JOURNAL PAPER

Salma Akter, M. Shaminur Rahman, Hazrat Ali, Benjamin Minch, Kaniz Mehzabin, Md. Moradul Siddique, Syed Md. Galib, Farida Yesmin, Nafisa Azmuda, Nihad Adnan, Nur A. Hasan, Sabita Rezwana Rahman, Mohammad Moniruzzaman & Md Firoz Ahmed, Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast, Scientific Reports volume, 13, 15976, 2023. doi: https://doi.org/10.1038/s41598-023-43306-4

The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB’s eastern coast, viz., Saint Martin and Cox’s Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox’s Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox’s Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox’s Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.

 

Nihad Adnan, Md Ahsanul Haq, Taslima Akter Tisha, Shahad Saif Khandker, Mohd Raeed Jamiruddin, SM Shafiul Alam Sajal, Salma Akter, Md Firoz Ahmed, Rubhana Raqib, Mohib Ullah Khondoker, Nafisa Azmuda, Mainul Haque, Md Ahsanul Haq, Optimizing SARS-CoV-2 Immunoassays for Specificity in Dengue-Co-Endemic Areas, Cureus, 15, 10, pp.e47683, 2023. doi: 10.7759/cureus.47683

Introduction: The overlap in clinical presentation between COVID-19 and dengue poses challenges for diagnosis in coendemic regions. Furthermore, there have been reports of antibody cross-reactivity between SARS-CoV-2 and dengue. Our research aims to evaluate SARS-CoV-2 antigens for serological testing while reducing the possibility of cross-reactivity with anti-dengue antibodies. Method: Two hundred and ten serum samples were collected from 179 patients and divided into four panels. Panels 1 and 2 consisted of COVID-19-negative healthy donors (n=81) and pre-pandemic dengue patients (n=50), respectively. Alternatively, Panel 3 (n=19) was composed of reverse transcription-quantitative polymerase chain reaction (RT-qPCR)-positive samples collected within two weeks of COVID-19 symptom onset, while Panel 4 (n=60) was composed of positive samples collected after two weeks of symptom onset. Previously developed and characterized in-house SARS-CoV-2 spike-1 (S1), receptor binding domain (RBD), and nucleocapsid (N) immunoglobin G (IgG)-enzyme-linked immunosorbent assay (ELISA) assays were used for the study. Results: Six dengue-positive sera cross-reacted with the RBD of SARS-CoV-2. However, only one dengue-positive sera cross-reacted with the S1 and N proteins of SARS-CoV-2. Co-immobilization of S1 and RBD in different ratios revealed an 80:20 (S1:RBD) ratio as optimal for achieving an overall 96.2% sensitivity with the least cross-reaction to anti-dengue antibodies. Conclusion: Our findings indicated that SARS-CoV-2 RBD-based immunoassays present more cross-reactivity with antidengue antibodies than S1 and N proteins. Furthermore, co-immobilization of S1 and RBD reduces the cross-reactivity with anti-dengue antibodies compared to RBD, thereby increasing the immunoassay specificity without affecting overall sensitivity for the dengue-endemic areas. 

 

Mohammad Moniruzzaman Benjamin Minch, Salma Akter, Alaina Weinheimer, M. Shaminur Rahman, Md Anowar Khasru Parvez, Sabita Rezwana Rahman, Md Firoz Ahmed, Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal, mSphere, 8, 6, 2023. doi: https://doi.org/10.1128/msphere.00407-23

The Bay of Bengal (BoB) is the world’s largest bay, offering essential services like fishing and recreation while holding significant economic value for coastal communities. However, the BoB faces environmental challenges from monsoons, freshwater inputs, rising sea levels, and intensified cyclones due to climate change. Human activities such as tourism and development also impact the region, necessitating a global change perspective. Despite its importance, microbial diversity and ecology in the BoB remain largely unexplored. We focused on large and cell-associated viruses (i.e., originating from the cellular size fraction), particularly giant viruses and large phages in two BoB coastal sites: Cox’s Bazar, a populated beach with freshwater influences, and Saint Martin Island, a less affected resort island. Metagenomic sequencing reveals a higher abundance and diversity of viruses in Cox’s Bazar and presence of viruses that suggest freshwater intrusion and runoff. We identified 1962 putative phage genomes (10–655 kbp). Notably, 16 “large” phages >100 kbp were found in Saint Martin, and a terminase large subunit marker gene phylogeny revealed substantial diversity of large phages along the BoB coast. The BoB virome encodes diverse functionalities, with a greater presence of auxiliary metabolic genes in the Cox’s Bazar viral community. Additionally, five giant virus genomes (phylum Nucleocytoviricota) encoding various functionalities are reconstructed from Cox’s Bazar (83–876 kbp). This pioneering study revealing the viral diversity and host interactions in coastal BoB lays the foundation for future investigations into viral impact on biogeochemical cycles and the microbial food web in this understudied environment.

 

Nihad Adnan, Mohib Ullah Khondoker, M Shaminur Rahman, M Firoz Ahmed, Shahana Sharmin, Nadim Sharif, Nafisa Azmuda, Salma Akter, Shamsun Nahar, Taslin Jahan Mou, Mahfuza Marzan, Syeda Moriam Liza, Nowshin Jahan, Tamanna Ali, Shahad Saif Khandker, Maha Jam, Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh, 10, pp.10, 2021. doi: https://doi.org/10.1128/MRA.00124-21

Here, we report the coding-complete genome sequences of nine clinical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and their mutations. The samples were collected from nine Bangladeshi coronavirus disease 2019 (COVID-19) patients. We have identified the E484K escape mutation and the S359T mutation within the spike protein coding region of the sequenced genomes.

 

Raeed Jamiruddin, Ahsanul Haq, Mohib Ullah Khondoker, Tamanna Ali, Firoz Ahmed, Shahad Saif Khandker, Irfan Jawad, Rubel Hossain, Sohel Ahmed, Sabita Rezwana Rahman, Mamun Mustafi, Taku Kaitsuka, Masayasu Mie, Kazuhito Tomizawa, Eiry Kobatake, Mainul Haqu, Antibody response to the first dose of AZD1222 vaccine in COVID-19 convalescent and uninfected individuals in Bangladesh, Expert review of vaccines, 20, 12, pp.1651-1660, 2021. doi: https://doi.org/10.1080/14760584.2021.1977630

Vaccination with the Oxford-AstraZeneca COVID-19 vaccine (AZD1222) initially started in the UK and quickly implemented around the Globe, including Bangladesh. Up to date, more than nine million doses administrated to the Bangladeshi public. Herein, we studied the antibody response to the first dose of AZD1222 in 86 Bangladeshi individuals using in-house ELISA kits. Study subjects were categorized into two groups, convalescent and uninfected, based on prior infection history and SARS-CoV-2 nucleocapsid-IgG profiles. All the convalescent individuals presented elevated spike-1-IgG compared to 90% of uninfected ones after the first dose. Day >28 post-vaccination, the convalescent group showed six times higher antibody titer than the uninfected ones. The most elevated antibody titers for the former and later group were found at Day 14 and Days >28 post-vaccination, respectively. The spike-1-IgA titer showed a similar pattern as spike-1-IgG, although in a low-titer. In contrast, the IgM titer did not show any significant change in either group. High antibody titer in the convalescent group, signify the importance of the first dose among the uninfected group. This study advocates the integration of antibody tests in vaccination programs in the healthcare system for maximizing benefit.

 

Mst Fatema Khatun, Md Abu Sayem Khan, Md Firoz Ahmed, Md Majibur Rahman, Sabita Rezwana Rahman, Assessment of foodborne transmission of Salmonella enteritidis in hens and eggs in Bangladesh, Veterinary Medicine and Science, 8, 5, pp.2032-2039, 2022. doi: https://doi.org/10.1002/vms3.874

Salmonella is considered one of the leading causes of foodborne illnesses worldwide. Information about the transmission of pathogens to poultry and poultry products is necessary to implement control measures for reducing both human exposure and economic loss. The aim of this study was to analyze and evaluate the transmission characteristics of Salmonella enteritidis to laying-type hen flocks and their laid eggs. For this purpose, 15 pairs of laying hens were used in which each pair consisted of one inoculated and one contact exposed hen. The eggs and cloacal swabs from these hens were subsequently analyzed. Of the 15 in-contact hens tested, 60% were found to be positive for S. enteritidis within 61 days postinoculation, of which 26.7% transmission occurred within the first 31 days postinoculation. Among the collected laid eggs tested, S. enteritidis was detected on 58% eggshells and 5.33% eggs internal contents. We also observed a 33.33% reduction in egg production from S. enteritidis-infected hens. In a cross-contamination study, we demonstrated that an experimentally inoculated container can act as a potential source of Salmonella spp. infection. Our results will help establish effective monitoring programs to reduce the transmission of Salmonella spp. in poultry and poultry products.

 

T Hossain, MAS Khan, MF Ahmed, SR Rahman, Prevalence and molecular detection of multidrug-resistant Salmonella spp. isolated from eggshells in the local markets of Dhaka, Bangladesh, International Journal of One Health, 8, 2, pp.101-107, 2022. doi: www.doi.org/10.14202/IJOH.2022.101-107

Salmonella spp. are frequently associated with various parts of the egg, including the shell, and cause foodborne outbreaks worldwide. Antibiotic-resistant Salmonella spp. pose serious threats to human and animal health; therefore, preventive measures against these pathogens are important. This study aimed to isolate and characterize Salmonella spp. from eggshell samples from different local markets in Dhaka, Bangladesh. Salmonella spp. were recovered from eggshells by enrichment culture and biochemical tests and characterized through molecular amplification of Salmonella-specific genes. Antibiotic sensitivity testing and molecular detection of isolates were performed by disk diffusion method and polymerase chain reaction (PCR), respectively. The invA, fliC, and sdfI genes were used in PCR to identify the genus Salmonella, and the species Salmonella Typhimurium and Salmonella Enteritidis, respectively. The prevalence of Salmonella spp. was recorded as 40%, in which S. Typhimurium was the predominant serotype. PCR analysis revealed that 100%, 59%, and 13.6% of these isolates possessed the invA, fliC, and sdfI genes, respectively. The isolates exhibited multidrug resistance phenotypes, with resistance (95.5%) toward tetracycline, sulfamethoxazole, and clindamycin and sensitivity (86.3%) toward chloramphenicol. The findings of this study reflect the potential of eggs as a reservoir of multidrug-resistant Salmonella spp.; therefore, we recommend the careful handling of eggs to avoid contamination from farm to market.

 

Anna Albecka, Danielle J. Owen, Lyudmila Ivanova, Juliane Brun, Rukayya Liman, Laura Davies, M. Firoz Ahmed, Susanna Colaco, Michael Hollinshead, Stephen C. Graham , Colin M. Crump, Dual Function of the pUL7-pUL51 Tegument Protein Complex in Herpes Simplex Virus 1 Infection., doi: https://doi.org/10.1128/jvi.02196-16

The tegument of herpesviruses is a highly complex structural layer between the nucleocapsid and the envelope of virions. Tegument proteins play both structural and regulatory functions during replication and spread, but the interactions and functions of many of these proteins are poorly understood. Here we focus on two tegument proteins from herpes simplex virus 1 (HSV-1), pUL7 and pUL51, which have homologues in all other herpesviruses. We have now identified that HSV-1 pUL7 and pUL51 form a stable and direct protein-protein interaction, their expression levels rely on the presence of each other, and they function as a complex in infected cells. We demonstrate that expression of the pUL7-pUL51 complex is important for efficient HSV-1 assembly and plaque formation. Furthermore, we also discovered that the pUL7-pUL51 complex localizes to focal adhesions at the plasma membrane in both infected cells and in the absence of other viral proteins. The expression of pUL7-pUL51 is important to stabilize focal adhesions and maintain cell morphology in infected cells and cells infected with viruses lacking pUL7 and/or pUL51 round up more rapidly than cells infected with wild-type HSV-1. Our data suggest that, in addition to the previously reported functions in virus assembly and spread for pUL51, the pUL7-pUL51 complex is important for maintaining the attachment of infected cells to their surroundings through modulating the activity of focal adhesion complexes.

2. Effect of risk factors on the prevalence of influenza infections among children of slums of Dhaka city.,

SR Rahman, MF Ahmed, MA Islam and MM Rahman. 2016. SpringerPlus. 5:602.

3. Antigenic and genetic characterization of Influenza b viruses in 2012 from slums, Dhaka, Bangladesh.,

MA Islam, N Sultana, MF Ahmed, MM Rahman, SR Rahman. 2015. Southeast Asian J Trop Med Public Health. 46(4):611-5.

4. Effects of Risk Factors on Anti-HBs Development in Hepatitis B Vaccinated and Nonvaccinated Populations.,

M Shaha, SA Hoque, MF Ahmed and SR Rahman. 2015. Viral Immunol. 28(4):217-221.

5. Prediction of new conserved epitopes in protein 3D model to neutralize influenza a virus strain H3N2 circulating in Bangladesh.,

M Shaha, MA Islam, AB Islam, MF Ahmed, MM Rahman and SR Rahman. 2015. Int. J. Curr. Res. Chem. Pharma. Sci, 2(3), pp.99-109.

6. A retrospective analysis of viral gastroenteritis in Asia.,

SK Dey, S Nahar, … MF Ahmed, .. A Farjana. 2014. Journal of Pediatric Infectious Diseases. 9(2):53-65.

7. Occurrence of urinary tract infection in adolescent and adult women of shanty town in Dhaka City, Bangladesh.,

SR Rahman, A Begum and MF Ahmed. 2014. Ethiop J Health Sci. 24(2):145-52.

8. Incidence of Methicillin Resistant Staphylococcus aureus in Burn Patients Admitted to Burn Unit, Dhaka Medical College Hospital, Bangladesh.,

MS Islam, MF Ahmed and SR Rahman. 2013. Advances in Microbiology. 3(6):498-503.

9. Incidence and antimicrobial susceptibility of Salmonella in slum children of Dhaka City, Bangladesh.,

MF Ahmed, SR Rahman. 2013.  Asian Jr. of Microbiol. Biotech. Env. Sc. Vol. 15, No. (3): 2013: 473-477.

10. Saccharification of Sugarcane Bagasse by Enzymatic Treatment for Bioethanol Production.,

MF Ahmed, SR Rahman and DJ Gomes. 2012.  Malaysian Journal of Microbiology, Vol 8(2):97-103.

11. Group A Streptococcal Sore Throat in periurban population of Bangladesh: A prospective study a antimicrobial susceptibility.,

T Azad, MS Islam, MF Ahmed and SR Rahman. 2011. Bangladesh Journal of Medical Science 17(2), pp. 121-126.

12. Prevalence of uropathogens and their drug resistance profile in diabetic and non-diabetic patients: a comparative study.,

MZ Abedin, MF Ahmed, L Jarin et. al. 2011. Bangladesh Journal of Medical Science 17(2), pp. 99-103.

13. Antimicrobial activity of extracts of Centella asiatica using different solvents.,

MAK Parvez, MSZ Shahriar, MMH Khan and MF Ahmed. 2010. Bangladesh Journal of Medical Science 16(2), pp. 145-149.

14. Distribution and resistance trends of Escherichia coli from urinary tract infections isolated in Dhaka city. Bangladesh,

MA Bashar, MF Ahmed, SR Rahman, DJ Gomes. 2009. Journal of Medical Science 15(2) pp. 13-18.

15. Multidrug-resistant bacterial infections of the urinary tract in children.,

MF Ahmed, MZ Abedin. 2009. Bangladesh Journal of Medical Science. 15(1):55-58.

16. Fuel Ethanol Production from Molasses by Some Indigenous Yeast Isolates.,

SH Sheela, MF Ahmed, DJ Gomes. 2008. Bangladesh Journal of Microbiology 25(2) pp. 129-133.

17. Antibiotic resistance of a clinical isolate of methicillin-resistant Staphylocuccus aureus against commonly used antibiotics.,

MSU Ahmed, MF Ahmed and SR Rahman. 2008. Bangladesh Journal of Medical Science 14(2) pp. 144-148.

 

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BOOK

Studies of viral and cellular proteins involved in herpes simplex virus type-1 egress,

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