Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.

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.

A comprehensive immunoinformatic analysis of chitin deacetylase's and MP88 for designing multi-epitope vaccines against Cryptococcus neoformans.

Cryptococcus neoformans causes life-threatening pneumonia and meningitis and is regarded as one of the leading killers of immunocompromised individuals. There is currently no vaccine against this pathogen. Recently, WHO placed it at the top among the critical priority groups in the fungal priority pathogens to accelerate the development of effective treatments. Numerous studies suggested the potential of subunit vaccines to overcome the challenges associated with live and inactivated whole-cell vaccines. Therefore, this study exploited integrated reverse vaccinology and immunoinformatic approach to construct and characterize multi-epitope vaccines targeting chitin deacetylases (Cda1, Cda2, Cda3) and MP88 of C. neoformans. 4 CTL, 8 HTL and 6 B cell epitopes were fused with different adjuvants and appropriate linkers to design two multi-epitope vaccines (VC1 and VC2). Both chimeric constructs were predicted to be highly antigenic, non-allergenic, non-toxic, soluble and had satisfactory physicochemical properties. Molecular docking and binding free energy calculation revealed strong binding interactions between vaccine constructs and human TLRs (TLR-2 and TLR-4). Classical MD Simulation and Normal mode analysis verified the stability of the vaccine-TLR complex in the biological environment. Codon adaptation, cloning and in silico expression suggested the efficient expression of recombinant vaccine proteins in E. coli. Both candidates also generated robust immune profiles comprising innate, adaptive and humoral immune responses. Taken together, experimental validations of our findings through extensive in vitro and in vivo testing might provide an effective vaccine for prophylactic control of C. neoformans.Communicated by Ramaswamy H. Sarma.

Genome Sequence of Genotype 1A Hepatovirus A Isolated from Plasma from a Haitian Child.

Genotype 1A hepatovirus A was identified by quantitative reverse transcription-PCR and isolated from plasma from a Haitian child with acute undifferentiated febrile illness and malaise. The strain was most closely related to Brazilian strains, consistent with recognized patterns of virus movement in the Caribbean region.

Use of Phages to Treat Antimicrobial-Resistant Salmonella Infections in Poultry.

Salmonellosis is one of the most common bacterial infections that impacts both human health and poultry production. Although antibiotics are usually recommended for treating Salmonella infections, their misuse results in the evolution and spread of multidrug-resistant (MDR) bacteria. To minimize the health and economic burdens associated with antimicrobial resistance, a novel antibacterial strategy that can obliterate pathogens without any adverse effects on humans and animals is urgently required. Therefore, therapeutic supplementation of phages has gained renewed attention because of their unique ability to lyse specific hosts, cost-effective production, environmentally-friendly properties, and other potential advantages over antibiotics. In addition, the safety and efficacy of phage therapy for controlling poultry-associated Salmonella have already been proven through experimental studies. Phages can be applied at every stage of poultry production, processing, and distribution through different modes of application. Despite having a few limitations, the optimized and regulated use of phage cocktails may prove to be an effective option to combat infections caused by MDR pathogens in the post-antibiotic era. This article mainly focuses on the occurrence of salmonellosis in poultry and its reduction with the aid of bacteriophages. We particularly discuss the prevalence of Salmonella infections in poultry and poultry products; review the trends in antibiotic resistance; and summarize the application, challenges, and prospects of phage therapy in the poultry industry.

Assessment of foodborne transmission of Salmonella enteritidis in hens and eggs in Bangladesh.

OBJECTIVES: 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. MATERIALS AND METHODS: 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. RESULTS: 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. CONCLUSIONS: Our results will help establish effective monitoring programs to reduce the transmission of Salmonella spp. in poultry and poultry products.

Draft genome analysis of a multidrug-resistant Pseudomonas aeruginosa CMPL223 from hospital wastewater in Dhaka, Bangladesh.

OBJECTIVES: Multidrug-resistant (MDR) clones of Pseudomonas aeruginosa can cause complicated infections in human. The emergence of ST664 of MDR P. aeruginosa has been reported in Nepal, Iran and China. Here, we present the draft genome analysis of a MDR P. aeruginosa CMPL223 isolated from hospital wastewater in Bangladesh to understand antimicrobial resistance trends and pathogenicity. METHODS: Cetrimide agar was used for isolation of P. aeruginosa. Polymerase chain reaction (PCR) was carried out for detection of biofilm and integron related genes. Bacterial susceptibility to antibiotics was determined by disc diffusion method. Sequencing of whole genomic DNA was performed using Illumina iSeq 100 platform. Following quality checking of raw reads, assembly and annotation of sequences, a wide array of in silico tools were used for characterization of draft genome. RESULTS: The isolate was a strong biofilm former, carried integron 1 in chromosomal DNA, and was predicted to be pathogenic. It belongs to sequence type ST664 and O7 serogroup. The assembled genome contained 12 acquired antimicrobial resistant (AMR) genes, 2 prophage regions, 240 virulence genes, 71 drug targets, 142 insertion sequences, and 1 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) array. The isolate was resistant to 21 out of 23 antibiotics, except colistin and imipenem. Comprehensive Antibiotic Resistance Database and ResFinder revealed that bacteria harboured blaOXA-50, blaOXA-796, blaPDC-374, fosA, tet(G), sul1, catB7, aph(3')-iib and ant(4')-IIb genes, conferring resistance to different classes of antibiotics. The results of in vitro characterization were consistent with the possible expression of detected antibiotic resistant genes through in silico analysis. CONCLUSION: Our data suggested the emergence of MDR P. aeruginosa ST664, which needs control measures for limiting its dissemination.

Antibody response to the first dose of AZD1222 vaccine in COVID-19 convalescent and uninfected individuals in Bangladesh.

BACKGROUND: 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. METHOD: 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. RESULTS: 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. CONCLUSION: 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.

Complete Genome Sequence of a Circulating Hepatitis B Virus Genotype C Strain Isolated from a Chronically Infected Patient Identified at an Outdoor Hospital in Bangladesh.

Hepatitis B virus (HBV) causes significant global health problems despite the presence of a potential vaccine. HBV chronic cases are increasing rapidly in developing countries like Bangladesh. Here, we report the complete genome sequence of an HBV genotype C strain isolated from a chronic patient identified at an outdoor hospital section.

Molecular analysis of amantadine-resistant influenza A (H1N1 pdm09) virus isolated from slum dwellers of Dhaka, Bangladesh.

Influenza is a highly contagious viral infection associated with excessive hospitalizations and deaths throughout the world. Continuous antigenic shift and drift is not only responsible for this devastating effect of influenza but also causes ineffectiveness of antiviral drugs and vaccines. In this study, we investigated the effectiveness of ribavirin, oseltamivir, and amantadine drugs in vitro against nine influenza A isolates collected during June 2012-August 2013 from different slums in Dhaka city. The effectiveness of these drugs was determined by measuring the inhibition of virus-induced cytopathic effect on MDCK cells through MTT assay (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). Our data showed that all nine influenza isolates (6 H1N1 pdm09 and 3 H3N2 subtypes) were completely susceptible to ribavirin (The 50% effective concentrations, EC50 3.0 µg/ml) and oseltamivir (EC50 0.35 µg/ml). When influenza A infection was challenged with amantadine drug, eight out of nine isolates (88%) demonstrated susceptibility to amantadine drug (EC50 0.30 µg/ml) while one H1N1 pdm09 isolate exhibited higher EC50 value (>10 µg/ml) beyond the cell tolerance level of drug (>5 µg/ml). Genetic analysis of transmembrane matrix protein 2 (M2), which is a target for the amantadine drug and vital for viral replication, showed a substitution of amino acid at position 31(S31 N) of that amantadine-resistant isolate indicating the possible reason of amantadine drug resistance.

Molecular epidemiology of hepatitis B virus isolated from Bangladesh.

BACKGROUND: Hepatitis B virus (HBV) is highly contagious and causes liver diseases. Globally more than 350 million people are chronically infected and among them above 80 % are from developing countries like Bangladesh. Resistance to existing drugs and vaccines are common phenomenon due to mutations in HBsAg 'a' determinant. Due to lack of data about mutations and subtypes of HBV in Bangladesh, this study strongly demands to be documented. Here, we determined the genotypes and subtypes of HBV prevalent in Bangladesh, and their genomic mutations associated with vaccine and drug resistance. RESULTS: Among 385 samples, a total of 54 (14 %) were found HBV positive, of which 19 samples were subjected to be sequenced. After bioinformatic analysis, we found Genotype D as predominant genotype (73.7 %) with subtypes ayw3 (64.3 %) and ayw2 (35.7 %), followed by genotype A with subtype adw2 (15.8 %), and then genotype C with subtype adr (10.5 %). A significant number of mutations (Thr118Val, Thr125Met, Thr126Ile, Pro127Thr, Ala128Val, Thr131Asn/Ser, Thr/Ser143Leu/Met) were found in 'a' determinant region which may admit resistance to the available vaccines and failure of HBsAg detection. CONCLUSIONS: This comprehensive study have clinical importance like disease diagnosis and treatment. It emphasizes HBV infected patients to do molecular diagnosis for choice of anti-viral drugs and effectiveness of vaccines for proper treatment.

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

BACKGROUND: Influenza viruses may cause severe acute respiratory illness among human population. People of densely populated areas, e.g., slum, are mostly affected by influenza viruses. Although potential vaccines to influenza viruses have been developed, infection rate is still high, therefore, increase the morbidity and mortality rate in slum areas. To treat these infections, slum dwellers including children and mothers do not get proper medication as well as vaccination. Hence, prevention remains to be the only mean to tackle such infections. Herein, we determined the prevalence of influenza infections among nutritionally deprived children and mothers of slum areas in Dhaka city and demonstrated the association with different risk factors like age, gender and socio-economic status. RESULTS: Nasopharyngeal swab samples and a short demography of all the participants suffering from influenza-like illness (ILI) were collected. The samples were subjected to RNA extraction and then real-time RT-PCR to detect influenza viruses. Among the ILI patients, about 87.9 % did not have knowledge about influenza infections and 80.5 % did not cover their noses during coughing as well as sneezing. Children were significantly infected by both influenza A and influenza B viruses, suggesting their vulnerability to these infections. Additionally, among the children with ILI, influenza infections were significantly associated with age below or equal to three years, very poor family incomes, practicing unhygienic habits and nutritional deficiency. CONCLUSIONS: This study suggests that proper vaccination, improved sanitary conditions and nutritional diet may help reduce the risk of influenza infections in slum areas.

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

Hepatitis B infection is still a major global health problem even though safe and effective vaccines have been available for more than 30 years. Although development of protective antibody to hepatitis B surface antigen (anti-HBs) is a common phenomenon after vaccination as well as natural infection, sometimes it does not appear even after complete vaccination. In the present study, whether the impairment of the development of anti-HBs in naturally infected and/or vaccinated populations is associated with immunomodulating risk factors (i.e., age, gender, smoking, and diabetes) and/or other risk factors (i.e., socioeconomic status, dental, and saloon exposure) was investigated through a cross-sectional study. Among 204 nonvaccinated patients, 132 (64.7%) tested positive for anti-HBc, indicating that they had been exposed to hepatitis B virus (HBV) at least once in their lifetime. Exposure to HBV (anti-HBc positive) was significantly higher among low-income people, dental exposed, and saloon users. Among anti-HBc positive patients, only 44 (33.3%) developed natural immunity with anti-HBs. Impairment in anti-HBs formation was found to be significantly high among cigarette smokers. However, no significant association of anti-HBs development was observed with age, gender, socioeconomic status, diabetes, dental exposure, and using saloon. Consistently, the frequency of developing protective anti-HBs (≥10 IU/L) among a vaccinated population was almost nine times less among smokers. These data suggest that anti-HBs development, either naturally or after vaccination, is significantly lower among smokers. It emphasizes the need to check the anti-HBs status in smokers after vaccination, and a booster vaccination should be administered if the anti-HBs antibody titer decreases below the protective level.

ANTIGENIC AND GENETIC CHARACTERIZATION OF INFLUENZA B VIRUSES IN 2012 FROM SLUMS, DHAKA, BANGLADESH.

Nasal and throat swab samples were collected from 400 subjects with influenza-like illness during June to September, 2012 from two heavily crowded slums, Rayerbazar and Hazaribagh, situated southeast of Dhaka, Bangladesh. Forty-one samples were positive for influenza B virus using quantitative RT-PCR, but no influenza A virus was detected. Antigenic characterization revealed that the influenza B viruses were of Yamagata and Victoria lineages, which was confirmed from genetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes. Co-circulation of influenza B viruses of both Yamagata and Victoria lineages in the slums of Dhaka indicates that introduction of a tetravalent vaccine formulation that includes both of these influenza B virus lineages would be more effective in this population.

Differences in lineage replacement dynamics of G1 and G2 rotavirus strains versus G9 strain over a period of 22 years in Bangladesh.

Group A rotaviruses (RVAs) have been a major cause of severe gastroenteritis in Bangladesh, mainly in children below the age of five. At the icddr,b, RVA strains collection and characterization dates back for more than 20 years. This sample collection was used to study the molecular evolution of the VP7 gene of G1, G2 and G9 RVA strains, which have been circulating in Bangladesh for most of this study period. The evolutionary rates (95% HPD) for G1, G2 and G9 were calculated to be 0.93×10(-3) (0.68-1.18), 1.45×10(-3) (1.12-1.78) and 1.07×10(-3) (0.78-1.39), respectively, which is in line with previous data for the RVA VP7 outer capsid protein, which is under strong negative selective pressure. Bayesian analyses revealed that for the G1 and G2 genotypes, one or multiple lineages co-circulated for one or a few seasons, frequently followed by replacement with genetically different lineages. This can be explained by the existence of a large variety of G1 and G2 RVA lineages and the rapid dissemination of different lineages across the globe. In contrast, circulating G9 lineages were rather closely related to each other across the study period and they were usually derived from variants circulating in the previous season(s). This is consistent with the fact that G9 RVAs have circulated in the human population for less than 20 years, and therefore their genetic diversity is much smaller, not resulting in the replacement of circulating G9 strains by highly divergent G9 lineages from abroad. Such different evolutionary dynamics for different RVA genotypes may alter their response to the selective pressure that might be exerted by the introduction of RVA vaccines and therefore a continued close monitoring is warranted.

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

BACKGROUND: Urinary tract infection (UTI) is commonly experienced by women of various age groups especially elderly ones. We planned to find out the prevalent microbial strains causing UTI in slum inhabitant adolescent and adult women in Dhaka City, Bangladesh. METHODS AND MATERIALS: Urine sample was collected from 462 UTI suspected female subjects. Pathogenic bacteria were identified using standard microbiological tests, and antimicrobial sensitivity profiles of the pathogens were determined. RESULTS: Bacteriuria was present in 9% of the subjects. A higher incidence (16.8%) of UTI was noted among adult women aged above 19 years. Escherichia coli (69%), Streptococcus spp. (15%) and Pseudomonas aeruginosa (7%) were more frequently isolated from the urine samples compared to Enterococcus faecalis (3%), Staphylococcus aureus (2%), Klebsiella pneumoniae (2%) and Hafnia alvei (2%). The E. coli isolates showed complete resistance to commonly used drugs, and 58% of these isolates were multidrug resistant (MDR). Minimum Inhibitory Concentration (MIC) values for ciprofloxacin ranged between 64µg/ml and 512µg/ml, and the Minimum Bactericidal Concentration (MBC) values against the isolates were 128µg/ml or above. Isolated strains of E. coli exhibited equal extent of ciprofloxacin resistance irrespective of the presence or absence of plasmid in them. CONCLUSION: The extent of drug resistance among the uropathogens if ignored may render them uncontrollable. This study suggests regular monitoring of drug resistance phenotype of the UTI pathogens to reduce the morbidity of female UTI patients and offer better treatment strategy in the healthcare sectors of Bangladesh.