Faculty of Biological Sciences

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    Adaptive Responses and Molecular Characterization of Chromium-Resistant Bacteria from Industrially Polluted Environments of Bangladesh
    (2025-12-15) Noimul Hasan Siddiquee
    Background: Industrial effluents released from tannery, dyeing and battery industry contribute largely to heavy metal pollution in both water and soil environments of Bangladesh. Chromium is one of the most problematic metals as it remains in the environment for long time and shows high toxicity, and its mobility increases under acidic conditions, making it risky for ecosystem and human health. Microorganisms subjected to such conditions frequently evolve adaptation methods that facilitate survival under metal stress, rendering them viable instruments for bioremediation. The goal of this study was to find bacteria that can live in or break down heavy metals and then make them more tolerant by passing them through higher and higher levels of heavy metals over and over again. Methods: Heavy metal degrading and tolerant bacteria were isolated from both water and soil samples collected from different industrial polluted areas of Savar, Dhaka. At first, the bacterial species were identified through selective media culture and common biochemical tests, and finally PCR analysis with species specific primers was used to confirm the identification. Potassium dichromate (K2Cr2O7) was used to test tolerance to chromium, the most prevalent heavy metal, in broth dilution and then plate counting. Adaptive evolution was prompted by successive exposure to progressively elevated chromium concentrations. Stress-driven morphological changes were examined by Gram staining, microscopy, and colony morphology was assessed visually on MacConkey agar. Results: Water samples showed a wide pH variation (1.01–7.50), with several sites being highly acidic and non-compliant with environmental standards. A total of 32 bacterial isolates were recovered, with Pseudomonas, Klebsiella, Escherichia coli, Aeromonas, and Acinetobacter as dominant genera. PCR confirmed most of the biochemically identified isolates. Among them, the survival of E. coli and Klebsiella spp. in chromium salt was recorded as high as 1.5 mM. After successive adaptation with increasing Chromium concentration, the MIC increased to 1.75 mM and 1.5 mM for E. coli and Klebsiella, respectively. Colony morphology changed significantly in Klebsiella under chromium stress, while E. coli showed no visible colony-level change. Adapted cells exhibited reduced cell size, irregular morphology, altered cellular arrangement, whitish- centered colony on the MacConkey plate22
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    Comparative Analysis of Antibiotic Resistance in Bacteria From Integrated and Non Integrated Fish Farms in Bangladesh
    (2025-12-15) Masiath Subha
    In Bangladesh,Farmers employ both integrated systems, where fish are raised alongside crops or livestock and non-integrated systems that concentrate solely on fish farming. Despite the potential dangers there is a lack of understanding regarding how antibiotic resistance differs between integrated and non-integrated fish farming systems in Bangladesh.This current study aims to compare bacterial resistance trends in these two types of farming systems, providing insights to encourage safer and more sustainable aquaculture practices.Twenty-four different Thai Pangas samples were collected from four integrated and four non-integrated fish farms across the Noakhali region, Bangladesh.The gut samples from each fish were collected and analyzed using standard microbiological techniques.Bacterial strains were identified through morphological, biochemical, and molecular methods.The isolates were then tested for antibiotic susceptibility against 15 different antibiotics using the Kirby-Bauer disk diffusion method. Furthermore, ESBLs, quinolone and tetracycline resistance genes were identified by using specific primers.Potential resistant isolates were selected and confirmed using 16S rRNA sequencing and phylogenetic analysis.A total of 90 isolates were identified from both integrated and non-integrated farms.The rate of antibiotic resistance was found to be 65% in integrated farms compared to 40 % in non-integrated farms. Among all isolates, E. coli exhibited the highest resistance rate at 22%,followed by Salmonella spp. at 19.50% and Proteus spp. at 15.8% in integrated farms.Conversely, non-integrated farms showed the highest resistance rates in E. coli (10%) and Klebsiella spp. (8%), and Proteus spp. (5%). Furthermore, major resistance genes such as tetA, blaCTX-M ,blaTEM, sul1 and qnr were detected in 47%, 35%, 23%,35% and 29% of isolates from integrated farms, respectively, while the corresponding percentages in non-integrated farms were 25%, 23%, 15% and 17%.In this finding, a greater occurrence of antibiotic resistance was noted in integrated farms than in non-integrated farms. Overall, the results will aid in the development of effective aquaculture practices (EAP) designed to reduce antimicrobial resistance in aquatic environment.
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    Integrative Genomic and Phenotypic Characterization of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae (ESBL-E) and Related Bacterial Species Isolated from Pediatric Diarrheal Cases in Bangladesh.
    (2025-12-15) ASH2305MS111M
    Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) pose a major global threat to antimicrobial therapy, particularly in pediatric populations where diarrheal diseases remain a leading cause of morbidity and mortality. This study provides an integrative genomic–phenotypic assessment of ESBL-producing pathogens isolated from diarrheal stool samples of hospitalized children (<8 years) in Bangladesh. A total of 38 bacterial isolates obtained from 32 samples were identified to the species level using MALDI-TOF MS, with Escherichia coli (47.37%) and Klebsiella pneumoniae (10.53%) being predominant. Whole genome sequencing (WGS) revealed genome sizes ranging from 3.36–6.63 Mb and 3,095– 6,056 annotated coding sequences. Genomic screening using ABRicate across five AMR databases identified ESBL-associated genes in 55.3% (21/38) of isolates. The bla CTX-M-15 gene was the most prevalent variant (76.19%), primarily among E. coli, followed by blaTEM and blaSHV alleles. Phenotypic ESBL detection via CLSI-recommended double-disk synergy testing confirmed ESBL activity in 39.5% of isolates. Genotype–phenotype concordance was 78.95%, with genotype-positive/phenotype-negative mismatches likely linked to silent gene expression, masking by co-produced β-lactamases, or complex resistance mechanisms. Plasmid replicon analysis identified diverse incompatibility groups, including IncF, IncI, IncHI, IncX, IncR, and Col plasmids, supporting the mobility and dissemination of ESBL genes. Virulence profiling showed substantial heterogeneity, with ESBL-positive isolates carrying multiple adhesion, iron acquisition, and stress-response determinants that may enhance pathogenic potential. This study represents one of the first comprehensive genomic–phenotypic investigations of ESBL-producing Enterobacteriaceae in pediatric diarrheal cases in Bangladesh. The predominance of bla CTX-M-15, the complexity of plasmid-mediated gene dissemination, and notable genotype–phenotype discrepancies underscore the need for integrated WGS-based surveillance alongside refined phenotypic diagnostics. These findings offer critical insights for early detection, infection control, and therapeutic decision-making in resource-limited healthcare settings.
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    ISOLATION AND CHARACTERIZATION OF CHROMIUM-TOLERANT BACTERIA FROM POULTRY EXCRETA
    (2025-12-15) TAHZIBUL ISLAM DIHAN
    Chromium (Cr) contamination represents a critical environmental challenge in Bangladesh, largely driven by the integration of tannery byproducts into poultry feed. This study aimed to isolate and characterize chromium- tolerant bacteria from poultry excreta to assess their potential for environmental bioremediation. Initial screening was conducted on Luria-Bertani (LB) agar enriched with 100 mg/L of potassium dichromate (K2Cr2O7). Five high-tolerance strains (ID-01, ID-09, ID-10, ID-11, and ID-14) were selected based on their growth performance across a concentration range of 100–500 mg/L over a 34-h period. The Cr (VI) reduction efficiency of these isolates was subsequently assayed using the 1,5-diphenylcarbazide colorimetric method. Among the isolates, ID-14 exhibited the highest reduction potential, reducing 98.17% of Cr(VI) at 100 mg/L, though efficiency decreased to 48.12% at 500 mg/L concentration. Biochemical characterization and antibiotic susceptibility testing (Kirby–Bauer method) assessed phenotypic traits and potential resistance co-selection, revealing multidrug-resistant phenotypes, notably in isolate ID-14 which exhibited the most extensive resistance profile, including Ampicillin, Levofloxacin, Ceftazidime & Oxacillin etc. Molecular identification of three top-performing isolates was achieved through 16S rRNA gene sequencing, which revealed that ID-11 matched with Proteus mirabilis, ID-10 with Staphylococcus xylosus & ID-09 with Staphylococcus cohnii. However, the most tolerant strain, ID-14, underwent Whole Genome Sequencing (WGS) to map the genetic architecture of its resistance determinants. WGS revealed that the isolate was Staphylococcus ureilyticus. Genomic analysis identified multiple metal resistance determinants, including chromium resistance genes such as chrA and cysk, which encode chromium efflux and reductive mechanisms, respectively. In addition, genomic mapping uncovered diverse antibiotic resistance genes (ARGs), including the fluoroquinolone resistance genes norA, norB, beta-lactam antibiotic resistance genes blaZ, fmtA, macrolide resistance genes mphC & msrA and multidrug resistance genes emrB & sdrM. Overall, these results identify potential indigenous bacterial candidates capable of mitigating heavy metal pollution and provide essential baseline genomic data for bioremediation strategies.
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    Molecular and Phenotypic Characterization of Virulent, Multidrug- Resistant, and Biofilm-Forming Salmonella spp. in Retail Fish
    (2025-12-15) NFH2305MS107F
    Fish is a widely consumed protein source in Bangladesh, yet retail markets often operate without adequate microbiological monitoring, increasing the risk of foodborne infections. Salmonella spp., a major zoonotic pathogen, is frequently associated with aquatic environments and poses a significant public health threat, particularly when antimicrobial resistance (AMR) and virulence factors converge. A total of 100 fish samples from six major retail markets in Noakhali, Bangladesh, were examined for the presence of Salmonella. Presumptive isolates were identified based on cultural and biochemical characteristics, followed by molecular confirmation using PCR targeting invA. Virulence genes (hilA, fimA), antimicrobial susceptibility against 14 antibiotics, AMR genes (blaTEM-1, blaCTX-M-1, tetA, sul1), and biofilm-forming ability were also assessed to evaluate pathogenic and resistance profiles. Among 145 presumptive isolates, 24 (16.55%) were confirmed as Salmonella spp. All 24 isolates carried the invA gene, while 95.8% and 79.2% possessed hilA and fimA, respectively, indicating substantial virulence potential. Antibiogram profiling revealed multidrug resistance, including complete resistance to ceftazidime (100%) and high resistance to ampicillin (75%) and levofloxacin (50%). PCR detection showed universal carriage of blaTEM-1 (100%), along with blaCTX-M-1 (50%), tetA (29.2%), and sul1 (29.2%). Biofilm assays demonstrated diverse adherence capacities, with several isolates classified as strong biofilm formers, suggesting enhanced environmental persistence and increased risk of cross-contamination. The identification of virulent, multidrug-resistant, and biofilm-forming Salmonella spp. in retail fish markets highlights significant risks to public health and food safety in Bangladesh. The coexistence of virulence genes, AMR determinants, and biofilm-forming capacity underscores the urgent need for improved hygiene practices, regulated antibiotic use in aquaculture, and enhanced surveillance of foodborne pathogens. Although serotyping and whole genome sequencing (WGS) could not be performed due to limited funding and time constraints, these advanced analyses are planned for future work to better understand the genetic diversity and epidemiology of circulating strains.
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    Molecular Characterization, Antimicrobial Resistance, Biofilm Formation, and Whole-Genome Sequencing of Vibrio spp. Isolated from Shrimp in Noakhali, Bangladesh
    (2025-12-15) Sajedul Islam
    Shrimp aquaculture is a vital economic sector in Bangladesh. Vibrio species are common foodborne pathogens that cause gastrointestinal tract inflammation. Multidrug resistance (MDR) in Vibrio spp. is a major health concern, especially in aquaculture and food chain. This research examined the prevalence, antimicrobial resistance (AMR), virulence characteristics, and biofilm- forming ability of Vibrio species in different retail shrimp samples from Noakhali, Bangladesh. A total of 241 shrimp samples were collected and studied through culture, molecular and whole- genome sequencing. Vibrio species were identified in 43.6% of samples, with 29.5% V. parahaemolyticus and 14.1% V. cholerae. Alarmingly, 70.5% of Vibrio isolates were multidrug- resistant (MDR) including significant resistance to ampicillin (88.6%), meropenem (81.9%), cefotaxime (71.4%), and ceftazidime (61.0%). Genotypic screening suggested the presence of ESBL genes bla-TEM (29.5%) and bla-SHV (10.6%). Biofilm production was positive in 62.9% of isolates, exhibiting interlink between biofilm strength and multidrug resistance. Virulence gene profiling demonstrated that all V. cholerae contain hlyA El Tor gene and tlh was prevalent in V. parahaemolyticus. Whole-genome sequencing of two severe MDR V. parahaemolyticus isolates identified a comprehensive array of antibiotic resistance genes, virulence factors, and genetic determinants associated with biofilm formation. These results underscore the intersection of pathogenicity, antibiotic resistance, and biofilm development in Vibrio species throughout the shrimp supply chain, constituting a significant public health issue. The study demonstrates the necessity for improved antimicrobial control, elevated hygiene standards, and ongoing surveillance to reduce public health hazards linked to contaminated seafood in Bangladesh.
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    Molecular Profiling of Hydrocarbon Degrading Microbial Communities of Petroleum Contaminated Soil in Noakhali Region, Bangladesh
    (2025-12-15) ASH2305MS106M
    Petroleum hydrocarbon contamination represents a persistent environmental challenge due to its ecological toxicity and long-term impacts on soil health and microbial communities. Despite increasing vulnerability to petroleum pollution in Bangladesh, particularly in coastal and transport- linked regions, the microbial ecology of contaminated soils in Noakhali remains poorly understood. This study investigated the diversity, functional potential, and antimicrobial resistance profiles of indigenous microbial communities inhabiting petroleum-contaminated soils from selected filling stations in Noakhali, Bangladesh, using an integrated culture-dependent and 16S rRNA gene-based metagenomics approach. Selective enrichment using Mineral Salt Medium supplemented with diesel resulted in the isolation of 33 potential hydrocarbon-degrading bacterial strains. Morphological, Gram-staining, and biochemical characterization identified Pseudomonas spp. as the dominant genus, including Pseudomonas aeruginosa, alongside Klebsiella, Acinetobacter, Enterobacter, Hafnia, Bacillus, Staphylococcus, Micrococcus, and Streptococcus species. Functional screening revealed strong lipase and biosurfactant production by Pseudomonas aeruginosa. Antimicrobial susceptibility testing demonstrated site-specific resistance patterns, with the highest resistance observed at Sonapur Filling Station, suggesting localized anthropogenic pressure. High-throughput sequencing of the 16S rRNA gene identified 172 unique Amplicon Sequence Variants (ASVs). Alpha diversity analyses revealed the highest microbial richness at Alexander Filling Station (AFS). Taxonomic analysis revealed that the microbial communities were predominantly composed of Bacteroidota and Proteobacteria, with notable representation of hydrocarbon-degrading lineages such as Pseudomonas, Rhodococcus, and Acinetobacter, while Prevotella and Pseudomonas emerged as the most abundant genera. Predicted functional profiling indicated enrichment of key metabolic pathways and genes involved in alkane and aromatic hydrocarbon degradation, nitrogen and sulfur cycling, and antibiotic resistance, with AFS exhibiting the highest hydrocarbon-degrading potential. This study provides the first comprehensive molecular insight into petroleum-contaminated soils of Noakhali and underscores the ecological significance of indigenous microbial communities for site-specific, sustainable bioremediation strategies in Bangladesh.
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    Whole Genome and Phenotypic Approaches to Study Vibrio cholerae Pathogenicity and Survival Mechanisms
    (2025-12-15) BFH2305MS102F
    ii Abstract Despite Vibrio cholerae causing epidemic and pandemic cholera has been well-established in brackish water environments, the aquatic reservoir is often debated because the bacterium is rarely, if ever, isolated from surface water by culturing methods. Non-culturable state has been proposed as a survival strategy for V. cholerae wherein it can change shape from curved rod to coccoid, as detected by Direct Fluorescent Antibody (DFA) assay. Recent studies showed V. cholerae O1 cells in the aquatic habitat, persisting mostly as coccoid cells in clusters of biofilms comprising non-culturable cells that can regain culturalabity upon animal challenge to initiate seasonal cholera. In this study, we have attempted to isolate and detect the bacterium from water samples collected fortnightly from household ponds and nearby canals in the coastal area of Noakhali, Bangladesh. Serotyping and molecular approaches were employed to identify V. cholerae O1. Polymerase Chain Reaction (PCR) was employed to detect the virulence- specific genes and Multilocus Sequence Typing (MLST) of the bacterium. Whole Genome Sequencing (WGS) was performed for further characterization of the isolated V. cholerae strains. In addition, a laboratory microcosm was constructed to observe the impact of temperature on growth response of the bacterium. Of 11 V. cholerae isolated from water samples collected during May - October, 2024, nine proved positive for serogroup O1, as they carried specific genes: ompW, rfbO1, tcpA, toxR, viuB, but, all were non-toxigenic having no ctxA encoding cholera toxin subunit A. Two isolates were non-O1/non-O139 having ompW only. Furthermore, MLST analysis confirmed these nine V. cholerae O1 as sequence type 69 (ST-69), whereas the two non-O1/non-O139 as ST-982. WGS data showed the presence of pathogenicity and related genes, including acfA, acfB, acfC, acfD, hlyA, makA, nanH, tagA, toxR, vasX, tcp etc., but lacked the CTX prophage. Some of these isolates also had multiple antimicrobial resistance genes for ampicillin, ceftazidime, and sulfamethoxazole suggesting multidrug resistance. Biofilm assays revealed that V. cholerae O1 isolates having all biofilm genes (including mshABCDEFGHIJKMN, omp U) failed to form a typical biofilm ring on a borosilicate glass tube, suggesting additional regulatory or structural factors that may influence the biofilm development. V. cholerae non-O1/non-O139 isolates lacked the key biofilm genes mshD and ompU and displayed no ring formation. Microcosm study revealed that at 37ºC, V. cholerae O1 grew actively isolates grew actively up to 49 days, whereas non O1/ non O139 strains became non-culturable after 35 days. In Microcosm at 4ºC, O1 cells failed to retain active growth state after 7 days, whereas the non-O1/non-O139 were active until 14 days. The overall results presented in this study might reflect the pathogenicity status, aquatic reservoir and possible transition from toxigenic to non-toxigenic strains, including the growth response and mechanism of the survival of V. cholerae O1 in the aquatic environment of the coastal areas of Noakhali, Bangladesh.