Multidrug resistance pattern and molecular epidemiology of pathogens among children with diarrhea in Bangladesh, 2019-2021.

Antimicrobial and multidrug resistance (MDR) pathogens are becoming one of the major health threats among children. Integrated studies on the molecular epidemiology and prevalence of AMR and MDR diarrheal pathogens are lacking. A total of 404 fecal specimens were collected from children with diarrhea in Bangladesh from January 2019 to December 2021. We used conventional bacteriologic and molecular sequence analysis methods. Phenotypic and genotypic resistance were determined by disk diffusion and molecular sequencing methods. Fisher's exact tests with 95% confidence intervals (CIs) was performed. Prevalence of bacterial infection was 63% (251 of 404) among children with diarrhea. E. coli (29%) was the most prevalent. E. coli, Shigella spp., V. cholerae, and Salmonella spp., showed the highest frequency of resistance against ceftriaxone (75-85%), and erythromycin (70-75%%). About 10-20% isolates of E. coli, V. cholerae and Shigella spp. showed MDR against cephem, macrolides, and quinolones. Significant association (p value < 0.05) was found between the phenotypic and genotypic resistance. The risk of diarrhea was the highest among the patients co-infected with E. coli and rotavirus [OR 3.6 (95% CI 1.1-5.4) (p = 0.001)] followed by Shigella spp. and rotavirus [OR 3.5 (95% CI 0.5-5.3) (p = 0.001)]. This study will provide an integrated insight of molecular epidemiology and antimicrobial resistance profiling of bacterial pathogens among children with diarrhea in Bangladesh.

Development of high temperature simultaneous saccharification and fermentation by thermosensitive Saccharomyces cerevisiae and Bacillus amyloliquefaciens.

Scarcity of energy and pollution are two major challenges that have become a threat to all living things worldwide. Bioethanol is a renewable, ecological-friendly clean energy that may be utilized to address these issues. This study aimed to develop simultaneous saccharification and fermentation (SSF) process through high temperature-substrate adaptation and co-cultivation of S. cerevisiae with other potential amylolytic strains. In this study, we adapted our previously screened thermosensitive Saccharomyces cerevisiae Dj-3 strain up-to 42 °C and also screened three potential thermotolerant amylolytic strains based on their starch utilization capability. We performed SSF fermentation at high temperature by adapted Dj-3 and amylolytic strains using 10.0% starch feedstock. Interestingly, we observed significant ethanol concentration [3.86% (v/v)] from high temperature simultaneous saccharification and fermentation (HSSF) of adapted Bacillus amyloliquefaciens (C-7) and Dj-3. We attribute the significant ethanol concentration from starch of this HSSF process to C-7's high levels of glucoamylase activity (4.01 U/ml/min) after adaptation in starch (up-to 42 °C) as well as Dj-3's strong glucose fermentation capacity and also their ethanol stress tolerance capability. This study suggests the significant feasibility of our HSSF process.

A Systematic Review on COVID-19 Vaccine Strategies, Their Effectiveness, and Issues.

COVID-19 vaccines are indispensable, with the number of cases and mortality still rising, and currently no medicines are routinely available for reducing morbidity and mortality, apart from dexamethasone, although others are being trialed and launched. To date, only a limited number of vaccines have been given emergency use authorization by the US Food and Drug Administration and the European Medicines Agency. There is a need to systematically review the existing vaccine candidates and investigate their safety, efficacy, immunogenicity, unwanted events, and limitations. The review was undertaken by searching online databases, i.e., Google Scholar, PubMed, and ScienceDirect, with finally 59 studies selected. Our findings showed several types of vaccine candidates with different strategies against SARS-CoV-2, including inactivated, mRNA-based, recombinant, and nanoparticle-based vaccines, are being developed and launched. We have compared these vaccines in terms of their efficacy, side effects, and seroconversion based on data reported in the literature. We found mRNA vaccines appeared to have better efficacy, and inactivated ones had fewer side effects and similar seroconversion in all types of vaccines. Overall, global variant surveillance and systematic tweaking of vaccines, coupled with the evaluation and administering vaccines with the same or different technology in successive doses along with homologous and heterologous prime-booster strategy, have become essential to impede the pandemic. Their effectiveness appreciably outweighs any concerns with any adverse events.

Molecular Epidemiology, Evolution and Reemergence of Chikungunya Virus in South Asia.

Chikungunya virus (CHIKV) is a vector (mosquito)-transmitted alphavirus (family Togaviridae). CHIKV can cause fever and febrile illness associated with severe arthralgia and rash. Genotypic and phylogenetic analysis are important to understand the spread of CHIKV during epidemics and the diversity of circulating strains for the prediction of effective control measures. Molecular epidemiologic analysis of CHIKV is necessary to understand the complex interaction of vectors, hosts and environment that influences the genotypic evolution of epidemic strains. In this study, different works published during 1950s to 2020 concerning CHIKV evolution, epidemiology, vectors, phylogeny, and clinical outcomes were analyzed. Outbreaks of CHIKV have been reported from Bangladesh, Bhutan, India, Pakistan, Sri Lanka, Nepal, and Maldives in South Asia during 2007-2020. Three lineages- Asian, East/Central/South African (ECSA), and Indian Ocean Lineage (IOL) are circulating in South Asia. Lineage, ECSA and IOL became predominant over Asian lineage in South Asian countries during 2011-2020 epidemics. Further, the mutant E1-A226V is circulating in abundance with Aedes albopictus in India, Bangladesh, Nepal, and Bhutan. CHIKV is underestimated as clinical symptoms of CHIKV infection merges with the symptoms of dengue fever in South Asia. Failure to inhibit vector mediated transmission and predict epidemics of CHIKV increase the risk of larger global epidemics in future. To understand geographical spread of CHIKV, most of the studies focused on CHIKV outbreak, biology, pathogenesis, infection, transmission, and treatment. This updated study will reveal the collective epidemiology, evolution and phylogenies of CHIKV, supporting the necessity to investigate the circulating strains and vectors in South Asia.

Prevalence and impact of comorbidities on disease prognosis among patients with COVID-19 in Bangladesh: A nationwide study amid the second wave.

BACKGROUND: Socio-demographics and comorbidities are involved in determining the severity and fatality in patients with COVID-19 suggested by studies in various countries, but study in Bangladesh is insufficient. AIMS: We designed the study to evaluate the association of sociodemographic and comorbidities with the prognosis of adverse health outcomes in patients with COVID-19 in Bangladesh. METHODS: A multivariate retrospective cohort study was conducted on data from 966 RT-PCR positive patients from eight divisions during December 13, 2020, to February 13, 2021. Variables included sociodemographic, comorbidities, symptoms, Charlson comorbidity index (CCI) and access to health facilities. Major outcome was fatality. Secondary outcomes included hospitalization, duration of hospital stay, requirement of mechanical ventilation and severity. RESULTS: Male (65.8%, 636 of 966) was predominant and mean age was 39.8 ± 12.6 years. Fever (79%), dry cough (55%), and loss of test/smell (51%) were frequent and 74% patients had >3 symptoms. Fatality was recorded in 10.5% patients. Comorbidities were found in 44% patients. Hypertension (21.5%) diabetes (14.6%), and cardiovascular diseases (11.3%) were most prevalent. Age >60 years (OR: 4.83, 95% CI: 2.45-6.49), and CCI >3 (OR: 5.48, 95% CI: 3.95-7.24) were predictors of hospitalizations. CCI >4 (aOR: 3.41, 95% CI: 2.57-6.09) was predictor of severity. Age >60 years (aOR: 3.77, 95% CI: 1.07-6.34), >3 symptoms (aOR: 2.14, 95% CI: 0.97-4.91) and CCI >3 vs. CCI <3 (aOR: 5.23, 95% CI: 3.77-8.09) were independently associated with fatality. CONCLUSIONS: Increased age, >3 symptoms, increasing comorbidities, higher CCI were associated with increased hospitalization, severity and fatality in patients with COVID-19.

Prevalence and impact of diabetes and cardiovascular disease on clinical outcome among patients with COVID-19 in Bangladesh.

BACKGROUND: Patients with coronavirus disease-2019 (COVID-19) with preexisting diabetes and cardiovascular metabolic diseases have higher fatality rate. The circulation of new variants with emerging clinical characteristics requires more studies focusing the impact of preexisting health conditions on outcome of COVID-19 accurately. AIMS: Main aim of this study was to investigate the impact of diabetes and cardiovascular disease (CVD) on disease prognosis and severe health outcomes among patients with COVID-19. METHODS: A retrospective study was performed on 799 patients with COVID-19 during December 10, 2020, to February 10, 2020 in Bangladesh. Logistic regression analysis was performed for age, sex, diabetes, CVD and symptoms on fatality. Kaplan-Meier survival analysis was conducted to predict the survival rate. RESULTS: Fatality was detected in 40% (318 of 799) patients with COVID-19. Among 318 fatalities, 90.6% were detected in patients with CVD and 74.5% in patients with diabetes. Case fatality rate was highest in patients with COVID-19, CVD and diabetes (94, 184 of 195). Fever (91%) and dry cough (71%) were the most frequent symptoms. CVD (42.2%), diabetes (32.7%) and obesity (18%) were prevalent. The highest odds of risk was detected in patients with COVID-19, CVD and diabetes (OR: 6.98, 95% CI, 4.21 to 7.34). Female patients had the highest survival rate. CONCLUSIONS: In this study, 318 fatality was seen in 799 patients with COVID-19. The highest odds of fatality risk was detected in patients with COVID-19, CVD and diabetes. The risk increased many folds when CVD and diabetes coexisted in patients.

Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan.

Although vaccines have become available, emergence and rapid transmission of new variants have added new paradigm in the coronavirus disease-2019 (COVID-19) pandemic. Weather, population and host immunity have been detected as the regulatory elements of COVID-19. This study aims to investigate the effects of weather, population and host factors on the outcome of COVID-19 and mutation frequency in Japan. Data were collected during January 2020 to February 2021. About 92% isolates were form GR clades. Variants 501Y.V1 (53%) and 452R.V1 (24%) were most prevalent in Japan. The strongest correlation was detected between fatalities and population density (rs = 0.81) followed by total population (rs = 0.72). Relative humidity had the highest correlation (rs = -0.71) with the case fatality rate. Cluster mutations namely N501Y (45%), E484K (30%), N439K (16%), K417N (6%) and T478I (3%) at spike protein have increased during January to February 2021. Above 90% fatality was detected in patients aged >60 years. The ratio of male to female patients of COVID-19 was 1.35:1. This study will help to understand the seasonality of COVID-19 and impact of weather on the outcome which will add knowledge to reduce the health burden of COVID-19 by the international organisations and policy makers.

Environmental correlation and epidemiologic analysis of COVID-19 pandemic in ten regions in five continents.

BACKGROUND: Coronavirus disease-2019 (COVID-19) has caused worldwide health emergencies during the last 6 months of 2020. Within very short time, severe acute respiratory coronavirus-2 (SARS-CoV-2) has infected over 64,516,333 people with 1,493,264 fatalities in 210 countries and regions. Previous studies have reported that environmental factors can affect the viability and transmission of SARS-CoV-2. This study aimed to determine the correlation of environmental factors with COVID-19 pandemic and epidemiology of COVID-19 across nine countries in five continents. METHODS: Both environmental and health data were retrieved from various databases during January 1, 2020 to June 30, 2020. Mean value of environmental factors were calculated for weekly and daily cases and fatalities. Spearman correlation test was conducted. RESULTS: In this study, most of the COVID-19 cases and fatalities were detected from regions (New York, Madrid, Lombardy, London and Sau Paulo) with 7 °C-25 °C mean temperature per day, 3 to 6 mean UV index per day and 14 km/h to 22 km/h mean wind velocity per day. Both cases and fatalities increased significantly after removing lockdown in Bangladesh, India, Brazil and South Africa. Over 50% COVID-19 patients were asymptomatic in every country except Brazil and Australia. Fever (>50%) was the most common symptom followed by cough (45%), tiredness (38%) and sore throat (30%), respectively. In India and Bangladesh over 70% of cases were reported in male. Significant correlation of COVID-19 cases with temperature and UV were detected in London, Lombardy, Madrid, New York and Dhaka. CONCLUSION: This is one of the first cross-country epidemiologic and correlation studies between environmental factors and COVID-19 pandemics. This study will help both local and international health organizations and policy makers to face the COVID-19 challenge.

Molecular epidemiology and genetic diversity of norovirus infection in children with acute gastroenteritis in Bangladesh, 2014-2019.

Acute gastroenteritis (AGE) is one of the most common diseases in children, and it continues to be a significant cause of morbidity and mortality worldwide. Norovirus is one of the major enteropathogens associated with both sporadic diarrhea and outbreaks of gastroenteritis. This study aims to investigate genotype diversity and molecular epidemiology of norovirus in Bangladesh. A total of 466 fecal specimens were collected from January 2014 to January 2019 from children below 5 years old with AGE in Bangladesh. All samples were analyzed by reverse transcriptase polymerase chain reaction to detect norovirus, and sequence analysis was conducted if found positive. Norovirus was detected in 5.1% (24 of 466) fecal specimens. Norovirus genotype GII.7 was predominant (62.5%, 15 of 24), followed by GII.3 (37.5%, 9 of 24). Coinfection between rotavirus and norovirus was found in 7 of 24 positive cases. Diarrhea (93.7%) and dehydration (89%) were the most common symptoms in children with AGE. About 80% of the positive cases were detected in children aged under 24 months. One seasonal peak (87.5% infection) was detected in the winter. This study suggests that norovirus continues to be one of the major etiologies of children AGE in Bangladesh. This study will provide a guideline to assess the burden of norovirus infection in Bangladesh, which will assist to combat against AGE.

Molecular epidemiology and surveillance of circulating rotavirus among children with gastroenteritis in Bangladesh during 2014-2019.

Acute gastroenteritis is one of the major health problems in children aged <5 years around the world. Rotavirus A (RVA) is an important pathogen of acute gastroenteritis. The burden of rotavirus disease in the pediatric population is still high in Bangladesh. This study investigated the prevalence of group A, B, and C rotavirus (RAV, RBV, RCV), norovirus, adenovirus (AdV) and human bocavirus (HBoV) infections in children with acute gastroenteritis in Bangladesh from February 2014 to January 2019. A total of 574 fecal specimens collected from children with diarrhea in Bangladesh during the period of February 2014-January 2019 were examined for RAV, RBV and RCV by reverse transcriptase- multiplex polymerase chain reaction (RT- multiplex PCR). RAV was further characterized to G-typing and P-typing by RT-multiplex PCR and sequencing method. It was found that 24.4% (140 of 574) fecal specimens were positive for RVA followed by AdV of 4.5%. RBV and RCV could not be detected in this study. Genotype G1P[8] was the most prevalent (43%), followed by G2P[4] (18%), and G9P[8] (3%). Among other genotypes, G9P[4] was most frequent (12%), followed by G1P[6] (11%), G9P[6] (3%), and G11P[25] (3%). We found that 7% RVA were nontypeable. Mutations at antigenic regions of the VP7 gene were detected in G1P[8] and G2P[4] strains. Incidence of rotavirus infection had the highest peak (58.6%) during November to February with diarrhea (90.7%) as the most common symptom. Children aged 4-11 months had the highest rotavirus infection percentage (37.9%). By providing baseline data, this study helps to assess efficacy of currently available RVA vaccine. This study revealed a high RVA detection rate, supporting health authorities in planning strategies such as introduction of RVA vaccine in national immunization program to reduce the disease burden.

Molecular and epidemiological trends of human bocavirus and adenovirus in children with acute gastroenteritis in Bangladesh during 2015 to 2019.

Virus associated diarrhea remains one of the leading causes of children morbidity and mortality in Bangladesh. Human bocavirus (HBoV) has been reported as a potential pathogen of children's diarrhea worldwide. However, due to its frequent association with other gastroenteric pathogens, its role as diarrhea causative agent remains to be defined. This study focuses to detect the incidence of HBoV and adenovirus (AdV) and to determine the molecular and epidemiological characteristics of HBoV and AdV. Between January 2015 to January 2019, 290 fecal specimens were collected from diarrheal children in Bangladesh. All fecal specimens were tested for HBoV and AdV by conventional polymerase chain reaction and sequencing methods. HBoV was detected in 7.24% (21 of 290) of the stool samples, as a sole virus in 71.42% (15 of 21) of the positive samples. AdV was detected in 4.82% (14 of 290) of the samples. The most common clinical symptoms of HBoV infected patients were diarrhea (100%) and vomiting (57%). All of the isolates of HBoV were from HBoV1 and AdV were from AdV41, AdV5, AdV7, and AdV8. To the best of our knowledge, this is the first epidemiological and molecular analysis report of HBoV from clinical specimens in Bangladesh. In the future, more studies are needed to clarify the role of HBoV as diarrheal pathogens.

Molecular and Epidemiologic Analysis of Diarrheal Pathogens in Children With Acute Gastroenteritis in Bangladesh During 2014-2019.

BACKGROUND: Diarrheal disease is one of the leading causes of childhood morbidity and mortality in the 21st century in developing countries. Mainly infants and young children develop diarrheal diseases. This study aims to determine the incidence of diarrheal pathogens in children in Bangladesh. METHODS: During 2014 to 2019, 387 fecal specimens were collected from children with diarrhea in Bangladesh. Bacterial pathogens were detected by conventional bacteriologic, biochemical and molecular sequence analysis methods. DNA virus and RNA virus (diarrheal viruses) were detected using polymerase chain reaction and reverse transcriptase polymerase chain reaction, respectively and confirmed by molecular sequence analysis. RESULTS: Bacterial infections were detected in 39.27% (152 of 387) of the stool samples. Escherichia coli was the most prevalent (17.3%) followed by Vibrio cholerae (13.5%), Salmonella spp. (4.9%) and Shigella spp. (3.6%). From 387 fecal specimens tested, 42.4% (164 of 387) were positive for viral infections. Rotavirus was the most prevalent (26.3%), followed by adenovirus (5.7%), norovirus (5.4%) and human bocavirus (4.9%). Dual infection between rotavirus and E. coli accounted for the largest portion of coinfection (48%). Diarrhea (77%) and abdominal pain (65%) were most common followed by vomiting (63%), fever (43%) and dehydration (39%). E. coli and V. cholerae were most resistant against ciprofloxacin (62.7%) and tetracycline (88.5%). qnrA and sul4 resistance genes were isolated from these pathogens. CONCLUSIONS: Data from this study underline the high incidence of diarrheal pathogens and presence of antibiotics resistance genes in a pediatric population in Bangladesh.

Clinical Characteristics and Diagnostic Challenges of COVID-19: An Update From the Global Perspective.

Clinical characteristics are essential for the correct diagnosis of diseases. The current review aimed to summarize the global clinical characteristics of the COVID-19 patients systematically and identify their diagnostic challenges to help the medical practitioners properly diagnose and for better management of COVID-19 patients. We conducted a systematic search in PubMed, Web of Science, Scopus, Science Direct, and Google Scholar databases for original articles containing clinical information of COVID-19 published up to 7th May 2020. Two researchers independently searched the databases to extract eligible articles. A total of 34 studies from 8 different countries with 10889 case-patients were included for clinical characteristics. The most common clinical symptoms were cough 59.6, fever 46.9, fatigue 27.8, and dyspnea 20.23%. The prominent laboratory findings were lymphocytopenia 55.9, elevated levels of CRP 61.9, aspartate aminotransferase 53.3, LDH 40.8, ESR 72.99, serum ferritin 63, IL-6 52, and prothrombin time 35.47%, and decreased levels of platelets 17.26, eosinophils 59.0, hemoglobin 29, and albumin 38.4%. CT scan of the chest showed an abnormality in 93.50% cases with bilateral lungs 71.1%, ground-glass opacity 48%, lesion in lungs 78.3%, and enlargement of lymph node 50.7%. Common comorbidities were hypertension, diabetes, obesity, and cardiovascular diseases. The estimated median incubation period was 5.36 days, and the overall case fatality rate was 16.9% (Global case fatality outside China was 22.24%: USA 21.24%, Italy 25.61%, and others 0%; whereas the case fatality inside the Hubei Province of China was found to be 11.71%). Global features on the clinical characteristics of COVID-19 obtained from laboratory tests and CT scan results will provide useful information to the physicians to diagnose the disease and for better management of the patients as well as to address the diagnostic challenges to control the infection.

Bacteriological assessments of foodborne pathogens in poultry meat at different super shops in Dhaka, Bangladesh.

Poultry is now considered as a major fast-growing source of meat in the world. The consumers demand safe and hygienic products without contamination with pathogenic microorganisms when the production and consumption of poultry meat is gradually increasing. The present study was conducted to assess the bacterial contamination of dressed chicken collected from different supershops in Dhaka, Bangladesh. The chicken samples from S1, S2, M1, M2 and A supershops were analyzed to determine the enteropathogenic bacteria in poultry meat. Three genera of bacteria were isolated from all of the chicken meat samples. These enteropathogens from various organs of dressing chickens were also enumerated. The isolates were presumptively identified as E. coli, Salmonella spp., and Shigella spp. by conventional culture method. The three enteropathogens were subjected to PCR assay for their confirmation as virulent enteropathogens. Only E. coli isolates were confirmed as pathogenic E. coli (Enterotoxigenic), other isolates were not confirmed as virulent Salmonella spp., Shigella spp.. Results of this study demonstrated that more cautions are recommended for personnel hygiene in processing and handling of poultry and poultry products to prevent occurrence of enterotoxigenic E. coli in dressed poultry meat sold by the supershops in Bangladesh.

Analysis of reading frame and expressional regulation of randomly selected promoter-proximal genes in Escherichia coli.

The expression of seventy-seven randomly cloned genes of Escherichia coli was examined following a variety of treatments including heat shock, glucose starvation, phosphate starvation, ammonium starvation or osmotic shock, with the aid of lacZ reporter gene protein fusions on multicopy plasmids. Two of 77 genes (amr and yigL) had not previously been identified as protein encoding open-reading frames (ORFs) in annotations of the E. coli genome database. Thirteen genes exhibited significant changes in expression in response to at least one of the treatments, and six of them appeared to be controlled by more than one sigma (sigma) factor of RNA polymerase. This study thus allows us not only to identify the reading frame of the genomic genes but also to support the hypothesis earlier proposed that a significant proportion of genes in E. coli are involved in adaptations to various stresses to which the organism is likely to be exposed in the environment.

Characterization of the ves gene, which is expressed at a low temperature in Escherichia coli.

A gene, designated ves, that is expressionally responsive to temperature was found in Escherichia coli. Experiments with a single-copy lacZ operon fusion and primer extension analysis revealed that ves was expressed at a low temperature with a peak around 25 degrees C but was hardly expressed at 42 degrees C. After a temperature downshift, the mRNA level increased until 6 to 12 h and then decreased. Consistently, an A + T-rich sequence similar to UP elements seen in cold-shock inducible cold-shock protein (Csp) genes was found up-stream of the ves promoter, and its 5'-untranslated region was found to share similarity with those of the cold-shock inducible and cold-adaptive cspA and cspB genes. Additionally, a putative down-stream box, which also exists in cold-inducible proteins, was found. The ves product was identified by overproduction and determination of its N-terminal sequence. Similarity of the C-terminal portion of Ves to the CspA family suggests that Ves belongs to this family. The results of gene-disruption experiments suggest that ves is not essential for E. coli.