Thesis (Bachelor of Science in Microbiology)
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Item A bacteriological study of public bus and bus stop surfaces in Dhaka: identifying GLASS pathogens and analyzing their antibiotic resistance pattern(BRAC University, 2026-01) Rahman, Britney; leen, Isha; Anwar, Mahmuda; Mokaddas, Mohosina; Haque, Fahim Kabir MonjurulDue to overcrowding, humid environment and unsanitary conditions, public buses of Dhaka city can be a probable reservoir for pathogenic and antimicrobial resistant bacteria. This study focuses on identifying the Global Antimicrobial Resistance and Use Surveillance System (GLASS) guidelines’ priority bacteria in common touch surfaces of buses and bus stops, and providing a proper insight on the antimicrobial resistance (AMR) pattern of these bacteria. Samples collected from seats, grab rails and bus stops were spread on different selective media. Based on colony morphology bacteria were presumptively selected, then polymerase chain reaction (PCR) was performed. Upon identification of target bacteria, the analysis of their AMR pattern was done using Kirby-Bauer disc diffusion method. Among the 30 samples, 60.0% were positive for Klebsiella pneumoniae, 36.7% for Vibrio species, 33.3% for Acinetobacter baumannii, 20% for Staphylococcus epidermidis, 16.7% for Enterococcus spp. and/or P. aeruginosa, and 10.0% for Staphylococcus aureus and/or Salmonella species. Samples taken from cloth surfaces had the highest bacterial count, while acrylic paint and steel surfaces had a relatively lower count. Among the nine bacteria, all bacteria except for A. baumannii, Salmonella species and P. aeruginosa showed an alarmingly high level of multidrug-resistance, with K. pneumoniae showing the highest resistance, 95%. The detection of multidrug-resistant bacteria in public buses, emphasise these transportation as being an important reservoir for clinically significant pathogens and the dissemination of antimicrobial resistance genes to the environmental microbiome. The findings of this study call for an urgent need for improving the overall conditions of buses and ensuring proper cleaning practices in public transports.Item A comparative analysis of expanded quantitative urine culture and standard urine culture methods in patients with urinary tract infections(BRAC University, 2026-01) Srabony, Tajri Hasan; Kunder, Stella Bijoyee; Shafi, K M Abdullah Hel; Deen, Nadia SultanaUrinary tract infections (UTI) are one of the most common bacterial infections of humans. Accurate diagnosis of the cause of UTI is necessary for effective treatment. Even though clinically Standard Urine Culture (SUC) is common for detecting bacterial presence in urine samples, latest reports show that Expanded Quantitative Urine Culture (EQUC) provides better diagnostic sensitivity compared to SUC. To test this, SUC and EQUC methods were compared to analyse bacterial load and diversity using urine samples collected from 20 patients with UTI symptoms and 20 healthy controls in this study. Samples were diluted and inoculated on nutrient agar, HiChrome UTI agar, MacConkey agar and blood agar for SUC method, then incubated at 37°C for 24 hours under aerobic conditions. On the other hand, for EQUC, in addition to all the media, chocolate agar was used with different conditions like carbon-enriched, anaerobic environment with incubation at 37°C for 48 hours. Colony characteristics and polymerase chain reaction (PCR) were performed for bacterial detection. Antibiotic susceptibility test was conducted by the Kirby-Baur method. On nutrient agar medium, EQUC yielded 5-fold higher bacteria than SUC and portrayed higher bacterial diversity. While several bacterial species for example, klebsiella spp., Staphylococcus aureus, and Pseudomonas aeruginosa was detected by SUC and EQUC based on colony characteristics, EQUC exclusively detected the presence of Staphylococcus haemolyticus. Seventy-five percent of presumptive Klebsiella and 73.3% of presumptive E. coli were confirmed by PCR. AST was performed on E. coli and Klebsiella. Notably, bacteria grown via EQUC showed a diverse resistance pattern compared to SUC. Further molecular diagnoses will be performed to validate these findings.Item Detection and antimicrobial resistance profiling of nosocomial bacterial pathogens in two tertiary care hospitals of Dhaka, Bangladesh(BRAC University, 2026-02) Rahman, Arifa; Palma, Delcy Margarate; Pratyasha, Tahrim Hossain; Monjurul Haque, Fahim KabirNosocomial infections remain a significant global health burden, posing persistent challenges in hospital settings, including in Bangladesh. Prompt identification of causative agents and appropriate antimicrobial therapy are essential, as delayed or inadequate treatment increases patient morbidity and mortality. This study investigated the prevalence and antimicrobial resistance patterns of most ESKAPE pathogens- Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, —excluding Enterococcus faecium and Enterobacter species, known for high virulence and multidrug resistance in hospital-acquired infections worldwide. However, Escherichia coli was included in this study as it was one of the most prevalent bacteria found in the hospital environment. Environmental swabs were collected from high-touch surfaces, including bed rails, bed sheets, nursing tables, and saline stands, across ICU, NICU, and children’s wards of two tertiary hospitals in Dhaka. Samples were serially diluted, cultured on selective media, and presumptively identified by colony morphology, with confirmation via polymerase chain reaction (PCR) and gel electrophoresis. Antimicrobial susceptibility was assessed using the Kirby–Bauer disc diffusion method. From 22 samples, Klebsiella pneumoniae was most prevalent (36.6%), followed by Staphylococcus spp. and Escherichia coli (18.18%). Acinetobacter baumannii (13.64%), and Pseudomonas aeruginosa (9.1%) with the lowest amount of prevalence. High resistance was noted against Beta-lactams (41.18% – 64.71%) and macrolides (47.06%), while lower resistance was found against carbopenem. MDR rates were highest in Staphylococcus species and Escherichia coli (100%), followed by Klebsiella pneumoniae (75%), Pseudomonas aeruginosa (50%), and Acinetobacter baumannii (33.3%). These findings underscore the urgent need for continuous surveillance, stringent infection control, and rational antibiotic use to mitigate multidrug-resistant pathogens in hospital environments.Item Analysis of antimicrobial resistance in acinetobacter baumannii and klebsiella pneumoniae from patients with wound infections(BRAC University, 2025-12) Farid, Tanzim Bin; Haque, Fahim Kabir MonjurulThis study assessed the antimicrobial resistance profiles, key resistance genes, and hemolytic phenotypes of the organisms Acinetobacter baumannii and Klebsiella pneumoniae isolated from 61 pre-surgical traumatic leg wound samples in Dhaka. Of the specimens, 34 (55.7%) yielded target organisms: 15 A. baumannii and 19 K. pneumoniae. Both species demonstrated extremely high multidrug non-susceptibility across all tested antibiotic classes, with A. baumannii showing complete resistance to several agents. Colistin and Tigecycline remained the only antibiotics with comparatively lower resistance. All isolates exhibited γ-hemolysis, indicating the absence of RBC lysis. Molecular testing confirmed the presence of class 1 and class 2 integron integrase genes in A. baumannii, supporting the observed co-resistance patterns. These findings underscore a severe local resistance burden that compromises empiric therapy, highlight the need for routine culture-guided management, and emphasize the importance of strengthened antimicrobial stewardship and infection-control measures in trauma care settings.Item Assessment of airborne bacterial pathogens and antimicrobial resistance in selected urban areas of Dhaka city(BRAC University, 2025-12) Sami, Md. Kawser Bhuiyan; Haque, Fahim Kabir MonjurulAirborne microorganisms in urban environments pose a substantial but often neglected public health risk, particularly in densely populated cities such as Dhaka, where intense human activity, traffic congestion, and inadequate environmental controls can facilitate the spread of pathogenic bacteria. This study investigated the presence, spatial distribution, and antimicrobial resistance patterns of selected airborne bacterial pathogens across ten locations in Dhaka city, including Badda, Khilgaon, Aftabnagar, Mohakhali, Mirpur-10, Mirpur-12, Hatirjheel, Farmgate, Panthapath, and TB Gate Quarter. Air samples were analyzed for Pseudomonas spp., Klebsiella spp., Staphylococcus aureus, Acinetobacter baumannii, and Escherichia coli using selective culture methods followed by molecular confirmation through DNA extraction, polymerase chain reaction (PCR), and gel electrophoresis, yielding characteristic amplicons of 618 bp, 130 bp, 279 bp, 353 bp, and 585 bp, respectively. The distribution of airborne bacteria varied notably among sites, with Khilgaon showing the highest diversity of detected pathogens, while Hatirjheel samples showed no detectable target organisms. Antibiotic susceptibility testing revealed an alarming prevalence of multidrug resistance among all isolates, as Staphylococcus aureus exhibited 100% resistance to all tested antibiotics, E. coli and Klebsiella pneumoniae showed complete resistance to most antibiotics with only partial sensitivity to nitrofurantoin and trimethoprim, and both Pseudomonas spp. and A. baumannii demonstrated extensive resistance, remaining mainly susceptible to last-resort antibiotics such as colistin and selected fluoroquinolones. Overall, the findings highlight the presence of multidrug-resistant airborne bacterial pathogens in Dhaka’s urban air and underscore the urgent need for routine air quality surveillance and strengthened public health and antimicrobial resistance control strategies.Item Occurrence and antibiotic resistance pattern of gram-negative bacteria isolated from restaurant table surfaces(BRAC University, 2026-01) Deen, Nadia SultanaPathogenic bacteria present on frequently touched surfaces represent a significant public health concern, particularly due to their potential to spread antibiotic-resistant infections. This study aimed to isolate and characterize pathogenic bacteria from restaurant (15 restaurant table surfaces) in Dhaka city and to evaluate their antibiotic susceptibility patterns. A total of Acinetobacter, Escherichia coli (N=5), Salmonella spp. (N=6), Shigella spp. (N=15), Vibrio spp. (N=14), Klebsiella pneumoniae (N=18), and Staphylococcus aureus (N=1) were analyzed against six commonly used antibiotics: Vancomycin, Amoxicillin, Azithromycin, Cefepime, Kanamycin, and Tetracycline. All Gram-negative isolates demonstrated 100% resistance to Vancomycin, indicating its ineffectiveness against these organisms. High resistance to Amoxicillin was observed among E. coli (80%), Salmonella spp. (83%), Shigella spp. (87%), Vibrio spp. (64%), and K. pneumoniae (83%). In contrast, Kanamycin, Cefepime, and Tetracycline showed comparatively higher effectiveness, particularly against E. coli, Shigella spp., Vibrio spp., and K. pneumoniae. Klebsiella pneumoniae exhibited the highest sensitivity to Cefepime (84%), while Shigella spp. showed notable sensitivity to Kanamycin (80%) and Cefepime (74%). Intermediate susceptibility was most prominent for Azithromycin and Cefepime across several isolates, especially in Salmonella spp. and Vibrio spp. The single Staphylococcus aureus isolate showed complete resistance to Vancomycin and Amoxicillin but remained fully sensitive to Azithromycin, Cefepime, and Tetracycline. Although identification and resistance profiling were based on conventional microbiological and phenotypic methods, molecular confirmation using polymerase chain reaction (PCR) targeting species-specific genes and antibiotic resistance determinants would further enhance the accuracy and reliability of pathogen identification. Overall, the findings highlight the presence of multidrug-resistant pathogenic bacteria on restaurant table surfaces, emphasizing the need for improved hygiene practices, molecular surveillance, and continuous monitoring of antibiotic resistance to reduce public health risks.Item A comparative assessment of bacterial load and other high-risk factors of necrotizing enterocolitis among neonates in Bangladesh(BRAC University, 2026-01) Shanta, Nusrat Jahan; Tabassum, Ummay Sumaiya; Deen, Nadia SultanaNecrotizing enterocolitis (NEC) is a serious inflammatory disease of the gastrointestinal tract that mainly affects preterm, low birth weighted neonates and remains an important cause of neonatal morbidity and mortality. In Bangladesh, evidence describing both intestinal bacterial burden and clinical high risk factors in NEC is still limited. This case-control study assessed bacterial load, different bacterial detection, and high risk factors among neonates in Bangladesh. A gender and gestational age matched case-control study was conducted at Ad-din Medical College Hospital, Bangladesh. The study population consisted of 66 preterm neonates (gestational age 28 to 36 weeks, birth weight up to 1.5 kg), including 33 NEC cases and 33 non-NEC controls. NEC cases were identified during sample collection based on key clinical features, including a positive occult blood test (OBT), abdominal distension, and the presence of bubble gas. Stool specimens were cultured on selective and differential media to measure bacterial load (CFU/ml) and to identify presumptive organisms based on colony morphology. PCR was performed to identify Escherichia coli and Klebsiella pneumoniae; PCR for other suspected organisms could not be performed due to unavailability of primers. To assess the significance of crude and adjusted odds ratio (aOR) of clinical relevance, Fisher’s test and Chi-square test were applied. Compared with NEC cases, controls showed a higher overall bacterial load, with a mean load of 1.25 × 107 CFU/ml in NEC and 2.21 × 107 CFU/ml in controls, representing an approximately 1.8 times higher load in the control group. However, PCR based detection identified E. coli and K. pneumoniae more frequently in NEC cases than in non-NEC. Growth on selective media suggested organisms such as Staphylococcus epidermidis, Staphylococcus saprophyticus, and Pseudomonas aeruginosa, along with several unidentified isolates. Several factors were analyzed including congenital heart disease, cardiogenic shock sepsis, formula feeding, breastfeeding, seizures and blood transfusion, only both type feeding demonstrated statistically significant difference between two groups (aOR: 0.8254; 95% CI: 0.2280-2.719; p < 0.05). Moreover, multidrug resistance was common in K. pneumoniae and E. coli isolates, and E. coli showed higher antimicrobial resistance. Our findings provide insight into clinical and microbiological parameters that may be useful for characterizing NEC. Because NEC is a complex inflammatory condition, further studies examining how multiple risk factors interact are needed to help lower the risk and impact of this devastating disease.Item ORAL candidosis in intensive care unit patients a comprehensive review (2005–2025)(BRAC University, 2025-12) Zidan, Junhi; Haque, Fahim Kabir MonjurulOral candidosis is a common opportunistic mycotic infection in intensive care (ICU) with colonization rates quoted between 27% and 53% depending on when sampling occurs, the method of collection and the critical illness severity. It has been traditionally considered a focal mucosal infection, but increasing epidemiological data indicate oral candidosis represents a clinically relevant source of lower respiratory tract colonization and invasive candidemia, especially in mechanically ventilated adults (Nascimento et al., 2024; Noppè et al., 2024). The profound immune dysregulation of critical illness, broad-spectrum antibiotic exposure, invasive medical devices and impaired oral hygiene provide a conducive environment for such Candida overgrowth. This narrative review of literature accumulated over a period of 2 decades (2005-2025) sought to summarize the evidence on the epidemiology, microbiology, pathogenesis, risk factors for development, methods and tests employed in diagnosis, patterns of antifungal resistance as well as therapy and clinical outcomes related to oral candidosis among critically ill patients. Oral candidosis is considered as a marker for risk to systemic infection and its treatment. There is a clear need for improved epidemiological monitoring, standardized diagnostic pathways, integrated approaches to oral-care informed by specialist assessment and antifungal stewardship that are based on a secure evidence-base in order to reduce morbidity and mortality from this frequently overlooked complication of critical illness.Item Bacteriological comparison of oral swab samples collected from conventional cigarette smokers and e-cigarette smokers(BRAC University, 2025-11) Das, Indrajit; Sarwar, Istiak; Ahmed, Plabon; Deen, Nadia SultanaThis study explored the impact of Conventional Cigarette Smoker (CCS), Electronic Cigarette Smoker (ECS), and Conventional Cigarette Smoker+Electronic Cigarette Smoker (CCS+ECS) use on the oral microbiome in a population from Bangladesh, where clinical research on e-cigarette users remains scarce. Oral swab samples were collected from a total of 40 participants, including 10 e-cigarette users, 10 conventional cigarette smokers, 10 dual (E-Cigarette and Conventional Cigarette) users, and 10 non-smokers. Samples were cultured and Gram stained to identify the presence of Gram-positive and Gram-negative bacteria. In terms of culture-based study, Nutrient Agar (NA) medium and Blood Agar Plates (BAP) being used. The average total aerobic count on NA medium showed difference among the groups. The highest CFU/mL count were observed on CCS group (4.8 × 10⁹ CFU/ml), followed by NS group (4.6 × 10⁹ CFU/ml), CCS + ECS group (3.9 × 10⁹ CFU/ml) and ECS (2.8 × 10⁹ CFU/ml). In contrast, Blood Agar Plates (BAP), being enriched and capable of revealing hemolytic activity, provided an insight into bacteria that may be opportunistic or pathogenic whereas ECS showed the highest overall bacterial load, with BAP counts reaching 1.5 × 10⁷ CFU/mL. CCS and CCS+ECS had comparable levels, ranging from 6.0 to 6.5 × 10⁶ CFU/mL, while NS showed 7.7 × 10⁶ CFU/mL. A significant difference between the ECS group, CCS group (p = 0.02) and CCS + ECS group (p = 0.02), indicating that e-cigarette users may harbor a greater abundance of fastidious bacterial species compared to other groups. It was hypothesized that smoking and vaping would disturb the natural oral microbial balance, increasing suspected harmful bacteria. In this case, we did the Gram-staining method and the findings revealed that CCS and ECS exhibited a higher presence of Gram-negative bacteria compared to other groups. CCS displayed a dominance of Gram-positive bacteria, suggesting a unique microbial response to tobacco exposure. ECS showed a slightly decreased Gram-negative count compared to NS, although the NS and CCS+ECS shared similar microbial profiles overall. Despite noticeable changes in bacterial composition, overall microbial diversity remained relatively stable, implying that host-related factors like genetics and hygiene may also have played a role. These results highlighted the compounded risks of e-cigarette and conventional cigarette use, questioning the idea of vaping as a more secure substitute to smoking. The pressing need for preventive health interventions and continued investigation of the long-term oral health outcomes of smoking and vaping was highlighted by the research, particularly in emerging markets such as Bangladesh.Item Isolation of mobile colistin-resistance (mcr) gene-harboring Escherichia coli from chicken droppings in Dhaka(BRAC University, 2025-09) Rahman, Mohibur; Biswas, Nilanjana; Safa, Afrin Alam; Sabin, Tasmia; Deen, Nadia SultanaThe use of antibiotics in poultry industries across the low and middle-income countries is increasing rapidly, contributing to emergence of resistance against the last line of drug like colistin causing public health threat. Therefore, this study aimed to investigate the prevalence of Mobile Colistin Resistance (mcr) genes in E. coli isolated from the fecal samples of broiler chickens in Dhaka city. A total of 50 fecal samples were collected from food markets and residential areas of Dhaka city. The samples were processed and streaked onto selective media to presumptively isolate E. coli. The isolates were further confirmed by polymerase chain reaction (PCR) analysis, targeting 16s rRNA regions. Detection of mcr genes was performed by employing multiplex PCR of mcr-1 to mcr-5 and mcr-6 to mcr-9, while mcr-10 gene was amplified by singleplex standard PCR. Lastly, phenotypic expression was assessed by the broth microdilution method (BMD) to determine the minimum inhibitory concentration (MIC). A total of 47 E. coli isolates were presumptively isolated from selective media and subsequently 41 confirmed by PCR followed by plasmid-mediated detection of mcr resistance genes. Among E. coli isolates, 3 carried mcr-1 (7.3%), 33 mcr-3 (80.5%), 12 mcr-6 (29.3%), 2 mcr-7 (4.9%) 28 mcr-8 (68.3%) and 1 mcr-9 (2.4%), mcr-2, mcr-4, and mcr-10 were not detected in any of the isolates of E. coli. Phenotypic susceptibility testing of the isolates were carried out by using BMD method, revealing that most of the isolates harboring mcr genes are resistant to colistin at MIC up to 4 ug/mL. The high prevalence of various mcr genes, notably mcr-3 and mcr-8, indicated that colistin resistance had been extensively disseminated in bacteria from chickens. Such findings indicate industrial poultry chicken as a potential source of multidrug-resistant pathogens. 5