Department of Microbiology

Prevalence of Legionella spp. in various natural and processed water systems in Bangladesh and the development of an effective detection method

2026-08-04T00:00:00Z

Prevalence of Legionella spp. in various natural and processed water systems in Bangladesh and the development of an effective detection method Naher, Nazmun This thesis is submitted for the degree of Doctor of Philosophy

Occurrence and characterization of pathogenic bacteria producing β-lactamase in biomedical waste water from hospitals in Dhaka city

2026-08-03T00:00:00Z

Occurrence and characterization of pathogenic bacteria producing β-lactamase in biomedical waste water from hospitals in Dhaka city Mannan, Sultana Juhara Antimicrobial resistance (AMR), particularly among Gram-negative pathogens, presents a serious risk to environmental safety and public health worldwide. Hospitals are recognized as primary contributors to this crisis due to their release of high loads of antibiotics and resistant pathogens into waste water systems. This study focused on the detection, characterization, resistance pattern, and genomic analysis of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Escherichia. coli and Pseudomonas aeruginosa obtained from biomedical waste water collected from several major hospitals in Dhaka City, Bangladesh. A total of 300 waste water samples were collected from hospital effluents and analyzed through standard microbiological, phenotypic, and molecular techniques. Out of 184 isolates, 42.7% (n=38) were E. coli, 25.9% (n=23) were Acinetobacter baumannii, 25.9% (n=23) were P. aeruginosa and 5.6% (n=5) were Enterobacter cloacae. Antibiotic susceptibility testing revealed that E. coli and P. aeruginosa exhibited multidrug resistance (MDR), with notably high resistance rates against ampicillin, cefuroxime and ceftriaxone. Alarming resistance to meropenem, a last-line antibiotic, was also observed. Phenotypic confirmation of ESBL production using double-disc synergy method showed that 48.4% (n = 89) isolates were ESBL-positive. Carbapenemase activity was confirmed in isolates resistant to carbapenems. Multiplex polymerase chain reaction (PCR) indicated the existence of several key resistance genes: blaCTX-M (60%), blaTEM (48%), blaSHV (45%), and carbapenemase genes including blaNDM-1 (26%), blaOXA (22%), and blaKPC (18%). Plasmid profiling confirmed that many of these genes were plasmid-borne, indicating the likelihood of horizontal gene transfer across bacterial species in the waste water environment. In addition to phenotypic and molecular characterization, in silico docking analysis was employed to assess the binding affinities of clinically important β-lactam antibiotics (cefuroxime, ceftriaxone, and meropenem) against selected β-lactamase enzymes. Results indicated moderate binding affinities, with cefuroxime and ceftriaxone showing docking scores of –7.1 kcal/mol and –8.2 kcal/mol, respectively, against CTX-M-type enzymes. Modified derivatives with specific functional groups demonstrated enhanced binding, with docking energies improving up to –8.9 kcal/mol, suggesting that structural modification could potentially improve drug efficacy against resistant strains. Whole genome sequencing (WGS) of selected MDR isolates revealed comprehensive resistomes containing not only ESBL and carbapenemase genes but also multiple virulence Abstract 2 factors and transferable genetic materials, such as integrons and transposons. Several isolates contained co-localized resistance determinants, including blaCTX-M-15, blaNDM-1, and sul1 on the same plasmid structures, reinforcing the threat of horizontal gene transfer. A comparative analysis between isolates from hospital effluents and other urban water sources revealed significant genomic similarity, confirming the environmental spread of antimicrobial resistance genes (ARGs). The present study provides molecular insights into the structure-function relationship of antibiotics and β-lactamases, contributing to the larger field of drug redesign through computational approaches. Additionally, the findings emphasize the critical role that hospital waste water plays in the spread of multidrug-resistant bacteria and the pressing need for better waste management practices in densely populated urban centers. This integrated study—combining environmental microbiology, molecular diagnostics, bioinformatics, and structural biology—advances our understanding of the AMR burden in biomedical waste and presents a multidimensional strategy for surveillance, mitigation, and future therapeutic development. The outcomes emphasize the importance of adopting One Health frameworks and implementing robust environmental monitoring systems to address the escalating AMR threat at the human–environment interface. This thesis is submitted for the degree of Doctor of Philosophy.

Identification and Characterization of Microbial Signatures and Potential Biomarkers for Irritable Bowel Syndrome in Bangladesh

2026-08-03T00:00:00Z

Identification and Characterization of Microbial Signatures and Potential Biomarkers for Irritable Bowel Syndrome in Bangladesh Shakil, Md. Shahriar Kabir Introduction: Irritable Bowel Syndrome (IBS) is a functional gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, metagenomic studies integrating taxonomic, functional, resistome, virulome, and genome-resolved analyses in Bangladeshi IBS patients are limited. This study applied whole-metagenome sequencing (WMS), comparative genomics, and machine-learning (ML) approaches to characterize gut microbiome alterations in IBS patients relative to healthy controls (HC). Materials and Methods: A total of thirty (n=30) stool samples were collected from IBS-diagnosed patients (n=20) and HC (n=10) at the National Gastroliver Institute & Hospital, Mohakhali, Dhaka, Bangladesh. Of these, based on the quality and concentration of extracted total genomic DNA, ten IBS samples (n=10) and six HC samples (n=6) were selected for WMS. Sequencing was performed using the Illumina Next Generation Sequencing (MiSeq 4000) platform. The raw FASTQ sequences were subjected to quality control using the Trimmomatic tool. Downstream analyses were performed using two complementary pipelines: the Chan Zuckerberg ID (CZID, formerly IDseq) for host filtering, taxonomic profiling, diversity metrics, and assembly, as well as the Kraken2-based workflow for antimicrobial resistance (AMR) and virulence factor genes detection. Metagenome Assembled Genomes (MAGs) were reconstructed using MEGAHIT, MetaBAT2, and MaxBin2. Comparative global analysis involved a total of 1,109 samples (HC=492; IBS=617), comprising 1,093 publicly available gut metagenomes from across all continents, along with the Bangladeshi samples (n=16). ML models were trained on combined global and local taxonomic datasets after normalization, feature selection, and hyperparameter optimization. Results: IBS patients exhibited clear dysbiosis in their gut microbiome characterized by a marked reduction of Actinobacteria, especially Bifidobacterium spp., and increased abundance of Firmicutes and pathobionts such as Klebsiella pneumoniae, Enterobacter cloacae, and Sutterella wadsworthensis. Notably, multiple Bifidobacterium species, including B. breve, B. bifidum, B. catenulatum, B. pseudocatenulatum and B. longum subspecies, were significantly enriched in the HC samples compared to IBS patients. AMR profiling revealed a relatively higher prevalence of tetracycline, macrolide, and β-lactam resistance genes in IBS samples. MAG analysis recovered 392 genomes, with IBS-derived MAGs harboring more AMR and virulence genes. Comparative Page | ii analysis of global datasets, including Bangladeshi samples, revealed significantly lower alpha diversity in IBS patients supported with Chao1 (p-value: 2.6226e-05), ACE (p-value: 1.8209e-05), and Observed (p-value: 3.0546e-05) indices, indicating higher species richness in HC. Beta diversity analysis showed clear and distinct clustering of IBS and HC samples, reflecting significant differences in overall community composition. LEfSe analysis (LDA score > 2.5, p < 0.05, FDR-adjusted) identified distinct microbial signatures between IBS patients and HC groups, with healthy individuals enriched in Bacteroides spp. (B. stercoris, B. uniformis) and Bifidobacterium catenulatum. In contrast, IBS patients showed increased abundances of Klebsiella, Roseburia, Faecalibacterium, and uniquely associated taxa including Collinsella aerofaciens, Klebsiella pneumoniae, Streptococcus salivarius, and Clostridium spp. Among the developed ML models, Logistic Regression demonstrated superior IBS prediction performance with an accuracy of 0.80 (ROC-AUC 0.88). Conclusion: This multilayered metagenomic investigation revealed substantial microbial, functional, and genomic disruptions in Bangladeshi IBS patients, consistent with patterns observed in global datasets. The findings underscore the potential of microbiome-based ML models in early diagnosis and targeted therapeutics for IBS. Nevertheless, further studies with larger, multi-center, and longitudinal cohorts are warranted to validate these findings and resolve population- and subtype-specific microbiome signatures in IBS. This thesis is submitted for the degree of Doctor of Philosophy.

Insecticidal activity of indigenous Bacillus thuringiensis strains against Tephritids fruit fly pests affecting fruits and vegetables

2026-04-19T00:00:00Z

Insecticidal activity of indigenous Bacillus thuringiensis strains against Tephritids fruit fly pests affecting fruits and vegetables Bari, Md. Abdul The extensive and indiscriminate use of synthetic chemical insecticides in agriculture and forestry has led to several unintended and detrimental consequences, including environmental pollution, the development of pest resistance, the mortality of non-target organisms, and negative public health effects. These challenges are particularly pronounced in developing countries like Bangladesh, where pest infestations significantly reduce crop productivity and economic gains. As a sustainable and environmentally safer alternative, microbial biopesticides, particularly those derived from Bacillus thuringiensis (Bt), have emerged as a promising solution. Bt-based biopesticides are host-specific, biodegradable, and effective, offering significant potential to reduce chemical pesticide dependency. This study aimed to evaluate insecticidal activity of previously isolated, characterized and preserved indigenous Bacillus thuringiensis (Bt) strains from different eco-regions of Bangladesh against four economically important Tephritid fruit fly pests, Bactrocera dorsalis, B. zonata, Zeugodacus cucurbitae and Z. tau. These pests are known to cause extensive damage to fruits and vegetables, impacting local consumption, export opportunities, and national food security. A total of 44 Bt strains were isolated, identified, and screened through a comprehensive suite of phenotypic, genetic, proteomic, and toxicity analyses. The overarching goal was to identify highly potent Bt strains and validate their effectiveness under both laboratory and field conditions. Initial screening of the 44 native Bt isolates showed that 16 strains could induce greater than 50% and three potential strains JSd1, SaS6, and JDc1 exceeded 80% larval mortality in all four Tephritid species tested. Bt strain JSd1 consistently demonstrated the highest efficacy, inducing 97% mortality in B. dorsalis, 95% in B. zonata, 95% in Z. cucurbitae, and 92% in Z. tau, outperforming even the reference Btk HD-73 and Bts T84A1. Further toxicological analyses, including lethal concentrations (LC₅₀) and lethal time (LT₅₀) values, confirmed JSd1’s superior performance. LC₅₀ values ranged from 0.431 to 0.472 mg/ml and LT₅₀ values ranged between 54.09 and 55.17 hours, which are significantly lower than other strains, indicating high potency at reduced concentrations, while faster action and quicker pest knockdown. Beyond bioassays, the study also evaluated the biological quality parameters of insects exposed to Bt treatment infested with preferred hosts, which are critical in understanding sub-lethal effects and potential population suppression in pest communities. Bt JSd1, SaS6, and JDc1 significantly reduced pupal yield, pupal weight, adult emergence percentage, and flying ability iii across all four Tephritid species. For instance, Bt JSd1-treated groups consistently demonstrated the lowest pupal yield (as low as 99 ± 2.081 in Z. tau), lowest pupal weight (~8 mg), and lowest adult emergence (ranging from 39–53%). Emergence of malformed or half-emerged adults was also significantly higher in treated groups, while sex ratio distortion was minimal, suggesting that these strains primarily impacted general viability rather than sex-linked mortality. These results indicate a substantial decline in the reproductive and survival potential of these pest populations upon exposure to Bt biopesticides, making them highly effective components in Integrated Pest Management (IPM) strategies. To understand the genetic basis of its high efficacy, whole genome sequencing of Bt JSd1 was conducted. Genomic analysis revealed the presence of multiple Cry and Vip insecticidal genes, notably Cry22A and Vip3A, which are known for their effectiveness against Dipteran insects. Additionally, several virulence factors and biosynthetic gene clusters associated with secondary metabolite production were identified, contributing to the strain’s broad-spectrum insecticidal capability and environmental adaptability. This genetic richness further reinforces the potential of Bt JSd1 as a candidate for next-generation bioinsecticide development. Finally, field validation was carried out using the formulated Bt biopesticide (compared with chemical pesticides) on Solanum melongena (brinjal), a crop heavily impacted by the Eggplant Fruit and Shoot Borer (EFSB. Four-time foliar applications (Each of 100 ml volume containing 25.7 mg spore crystal mixture) of the Bt preparation reduced EFSB infestation to just 10%, compared to significantly higher levels in untreated controls, with no significant difference with the chemical pesticide. The average yield per plant increased from 1.45 kg (control) to 3.85 kg in the treated group, effectively matching or surpassing yields from chemically treated plots. Importantly, there were no observed negative impacts on beneficial insect populations or surrounding flora, highlighting the ecological safety of the product. Overall, this study provides compelling evidence for the viability and impact of indigenous Bt strains, particularly JSd1, as potent, safe, and affordable biocontrol agents, offering a sustainable solution to the challenges of chemical pesticide overuse, contributing to improved agricultural productivity, ecological health, and food security. Their local origin also enables domestic production and reduces reliance on imported formulations, supporting national bioeconomy goals. This thesis is submitted for the degree of Doctor of Philosophy.