Needle Aspiration Cytology (FNAC) of the swelling revealed few atypical cells and diagnosed as a case of malignant neoplasm. Later on surgical intervention was done in the form of wide excision and final histopathology report came as Synovial chondromatosis. No special treatment was given other than periodical follow up. The patient has been responding well. There was no clinical or radiographic evidence of recurrence.

Prevalences of Giardia lamblia and Cryptosporidium parvum infection in adults presenting with chronic diarrhoea

Giardia lamblia and Cryptosporidium parvum are both waterborne pathogens associated with diarrhoea in developing countries. In a recent study based at the Aga Khan University in Karachi, 334 adults aged 16-83 years (178 patients with chronic diarrhoea and 156 diarrhoea-free volunteers who acted as controls) were checked for infection with these parasites, using stool microscopy and/or PCR. Overall, 21 (6.3%) and 29 (8.7%) of the subjects were found positive for G. lamblia by microscopy and PCR, respectively, while the corresponding values for C. parvum were 13 (3.9%) and 14 (4.2%). Although, compared with the diarrhoea-free controls, the patients with diarrhoea were not significantly more likely to be found infected with Giardia, either by microscopy [15 (8.4%) v. six (3.8%); P=0.085] or PCR [19 (10.7%) v. 10 (6.4%); P=0.167], they were significantly more likely to be found infected with C. parvum, both by microscopy [11 (6.2%) v. two (1.3%); P=0.024] and by PCR [12 (6.7%) v. two (1.3%); P=0.014]. The 19 patients found PCR-positive for Giardia comprised 10 (67%) of the 15 found smear-positive for the same parasite but only nine (5%) of the 163 found smear-negative (k=0.545; P<0.001). Similarly, the 12 patients found PCR-positive for Cryptosporidium comprised all 11 (100%) patients found smear-positive for the same parasite but only one (0.6%) of the 167 found smear-negative (k=0.954; P<0.001). Although C. parvum was associated with chronic diarrhoea in the present study, the carriage of G. lamblia often appeared asymptomatic.