Resistance-guided isolation and characterization of antibiotic-producing bacteria from river sediments.

BACKGROUND: To tackle the problem of antibiotic resistance, an extensive search for novel antibiotics is one of the top research priorities. Around 60% of the antibiotics used today were obtained from the genus Streptomyces. The river sediments of Bangladesh are still an unexplored source for antibiotic-producing bacteria (APB). This study aimed to isolate novel APB from Padma and Kapotakkho river sediments having the potential to produce antibacterial compounds with known scaffolds by manipulating their self-protection mechanisms. RESULTS: The antibiotic supplemented starch-casein-nitrate agar (SCNA) media were used to isolate antibiotic-resistant APB from the river sediments. The colonies having Streptomyces-like morphology were selectively purified and their antagonistic activity was screened against a range of test bacteria using the cross-streaking method. A notable decrease of the colony-forming units (CFUs) in the antibiotic supplemented SCNA plates compared to control plates (where added antibiotics were absent) was observed. A total of three azithromycin resistant (AZR) and nine meropenem resistant (MPR) isolates were purified and their antagonistic activity was investigated against a series of test bacteria including Shigella brodie, Escherichia coli, Pseudomonas sp., Proteus sp., Staphylococcus aureus, and Bacillus cereus. All the AZR isolates and all but two MPR isolates exhibited moderate to high broad-spectrum activity. Among the isolates, 16S rDNA sequencing of NAr5 and NAr6 were performed to identify them up to species level. The analyses of the sequences revealed that both belong to the genus Streptomyces. CONCLUSIONS: The results from these studies suggest that manipulation of the self-resistance property of APB is an easy and quick method to search for novel APB having the potential to produce potentially novel antibacterial compounds with known scaffolds.

Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine.

Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a D-alanine-D-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to D-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and D-cycloserine binding pockets of Ddl.

A hospital-based study on complementary and alternative medicine use among diabetes patients in Rajshahi, Bangladesh.

BACKGROUND: The use of complementary and alternative medicine (CAM) among type 2 diabetes mellitus (T2DM) patients is increasing worldwide. It can affect optimum glycemic management. This study was to determine the rate and influencing factors of CAM use among diabetes patients as well as their effect on glycemic control. METHODS: This cross-sectional study was conducted among T2DM patients attending the outpatient department of Rajshahi Medical College Hospital. It is a tertiary hospital in the northern part of Bangladesh. A face-to-face interview with a pretested structured questionnaire was used for data collection. Chi-square (χ2) test and multivariate logistic regression model were used in this study for data analysis. RESULTS: Out of 244 T2DM patients, 86 (35.2%) used CAM. Multivariate logistic regression model showed that lower family income group (AOR = 8.7, 95% CI: 2.15-35.22, p-value 0.002), having no institutional education (AOR = 3.4, 95% CI: 1.17-9.87, p-value 0.025) and having diabetes for more than five years (AOR = 2.821, 95% CI: 1.34-5.94, p-value 0.006) were the most influential predictors of CAM use. The most commonly used CAMs were herbal products (67.4%) and homeopathic medicine (37.2%). Most of the CAM users (72%) were influenced by friends, neighbors, and family members. The most common reasons behind CAM use were reported to be the belief that CAM helped control diabetes better (44.2%) and easy availability and lower cost (27.9%). More than half of the users reported the efficacy of CAM as 'nothing significant', while others reported as somewhat good. 14% of CAM users experienced side-effects, especially gastrointestinal upset. It was observed that using CAM was associated with poor glycemic control (AOR = 2.25, 95% CI: 1.14-4.44, p-value 0.018). CONCLUSION: Our study demonstrated that some modifiable factors are associated with the use of CAM, and it cannot maintain good glycemic control. So, patients should be made aware of the ineffectiveness and bad effects of CAM by enhancing educational and poverty-alleviating programs.

The Transposon Registry.

Transposable elements in prokaryotes are found in many forms and therefore a robust nomenclature system is needed in order to allow researchers to describe and search for them in publications and databases. Here we provide an update on The Transposon Registry which allocates numbers to any prokaryotic transposable element. Additionally, we present the completion of registry records for all transposons assigned Tn numbers from Tn1 onwards where sequence data or publications exist.

Detection of Novel Integrons in the Metagenome of Human Saliva.

Integrons are genetic elements capable of capturing and expressing open reading frames (ORFs) embedded within gene cassettes. They are involved in the dissemination of antibiotic resistance genes (ARGs) in clinically important pathogens. Although the ARGs are common in the oral cavity the association of integrons and antibiotic resistance has not been reported there. In this work, a PCR-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral metagenomic DNA obtained from both the UK and Bangladesh. We identified a diverse array of gene cassettes containing ORFs predicted to confer antimicrobial resistance and other adaptive traits. The predicted proteins include a putative streptogramin A O-acetyltransferase, a bleomycin binding protein, cof-like hydrolase, competence and motility related proteins. This is the first study detecting integron gene cassettes directly from oral metagenomic DNA samples. The predicted proteins are likely to carry out a multitude of functions; however, the function of the majority is yet unknown.

ELISA with recombinant rKRP42 antigen using urine samples: a tool for predicting clinical visceral leishmaniasis cases and its outbreak.

We reported a highly sensitive and specific enzyme-linked immunosorbent assay (ELISA) that detects immunoglobulin G (IgG) in urine using rKRP42 antigen for the diagnosis of visceral leishmaniasis (VL). The ELISA was applied to study chronological change in antibody titers in five study areas in Rajshahi district, Bangladesh. A total of 585 subjects without a past VL history were examined at least three times in the 30-month follow-up period; of these subjects, 137 (23.4%) subjects became ELISA-positive at least one time during the study. Among the positive cases, 40 (29.2%) subjects developed clinical VL, and 31 (77.5%) of these subjects showed IgG titers of ≥ 1,000 U more than one time in the study period. Considering only the first ELISA results, 22 subjects with IgG titers of ≥ 1,000 U could be found, and 21 (95.5%) of these subjects turned out to be clinical cases. The high urinary IgG titers (≥ 1,000 U) will help predict possible clinical VL cases and thus, identify an outbreak in its earlier stage.

Antibacterial activities of actinomycete isolates collected from soils of rajshahi, bangladesh.

This study was performed to isolate actinomycete colonies having antibacterial activity from soil samples collected from different places around Rajshahi, Bangladesh. Thirty actinomycete colonies were isolated in pure culture from five soil samples using Starch-casein-nitrate-agar medium. The isolates were grouped in five color series based on their aerial mycelia color and screened for their antibacterial activity against a range of test bacteria. Sixteen isolates (53.3%) were found to have moderate to high activity against four gram-positive and four gram-negative bacteria. Since many isolates showed inhibitory activity against indicator bacteria, it is suggestive that Bangladeshi soil could be an interesting source to explore for antibacterial secondary metabolites.