Papers by M. Nazmul Hoque
Asian-Australasian journal of food safety and security, Apr 24, 2024
Organic dairy farming (ODF) is a method of dairy production that emphasizes the use of natural an... more Organic dairy farming (ODF) is a method of dairy production that emphasizes the use of natural and sustainable practices, aiming to minimize synthetic inputs, promote animal welfare, and protect the environment. The aim of this review is to elucidate the current status, challenges and prospects of the ODF in Bangladesh. Starting from the current situation, the challenges and future potential of the ODF are presented, as well as strategies to overcome the difficulties are also highlighted. The ODF has the great potential, challenges and opportunities in Bangladesh. This involves the production of milk, meat and dairy products using sustainable and organic practices. Farmers need certification, and challenges include limited awareness, access to organic inputs, and market demand. Government initiatives, training programs, and cooperative models can support the growth of the ODF. Market opportunities and ongoing research are essential considerations. Animals raised in the ODF systems are provided access to pasture or outdoor areas and are fed organic feed, which is free from synthetic additives, antibiotics and hormones. The transition to the ODF is driven by a combination of economic, environmental, and health-related motivations, aiming to produce dairy products in a more sustainable, economically viable and environmentally friendly manner. Organic dairy farmers prioritize the well-being of their animals and advocate for a natural environment, which is integral to animal welfare. The popularity of organic products, including meat, dairy, and value-added items, from these producers continues to rise, driven by the expanding organic market, higher prices for organic milk, and consumer preferences for products from more sustainable production systems. Despite a mammoth of challenges exist in the ODF, farmers need to implement and adhere to strict standards for organic products, animal welfare and the use of organic inputs to gain the full benefits of this sustainable farming system. This review article examines the present status of the ODF industry, emphasizing key considerations, management practices, challenges, and future prospects. It also provides insights into the relevant regulatory authorities, aiming to inform farmers and stakeholders in Bangladesh and beyond about ODF. However, there is a need for future research to concentrate on improving sustainability and efficiency within the ODF sector.
The emergence and spread of multidrug-resistant pathogens like Pseudomonas aeruginosa are major c... more The emergence and spread of multidrug-resistant pathogens like Pseudomonas aeruginosa are major concerns for public health worldwide. This study aimed to assess the prevalence of P. aeruginosa in clinical, environmental, and poultry sources in Bangladesh, along with their antibiotic susceptibility and the profiling of β-lactamase and virulence genes using standard molecular and microbiology techniques. We collected 110 samples from five different locations, viz., BAU residential area (BAURA; n = 15), BAU Healthcare Center (BAUHCC; n = 20), BAU Veterinary Teaching Hospital (BAUVTH; n = 22), Poultry Market (PM; n = 30) and Mymensingh Medical College Hospital (MCCH; n = 23). After overnight enrichment in nutrient broth, 89 probable Pseudomonas isolates (80.90%) were screened through selective culture, gram-staining and biochemical tests. Using genus-and species-specific PCR, we confirmed 22 isolates (20.0%) as P. aeruginosa from these samples. Antibiogram profiling revealed that 100.0% P. aeruginosa isolates (n = 22) were multidrug-resistant isolates, showing resistance against Doripenem, Penicillin, Ceftazidime, Cefepime, and Imipenem. Furthermore, resistance to aztreonam was observed in 95.45% isolates. However, P. aeruginosa isolates showed a varying degree of sensitivity against Amikacin, Gentamicin, and Ciprofloxacin. The blaTEM gene was detected in 86.0% isolates, while blaCMY, blaSHV and blaOXA, were detected in 27.0%, 18.0% and 5.0% of the P. aeruginosa isolates, respectively. The algD gene was detected in 32.0% isolates, whereas lasB and exoA genes were identified in 9.0% and 5.0% P. aeruginosa isolates. However, none of the P. aeruginosa isolates harbored exoS gene. Hence, this study provides valuable and novel insights on the resistance and virulence of circulating P. aeruginosa within the clinical, environmental, and poultry environments of Bangladesh. These findings are crucial for understanding the emergence of β-lactamase resistance in P. aeruginosa, highlighting its usefulness in the treatment and control of P. aeruginosa infections in both human and animal populations.
Scientific Reports
The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles i... more The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The ‘G’ clade was domina...
Microbiology Resource Announcements
This announcement provides the genome sequence of the biofilm-forming methicillin-resistant Staph... more This announcement provides the genome sequence of the biofilm-forming methicillin-resistant Staphylococcus aureus MTR_V1 strain isolated from a ready-to-eat food sample in Bangladesh. Our assembled genome had a length of 2.8 Mb, 27 contigs, two CRISPR arrays, 38 predicted antibiotic resistance genes, and 66 predicted virulence factor genes.
Frontiers in Pharmacology
Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous eff... more Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates.Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to ...
PLOS ONE
We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiom... more We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal spe...
Background: Arsenic (As) and its species are major pollutants in ecological bodied including grou... more Background: Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants. Results: Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MI...
Background: COVID-19 was declared a pandemic by the World Health Organization (WHO) on March 11, ... more Background: COVID-19 was declared a pandemic by the World Health Organization (WHO) on March 11, 2020. Unpredictable and peculiar characteristics of coronavirus left no single recommended treatment option apart from preventive actions. Bangladesh government adopts guidelines for the clinical management of mild, moderate, and severe cases of COVID-19 patients. Prescription error, the avoidable mistake, may cause havoc, especially for comorbid patients with diabetes and hypertension identified as a risky population group for COVID-19. Therefore, the present study was designed to evaluate the prescription errors, including the drug-drug interactions among the outdoor patients infected with the coronavirus. This study was carried out in outpatient departments of different hospitals in Bangladesh through a random sampling method between May 2021 and August 2021. Eighty prescriptions of COVID-19 patients were collected, among which 44 patients had comorbidity. Microsoft Excel 2016 program...
Advances in Virology
In this study, previously published Rab7 sequences from National Center for Biotechnology Informa... more In this study, previously published Rab7 sequences from National Center for Biotechnology Information (NCBI) have been investigated from chordates, mollusks, annelids, cnidarians, amphibians, priapulids, brachiopods, and arthropods including decapods and other groups. Among decapod crustacean isolates, amino acid variations were found in 13 locations. Penaeid shrimps had variations in positions 13 (I ⟶ J), 22 (T ⟶ A), 124 (G ⟶ X), and 149 (V ⟶ X) while interestingly the freshwater prawn and mitten crab both had amino acid substitutions in positions 87 (V ⟶ C) and 95 (T ⟶ S) along with the other disagreements in amino acid positions 178 (S ⟶ N), 201 (D ⟶ E), 181 (E ⟶ D), 182 (L ⟶ I), 183 (Y ⟶ G), 184 (N ⟶ H), and 198 (A ⟶ T). Among 100 isolates of Rab7 from organisms of various phyla, mutations were observed in several positions. These mutations caused variations in hydrophobicity and isoelectric point which impact the ligand-protein binding affinity. Some common mutations were found...
Research Square (Research Square), Oct 3, 2022
Background: Plant probiotic bacteria enhance growth and yield of crop plant when applied in appro... more Background: Plant probiotic bacteria enhance growth and yield of crop plant when applied in appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effects of growth, yield and bacteriome in roots and rhizosphere of rice by the application of BRRh-4 and BTL-M2 with varying doses of recommended N, P and K fertilizers. Results: Application of BRRh-4 and BTL-M2 strains also signi cantly increased seed germination, growth and yield of rice compared to untreated control. Interestingly, the grain yield of rice by these bacteria with 50% reduced recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these chemical fertilizers only. The metagenomics analysis by next generation sequencing revealed that the diversity in bacteriome were signi cantly higher (PERMANOVA, p = 0.0312) in the rice plants and rhizosphere soils that received both probiotic bacteria and chemical fertilizers compared to the rice plants treated with chemical fertilizers only. However, the diversity in bacteriome was more signi cant (p = 0.019, Kruskal-Wallis test) in the root bacteriome signature than in the rhizosphere soils. Out of 185 bacterial genera detected, Prevotellawas found to be the predominant genus in both soil and root metagenomes. However, the relative abundance of Prevotella remained twofold higher in the soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus(11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus(2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium(9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia(3.02). Conclusions: Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the rst time demonstrated that application of two plant growth promoting bacteria signi cantly improve growth, yield and increase the diversity of bacterial community in rice.
Journal of Global Antimicrobial Resistance
Objectives: Pseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of commun... more Objectives: Pseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of community-and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug resistant (MDR) P. aeruginosa DMC30b in order to elucidate the genetic diversity, molecular epidemiology, and underlying mechanisms for antimicrobial resistance and virulence. Methods: P. aeruginosa DMC30b was isolated from septic wound swab of a severe burn patient. Whole-genome sequencing (WGS) was performed under Ion Torrent platform. The genome was annotated using the SPAdes v. 3.12.01 in an integrated Genome Analysis Platform (IonGAP) for Ion Torrent sequence data. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). In-silico predictions of antimicrobial resistance genes (ARGs), virulence factor genes (VFGs) and metabolic functional potentials were performed using different curated bioinformatics tools. Results: P. aeruginosa DMC30b was classified as MDR and belongs to sequence type 244 (ST244). The complete genome size is 6,994,756 bp with a coverage of 76.76x, G+C content of 65.7% and a BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 100. The genome of P. aeruginosa DMC30b harboured two plasmids (e,g., IncP-6 plasmid p10265-KPC; 78,007 bp and ColRNAI_pkOIISD1; 9,359 bp), 35 resistomes (ARGs) conferring resistance to 18 different antibiotics (including four beta-lactam classes), and 214 VFGs. It was identified as the 167 th ST244 strain among ~ 5,800 whole-genome sequences of P. aeruginosa available in the NCBI database. Conclusion: P. aeruginosa DMC30b belongs to ST244 and was identified as the 167 th such isolate to be submitted to NCBI, and the first complete ST244 genome from Bangladesh. The complete genome data with high genetic diversity and underlying mechanisms for antimicrobial resistance and virulence of P. aeruginosa DMC30b (ST244) will aid in .
Magnaporthe oryzae is one of the most notorious fungal pathogens that causes blast disease in cer... more Magnaporthe oryzae is one of the most notorious fungal pathogens that causes blast disease in cereals and results in enormous loss of grain production. Many chemical fungicides are being used to control the pathogen but none of them are effective against blast disease. Thus, there is a demand to discover potential and safe natural biofungicides to manage blast disease successfully. To find out effective biofungicides, we performed in silico molecular docking analysis of some natural compounds targeting four enzymes namely, scytalone dehydratase, SDH1 (1STD), trihydroxynaphthalene reductase, 3HNR (YBV1), trehalose-6-phosphate synthase, Tps1 (6JBI) and isocitrate lyase, ICL1 (5E9G) of M. oryzae fungus that regulate melanin biosynthesis or appresorium formation. Thirty-nine natural compounds that previously reported to inhibit the growth of M. oryzae were subjected to rigid and flexible molecular docking against aforementioned enzymes followed by molecular dynamics simulation and free ...
Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree di... more Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through...
Journal of Pharmacognosy and Phytochemistry, 2015
The present study was designed to investigate antioxidant, antimicrobial and cytotoxic potential ... more The present study was designed to investigate antioxidant, antimicrobial and cytotoxic potential of pet ether, chloroform and methanol extracts of Ganoderma lucidum available in Bangladesh. Antioxidant activity of the extracts was evaluated using DPPH radical scavenging assay and determination of total phenolic content. Antibacterial and cytotoxic activities were studied using disc diffusion method and brine shrimp lethality bioassay respectively. Results showed that the methanol extract had highest antioxidant activity (IC50 value for DPPH was 47.58 μg/ml and total phenolic content was 167.9±3.252 in mg/g, Gallic acid equivalents) compared to the pet ether and chloroform extract. In antibacterial study, all the extracts showed mild to moderate activity with zone of inhibition ranging from 7 mm to 21 mm. In brine shrimp lethality bioassay, the LC50 values for pet ether, chloroform and methanol extracts were 941.88 μg/ml, 367.28 μg/ml and 295.8 μg/ml respectively which revealed weak ...
BioMed Research International, 2021
Campylobacter enteritis is the leading cause of gastroenteritis in humans worldwide including Ban... more Campylobacter enteritis is the leading cause of gastroenteritis in humans worldwide including Bangladesh. The objectives of this study were to estimate the prevalence and antimicrobial-resistance status of Campylobacter spp. in human diarrheal samples collected from Surya Kanta Hospital, Mymensingh, Bangladesh. In this study, we evaluated a total of 330 clinical samples for the presence Campylobacter spp. via cultural and biochemical tests and molecular assays. Furthermore, antimicrobial susceptibility testing for Campylobacter species was accomplished by the standard agar disc diffusion technique against eight commercially available antimicrobial agents. A pretested semistructured questionnaire was used to capture the data on socioanthropological factors from the diarrheal patients. Pearson’s chi-square test was performed, and a p value of <0.05 was considered for the level of significance. Nearly one in three diarrheal patients admitted in this hospital were infected with Campy...
Clinical Phytoscience, 2020
Background Thysanolaena maxima (Roxb.) Kuntze, a perennial grass plant, is usually distributed in... more Background Thysanolaena maxima (Roxb.) Kuntze, a perennial grass plant, is usually distributed in hilly regions of the Indian Subcontinent. Different parts of T. maxima have been used as herbal medicine by traditional healers of this region. In this present study, T. maxima plant extract has been screened for examination of its secondary metabolite content with their probable cytotoxic activity. Methods Secondary metabolites of the crude T. maxima plant extract were isolated by different chromatographic methods. The structures were elucidated by spectroscopic data (1H NMR, 13C NMR) as well as comparison with available literature sources. Antiradical activity by DPPH radical scavenging assay and antimicrobial activity by disc diffusion method of the fractions and cytotoxic activity by trypan blue exclusion method of the isolated compounds were also evaluated. Results Three phenolic compounds 4-hydroxybenzaldehyde (1), 4-hydroxycinnamic acid (2), 4-hydroxybenzoic acid (3) and two ster...
Pathogens, 2021
A cross-sectional survey was conducted in selected districts of Bangladesh to estimate prevalence... more A cross-sectional survey was conducted in selected districts of Bangladesh to estimate prevalence, risk factors, and molecular detection of Campylobacter isolates from 540 farmed cattle of 90 herds. As an individual sample, 540 feces, and as a pooled sample, 180 milk samples, 90 feed samples, 90 water samples, 90 manure samples, and 90 animal attendants’ hand-rinse water were collected and tested via culture, biochemical, and molecular assays. A pretested semi-structured questionnaire was used to collect herd-level data on risk factors with the herd owners. The herd-level data on risk factors were analyzed through univariate and multivariate analyses, and a p-value <0.05 was considered statistically significant for all analyses. Overall, farm-level prevalence of bovine Campylobacter was enumerated to be 53.3% (95% confidence interval [CI]: 42.5–63.9%). The feces sample was found to be a high level of contamination of 30.9% (95% CI: 27–35%) followed by the manure swab (pooled) at ...
Journal of Advanced Biotechnology and Experimental Therapeutics, 2021
The COVID-19 pandemic has altered global waste generation dynamics, which is a challenging task f... more The COVID-19 pandemic has altered global waste generation dynamics, which is a challenging task for poor countries having inefficient waste management system. On an average, 6,180 tons of medical waste (MW) during this COVID-19 pandemic is generated per month in the Dhaka city. This voluminous amount of MW generated in the Dhaka city is remained poorly managed, and thus, posing a serious threat to public health and environment. To protect any risk of spread of SARS-CoV-2 through MW, a concerted and prompt effort from municipal authorities, hospital administration, and concerned non-government organization (NGOs) is needed to adopt new ways of state-of-the-art, safe and cost-effective MW management system for the Dhaka city. Furthermore, research should be directed to find out other potential sources (e.g., inanimate objects or aquatic bodies) of SARS-CoV-2 infections to track it's spatial and temporal dynamics, and also to get early warning in case of future outbreaks.
Uploads
Papers by M. Nazmul Hoque