In a try to understand the pathogenesis, evolution and epidemiology of the SARS-CoV-2 virus, scientists from all over the world are tracking its genomic changes in real-time. Genomic studies can be helpful in understanding the disease dynamics. We have downloaded 324 complete and near complete SARS-CoV-2 genomes submitted in GISAID database from Bangladesh which were isolated between 30 March to 7 September, 2020. We then compared these genomes with Wuhan reference sequence and found 4160 mutation events including 2253 missense single nucleotide variations, 38 deletions and 10 insertions. The C>T nucleotide change was most prevalent (41% of all mutations) possibly due to selective mutation pressure to reduce CpG sites to evade CpG targeted host immune response. The most frequent mutation that occurred in 98% isolates was 3037C>T which is a synonymous change that usually accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp) and 23403A>G (D614G in spike protein). The P323L was reported to increase mutation rate and D614G is associated with increased viral replication and currently most prevalent variant circulating all over the world. We identified multiple missense mutations in B-cell and T-cell predicted epitope regions and/or PCR target regions (including R203K and G204R that occurred in 86% of the isolates) that may impact immunogenicity and/or RT-PCR based diagnosis. Our analysis revealed 5 large deletion events in ORF7a and ORF8 gene products that may be associated with less severity of the disease and increased viral clearance. Our phylogeny analysis identified most of the isolates belonged to the Nextstrain clade 20B (86%) and GISAID clade GR (88%). Most of our isolates shared common ancestors either directly with European countries or jointly with middle eastern countries as well as Australia and India. Interestingly, the 19B clade (GISAID S clade) was unique to Chittagong, which was originally prevalent in China. This reveals possible multiple introductions of the virus in Bangladesh via different routes. Hence, more genome sequencing and analysis with related clinical data is needed to interpret functional significance and better predict the disease dynamics that may be helpful for policy makers to control the COVID-19 pandemic.

Antimicrobial resistance (AMR) is a critical public health issue in Bangladesh, where antibiotic use is widespread but often unregulated. This nationwide cross-sectional study (2017–2020) analyzed data from 26 public and private laboratories across all divisions of the country. Standardized data on antimicrobial susceptibility testing (AST) were collected, curated, and analyzed using WHONET, QAAPT, and R software to assess resistance patterns in 232,329 bacterial isolates from various clinical specimens. Escherichia coli was the most common pathogen (32.5%), followed by Klebsiella sp. (15.5%) and Pseudomonas sp. (10.6%). Urine specimens comprised 50.3% of the tested samples, while blood and soft tissue/body fluids accounted for 12.1% and 24.8%, respectively. Patients aged 55 years and older represented the largest group (36.3%), highlighting their vulnerability to drug-resistant infections. Resistance to third-generation cephalosporins was alarmingly high in Escherichia coli (62.9% resistant to ceftriaxone), whereas carbapenem resistance remained relatively low (5.3% and 6.8% to imipenem and meropenem, respectively). Klebsiella sp. showed widespread resistance, though carbapenems remained relatively effective (imipenem resistance 20.3%, meropenem 21.7%). In contrast, Salmonella sp. remained largely sensitive to third-generation cephalosporins. However, 42% of Staphylococcus aureus isolates were methicillin-resistant (MRSA). This study underscores the urgent need for improved antibiotic stewardship, enhanced diagnostic capacity, and strengthened AMR surveillance to preserve treatment options in Bangladesh.

Introduction: Antimicrobial resistance (AMR) is a global public health issue, particularly in resource-limited, low- to middle-income countries like Bangladesh. In this study, we analyze and present four years of data on AMR from a tertiary care hospital in Bangladesh to inform policymakers and the wider community. Methods: In a retrospective cross-sectional study, we collected data for 4403 bacterial isolates reported between January 2017 and February 2020 at Mymensingh Medical College Hospital (MMCH), Bangladesh. All data were entered, cleaned, and analyzed using the software Stata Version-16.0, WHONET, a microbiology laboratory data management solution, and Quick Analysis of Antimicrobial Patterns and Trends (QAAPT), an AMR data visualization platform. Results: The bacteria were most commonly isolated from urine (71.66%, n = 3155), followed by pus (11.63%, n = 512), sputum (6.70%, n = 295), wound swabs (6.70%, n = 295), stool (1.91%, n = 84), endotracheal aspirate (1.20%, n = 53), and blood (0.20%, n = 9). Gram-negative bacteria predominated in all samples. Escherichia coli was the most common Gram-negative bacterium (31.30%, n = 1378), while Staphylococcus aureus was the most common Gram-positive bacterium (4.38%, n = 193). Antimicrobial susceptibility testing (AST) showed that multidrug resistance in Gram-negative bacteria such as E. coli, Klebsiella sp., and Acinetobacter sp. was common. S. aureus exhibited high resistance rates for beta-lactams, macrolides, and quinolones. In the urine samples, E. coli demonstrated high resistance to antibiotics like amoxicillin/clavulanic acid, ciprofloxacin, ceftriaxone, and cefuroxime (60–100%). Critical and high-priority pathogens as listed by the WHO constituted approximately 60% of the isolates. The AMR trends over three months showed increased resistance to amoxicillin/clavulanic acid for E. coli and to cefuroxime for Klebsiella sp. For S. aureus, the resistance to ciprofloxacin increased over three years, while the resistance to azithromycin decreased. Conclusions: There is a rise in bacterial resistance to the available antibiotics, with a significant prevalence of critical and high-priority pathogens in Bangladesh. We recommend vigilant AMR surveillance and stewardship programs to control the AMR in this country.

Surveillance is one of the effective tools to address antimicrobial resistance. In Bangladesh a countrywide antimicrobial resistance surveillance has been ongoing since 2016. The main objective of this surveillance is to formulate the guideline for clinicians and to assist policy makers to know the gravity of the AMR problem in Bangladesh. It is a case-based surveillance conducted by Institute of Epidemiology, Disease Control & Research (IEDCR) in nine sentinel sites where five types of clinical cases were selected according to case definition, and ten types of bacteria were identified from six types of preselected specimens. All the laboratory works were performed following the standard operating procedure supplied by the AMR surveillance Reference laboratory at IEDCR. Total 19,263 samples were processed during the period of March 2017 to March 2020 among which wound swab yielded highest growth (57%). E. coli was the highest (1717) isolated organism among the ten priority pathogens which showed highest sensitivity (91%) to Imipenem. Imipenem also showed higher sensitivity to most of the organisms. Third generation cephalosporin was found to be less sensitive to Escherichia coli (37%) and Klebsiella pneumoniae (28%); nevertheless, Salmonella species showed higher sensitivity (97%) to it. Acinetobacter calcoaceticus-baumannii complex isolated from ICU patients showed alarming resistance to all of the antibiotics including highest sensitive antibiotic Imipenem (29%). Salmonella species isolated from blood showed higher susceptibility to most of the antibiotics except ciprofloxacin (7%). Alarmingly, only 36% of the Staphylococcus aureus isolates showed susceptibility to cefoxitin indicates high prevalence of MRSA infection. The result of the surveillance representing the whole country is surely alarming as many of the bacteria are resistant to the commonly used as well as reserve groups of antibiotics. Concerted effort should be taken from all concerned authorities to curb the problem immediately.

Introduction: Antimicrobial resistance (AMR) is a critical global public health issue, leading to prolonged illness, increased morbidity and mortality, and rising healthcare costs. The effectiveness of antibiotics is diminishing due to the emergence of resistant bacterial strains. This study aimed to determine the bacterial profile and AMR patterns of clinical isolates at Uttara Adhunik Medical College Hospital (UAMCH), Dhaka. Methods: A retrospective study was conducted at UAMCH from January 2017 to December 2019. A total of 32,187 clinical specimens (urine, blood, stool, wound swabs/pus, and sputum) were processed, of which 4232 yielded positive cultures. Bacterial identification followed standard bacteriological methods, and antibiotic susceptibility was assessed using the Kirby–Bauer disc diffusion method per CLSI guidelines. Data analysis was conducted using WHONET and QAAPT. Results: The highest proportion of positive cultures was from urine (47.5%), followed by blood (35.0%) and wound swabs/pus (10.1%). The most common isolates were Escherichia coli (37.2%), Salmonella typhi (25.7%), and Klebsiella sp. (11.5%). Gram-negative bacteria showed high resistance to commonly used antibiotics such as amoxicillin/clavulanic acid, cefixime, and ceftriaxone, while the resistance rates were lower for gentamicin, amikacin, and meropenem. However, Acinetobacter sp. exhibited alarming resistance to all tested antibiotics. Conclusions: This study highlights concerning resistance patterns among bacterial isolates, emphasizing the need for ongoing AMR surveillance to inform treatment strategies and improve patient care in Bangladesh.