Draft-genome analysis provides insights into the virulence properties and genome plasticity of Vibrio fluvialis organisms isolated from shrimp farms and Turag river in Bangladesh.

Vibrio fluvialis is an opportunistic waterborne and seafood-borne enteric pathogen capable of causing severe diarrhea leading to death. This pathogen is endemic to Bangladesh, a country which is a major producer of cultured shrimp and wild-caught prawns. In this study, we carried out whole-genome sequencing of three V. fluvialis organisms isolated from shrimp farm and river sediment showing strong pathogenic characteristics in vivo and in vitro and compared their genomes against other V. fluvialis and related pathogenic species to glean insights into their potential as pathogens. Numerous virulence-associated genes including hemolysins, cytolysins, three separate Type IV pili, Types II and VI secretion systems, biofilm, and the V. cholerae pathogenesis regulating gene, toxR, were identified. Moreover, we found strain S-10 to have the propensity to acquire antibiotic resistance genes through horizontal gene transfer. These findings indicate that shrimp farms and rivers could be potential sources of V. fluvialis organisms which are an infection threat of public health concern.

Mutational profiles of marker genes of cervical carcinoma in Bangladeshi patients.

BACKGROUND: Cervical cancer is a gynecologic cancer type that develops in the cervix, accounting for 8% mortality of all female cancer patients. Infection with specific human papillomavirus (HPV) types is considered the most severe risk factor for cervical cancer. In the context of our socioeconomic conditions, an increasing burden of this disease and high mortality rate prevail in Bangladesh. Although several researches related to the epidemiology, HPV vaccination, and treatment modalities were conducted, researches on the mutation profiles of marker genes in cervical cancer in Bangladesh remain unexplored. METHODS: In this study, five different genomic regions within the top three most frequently mutated genes (EGFR, KRAS and PIK3CA) in COSMIC database with a key role in the development of cervical cancers were selected to study the mutation frequency in Bangladeshi patients. In silico analysis was done in two steps: nucleotide sequence analysis and its corresponding amino acid analysis. RESULTS: DNA from 46 cervical cancer tissue samples were extracted and amplified by PCR, using 1 set of primers designed for EGFR and 2 sets of primers designed for two different regions of both PIK3CA and KRAS gene. In total, 39 mutations were found in 26 patient samples. Eleven different mutations (23.91%), twenty-four different mutations (52.17%) and four mutations (8.7%) were found in amplified EGFR, PIK3CA and KRAS gene fragments, respectively; among which 1 (EGFR) was common in seven patient samples and 2 (PIKCA) were found in more than 1 patient. Our study shows that except for KRAS, the frequency of observed mutations in our patients is higher than those reported earlier in other parts of the world. Most of the exonic mutations were found only in the PIK3CA and EGFR genes. CONCLUSIONS: The study can be used as a basis to build a mutation database for cervical cancer in Bangladesh with the possibility of targetable oncogenic mutations. Further explorations are needed to establish future diagnostics, personalized medicine decisions, and other pharmaceutical applications for specific cancer subtypes.

An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.

Introduction: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility. Methods: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods. Results and discussion: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.

Multi-drug resistant gene mutation analysis in Mycobacterium tuberculosis by molecular techniques.

Background and Objectives: Rifampicin (RIF) and isoniazid (INH), two most potent antibiotics, are prescribed to cure tuberculosis. Mycobacterium tuberculosis, the causative agent of multidrug-resistant tuberculosis (MDR-TB), is resistant to these first-line drugs. Here, two molecular techniques were demonstrated such as PCR sequencing-based and GeneXpert assay for rapidly identifying MDR-TB. Materials and Methods: Pulmonary samples (sputum) were collected from 55 MDR-TB suspected patients from the National Tuberculosis Reference Laboratory (NTRL), Dhaka where the research work was partially accomplished and continued in the department of Microbiology, University of Dhaka, Bangladesh. We strived for sequencing technique as well as GeneXpert assay to identify mutations in rpoB and katG genes in MTB strains and sputum directly. Culture-based drug susceptibility testing (DST) was performed to measure the efficacy of the molecular methods employed. Results: When analyzed, rpoB gene mutations at codons 531 (54.54%), 526 (14.54%), and 516 (10.91%) were found by sequencing in 80% of the samples. Nucleotide substitution at katG315 (AGC→ACC) was spotted in 16 (76.19%) out of 21 samples. When comparing the sequencing results with DST, sensitivity and specificity were investigated to determine drug-resistance (rifampicin-resistance were 98 and 100% whereas isoniazid-resistance were 94 and 100% respectively). Additionally, as a point of comparison with DST, only 85.45% of RIF mono-resistant TB cases were accurately evaluated by the GeneXpert assay. Conclusion: This research supports the adoption of PCR sequencing approach as an efficient tool in detecting MDR-TB, counting the higher sensitivity and specificity as well as the short period to produce the results.

Occurrence and characterization of ß-lactamase-producing bacteria in biomedical wastewater and in silico enhancement of antibiotic efficacy.

Wastewater discharged from hospitals is a recognized contributor to the dissemination of antibiotic-resistant bacteria and their associated genetic traits into the environment. This study focused on the analysis of ß-lactamase-producing pathogenic bacteria within untreated biomedical wastewater originating from various hospitals in Dhaka City, Bangladesh, as well as in silico evaluation and structural activity relationship mentioned antibiotics were evaluated. In silico drug design techniques were applied to identify the relationship with how the functional group impacts the binding energy. Out of the 184 isolates obtained from well-established hospital sewage discharge points in Dhaka, 89 were identified as ß-lactamase positive. These bacteria were subjected to antimicrobial susceptibility testing using the VITEK-2 assay, and their profiles of extended-spectrum beta-lactamase (ESBL) production were determined through molecular methodologies. Among the ß-lactamase-positive isolates, considerable resistance was observed, particularly against ampicillin, Ceftriaxone, Cefuroxime, and Meropenem. The predominant resistant species included Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae. The study identified the prevalence of ESBL-producing genes, with blaNDM-1 being the most prevalent, followed by blaOXA-1, blaSHV, blaCTX-M, and blaKPC. None of the isolates carried the blaTEM gene. In addition to characterizing these bacteria, the research explored ways to enhance the binding energy of four existing antibiotics as new inhibitors through computational studies. The findings revealed significant improvements in binding energy. Specifically, Meropenem initially exhibited a binding energy of -7.5 kcal/mol, notably increasing to -8.3 kcal/mol after modification. With an initial binding energy was only -7.9 kcal/mol, Ampicillin experienced an enhancement, reaching -8.0 kcal/mol post-modification. Similarly, Ceftriaxone, with an initial binding energy of -8.2 kcal/mol, increased to -8.5 kcal/mol following structural adjustments. Finally, Cefuroxime, initially registering a binding energy of -7.1 kcal/mol, substantially increased to -8.9 kcal/mol after modification. This finding establishes a foundation for future investigations in the development of modified antibiotics to address the issue of antibiotic resistance. It presents prospective remedies for the persistent problem of antibiotic-resistant bacteria in healthcare and the environment.

Analysis of Different Prognostic Indicators for Malnutrition and Shigella flexneri Infection Among the Children in Bangladesh.

The present study investigates into some socio-economic, demographic, and nutritional features that can predispose Bangladeshi children to malnutrition and Shigella flexneri infection. Significant prognostic indicators associated with malnutrition were mother's illiteracy (unadjusted odds ratio, OR = 2.580; 95% confidence interval, CI = 1.134-5.867 and adjusted odds ratio, ORa, 3.814; 95% CI = 1.124-12.943), low birth weight (OR = 3.143; 95% CI = 1.2-8.232 and ORa = 2.404; 95% CI = 0.870-6.644) and poor socioeconomic status (OR = 2.549; 95% CI = 1.382-4.701 and ORa = 1.808; 95% CI = 0.852-3.838). Age was the strongest predictor for the acquisition of S. flexneri infection in the studied population (OR = 5.472; 95% CI = 2.583-11.592 and ORa = 5.808; 95% CI = 2.420-13.942). The severity of malnutrition was significantly (P = 0.033) related to seroprevalence of S. flexneri infection. To reduce malnutrition emphasis should be given on controlling the incidence of low birth weight, improving the literacy status especially of mothers and narrowing the gap between different socio-economic levels. Malnourished children should be examined for severity and direct intervention therapy should be given when necessary.

Local bacteriophage isolates showed anti- Escherichia coli O157:H7 potency in an experimental ligated rabbit ileal loop model.

Escherichia coli O157:H7 is considered among the most important recently emerged food-borne bacteria causing severe hemorrhagic diarrhea. Antibiotic treatment is not recommended as a prospective curative agent against this pathogen. Therefore, potency assessment of the local lytic phage isolates infecting E. coli O157:H7 as an alternate remedy to antibiotics was the principal concern of this study. Phage isolates against E. coli O157:H7 were checked by polymerase chain reaction for the presence of the virulence genes stx1 and stx2, and the safe phages were further screened in vitro for their capacity as biocontrol agents. Two bacteriophage strains, namely PAH6 and P2BH2, that had expressed potential antibacterial activity (P < 0.05) in vitro were selected for in vivo testing in ligated rabbit ileal loop models. Both phage isolates were capable of decreasing fluid accumulation in rabbit ileal loops along with reducing bacterial growth (r = 0.992). Combined application of the phages was found most satisfactory, reducing seven log cycles of bacterial growth. Consistent results in both in vivo and in vitro experiments demonstrate the applicability of bacteriophages as a rapid response tool against E. coli O157:H7. To our knowledge, this is the first successful application of the rabbit ileal loop test for therapeutic evaluation of bacteriophages.

Genotypic distribution and prevalence of human papillomavirus infection in an apparently healthy female population in Bangladesh.

Objective: Human papillomavirus (HPV) comprises around 120 genotypically related viruses, classified into low- and high-risk HPVs, which are capable of replicating inside the keratinocytes of skin or mucous membranes. Studies suggest that infections with HPV-16 or HPV-18 have a higher rate of developing cancer. The aim of our study was to detect HPV early, and to estimate the genotype-specific prevalence of HPV in apparently healthy and asymptomatic females in Bangladesh. Method: After cervical swab specimen collection, a VIA test was performed to identify any type of abnormality in the cervix. A multiplex PCR amplification of HPV DNA, using L1 consensus primer systems, was performed with type-specific primers, followed by sequencing to detect HPV genotypes. Result: Of the 417 females, 121 were found to be HPV positive. The most prevalent high-risk HPV genotypes were found to be HPV-16 and HPV-18. Different patient demographic parameters, such as age, socioeconomic status, education, and history of first intercourse, were also studied to establish correlations with HPV infection. Conclusion: Our results might provide some insights into factors that influence the development of cervical cancer. They might also help in guiding better patient management, increased public health awareness, further testing, and the implementation of existing vaccines.

Evaluation of plasma Epstein-Barr virus DNA as a biomarker for Epstein-Barr virus-associated Hodgkin lymphoma.

OBJECTIVES: Epstein-Barr virus is a tumorigenic virus and has been extensively studied as a causative agent for Hodgkin lymphoma. Although immunostaining of the tumor biopsy is the standard method for diagnosis of Epstein-Barr virus-driven Hodgkin lymphoma, the invasiveness of the procedure renders it difficult and less desirable for the patients. Therefore, we designed this study to evaluate the efficiency of plasma Epstein-Barr virus DNA detection as an alternative diagnostic and prognostic method for Epstein-Barr virus-associated Hodgkin lymphoma. METHODS: This analytical cross-sectional study was conducted during March 2017 to December 2018 including 43 Hodgkin lymphoma patients diagnosed histopathologically followed by the latent membrane protein-1 immunohistochemistry to determine their Epstein-Barr virus association. Plasma Epstein-Barr virus DNA in these samples was measured using quantitative polymerase chain reaction (qPCR). RESULTS: Of total, 29 (67.44%) patients tested positive for plasma Epstein-Barr virus DNA. On comparing results of latent membrane protein-1 immunohistochemistry (IHC) with plasma Epstein-Barr virus DNA, plasma Epstein-Barr virus DNA was found in 25 of 30 patients with latent membrane protein-1 expression and 4 of 13 patients without latent membrane protein-1 expression. The sensitivity and the specificity of plasma Epstein-Barr virus DNA detection with respect to latent membrane protein-1 IHC were found to be 83.33% and 69.23%, respectively (p = 0.0014). CONCLUSION: Determination of plasma Epstein-Barr virus DNA was found to be highly sensitive and specific in characterizing Epstein-Barr virus-associated Hodgkin lymphoma, suggesting that this diagnostic method holds promise as an alternative and more convenient method of diagnosis compared with tissue biopsy.

Analysis of immune responses and serological cross reactivities among Vibrio cholerae O1, Shigella flexneri 2a and Haemophilus influenzae b.

Antigenic determinants expressed on the bacterial cell surface are of importance in the serological characterization and microbiological diagnosis. The bacterial strains carrying these identical or similar antigenic epitopes might react with antibodies produced against other strains. In this study, strong immunogenicity and antigenic cross reactivity were demonstrated among V. cholerae O1, S. flexnerii 2a and H. influenzae b surface components. The enzyme linked immunosorbent assay (ELISA) results were supported by Western blot analysis, where at least 20 antigenic bands, were obtained in each of the reactions, when the surface components were reacted with the homologous antisera. The indirect ELISA results also demonstrated high degree of antigenic relatedness between the surface components of these species, where each surface component was reacted with the heterologous antisera. Western blot analysis also revealed cross reactions between the surface components suggesting common distribution of antigens/epitopes in these bacterial species. This study, thus, gave a clear idea of the level of antigenic sharing and variations among the pathogenic V. cholerae O1, S. flexneri 2a and H. influenzae b strains, which in future, may help in selecting a proper candidate for vaccines and immunodiagnostics development.

Epidemiology of Hepatitis B Virus Infection in Bangladesh: Prevalence among General Population, Risk Groups and Genotype Distribution.

Despite a considerable body of published research on hepatitis B in Bangladesh, researchers continue to lament the lack of reliable information about hepatitis B virus (HBV) infection epidemiology. The present review aims to provide a comprehensive survey of the literature with particular focus on a number of epidemiological questions, as well as a commentary on the trends of hepatitis B research as it has taken place in Bangladesh. The key themes to emerge from this review are: first, beyond noting a declining trend, it is difficult to provide conclusive estimates about HBV prevalence in the general population of Bangladesh. The majority of the studies, even the ones conducted on apparently healthy populations, fail to be adequately representative for the reasons explored in the article. Secondly, HBV infection in Bangladesh is sharply stratified across sociodemographic lines, which speaks to the role of awareness and risk exposure in HBV prevalence. Third, more research on occult infection rates is required to estimate the extent of risk posed by the current blood donation screening program, which relies exclusively on hepatitis B surface antigen as a biomarker. The same considerations apply for the comparative importance of vertical versus horizontal transmission and prevalence among particular risk groups like healthcare workers with high occupational exposure. Finally, while recent studies do allow us, albeit with some ambiguity, to draw conclusions about distribution of HBV genotypes in Bangladesh, there needs to be an added emphasis on molecular epidemiology. It is hoped that the present review, the first of its kind in Bangladesh, will serve as an up-to-date summary of the course HBV epidemiology research in Bangladesh has taken thus far, as well as crucial gaps to address going forward.

Analysis of immune responses against H pylori in rabbits.

AIM: To investigate the immunogenicity of H pylori proteins, to evaluate the production rate of anti H pylori IgG antibodies in relation to time and to demonstrate the fidelity of newly optimized in-house enzyme-linked immunosorbent assay (ELISA) technique as an alternative for H pylori infection assay. METHODS: In the present study, 100 microg of formalin-fixed H pylori whole cell antigens was injected into an experimental animal (New Zealand white female rabbit) intramuscularly on d 0, 16, 27 and 36. The first two doses were injected with adjuvants. On d 0, a serum sample was collected from the rabbit before immunization and this pre-immunized serum was used as a negative control for the whole study. To evaluate the immunogenic responses of the injected antigen, serum samples were collected from the rabbit at regular intervals up to d 42. The sera were analyzed using in-house ELISA and Western blot techniques. RESULTS: The production of anti H pylori IgG antibodies in the rabbit in response to the injected antigen increased almost exponentially up to d 14 and after that it was maintained at the same level until the last day (d 42). By analyzing the immune profiles of immunized sera, 11 proteins were identified to be immunogenic, among them 2 (approximately 100 kDa and 85 kDa) were most prominent. CONCLUSION: Analysis of the immune responses against pathogenic microorganisms like H pylori is necessary for the development of various diagnostic and preventive approaches. The results of this experiment reveal that the formalin-fixed H pylori whole cell antigens injected into the rabbit are highly immunogenic. These prominent proteins (approximately 100 kDa and 85 kDa) might have higher immunogenic effects among humans infected with H pylori and some of these immunogenic proteins can be included in diagnostic approaches based on serology and also for vaccine formulation. The in-house ELISA is a promising alternative compared to invasive techniques.

Prevalence of genotypes and subtypes of hepatitis B viruses in Bangladeshi population.

The genetic variability of hepatitis B virus (HBV) represents a challenge for the sensitivity of immunologic and molecular based assays. Based on sequence divergences in the entire genome of >8 %, HBV genomes have been classified into ten genotypes designated as A to J. The aim of this study was to determine HBV genotypes and subtype in samples of HBV infected patients in Bangladesh. The sera samples were collected from chronically infected HBV patients. At first the DNA positive HBV samples were screened by EIA in our laboratory and the 1063 bp region of surface gene was amplified, sequenced and genotyped by sequence analysis. The same sequences were also used for subtypes and mutational analyses. After that, genotyping was also carried out by nested PCR using genotype specific primers in the same region of HBV surface gene. A total of 39 samples were sequencing to find out the genotypes and subtypes. It was found that the prevalent genotype was genotype C (subgenotype C1) which accounted for 48.7 %. The other genotypes found were genotype A (23.1 %) and genotype D (28.2 %). Predominant subtypes in Bangladesh were adr (41 %) followed by subtype adw2 (28.2 %), ayw3 (25.6 %), and others. Additionally, genotyping was also done by nested PCR using type-specific primers. In this method, out of 17 samples 6 were found to be genotype C, followed by genotype D (4 of 17) and genotype A (3 of 17). In PCR-based genotyping system we also observed the mix genotypes; 3 samples contained both genotype A and D, and 2 samples contained both C and D. The genetic diversity of HBV and distribution of its genotypes and subtypes amongst Bangladeshi population were done in this study, which will help us to provide information regarding circulating genotypes in this region and also help physicians to prescribe proper antiviral/interferon therapy.

Genome Sequence of Bacillus anthracis Strain Tangail-1 from Bangladesh.

Soil was collected in July 2013 at a site where a cow infected with anthrax had been the month before. Selective culturing yielded Bacillus anthracis strain Tangail-1. Here, we report the draft genome sequence of this Bacillus anthracis isolate that belongs to the canonical A.Br.001/002 clade.

Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe.

The zoonosis anthrax caused by the bacterium Bacillus anthracis has a broad geographical distribution. Active enzootic areas are typically located away from central and northern Europe where cases of the disease occur only sporadically and in limited numbers. In contrast, a few out of the 64 districts of Bangladesh are hyper-endemic for anthrax and there the disease causes major losses in live-stock. In this study we genotyped eight strains of B. anthracis collected from the districts of Sirajganj and Tangail in 2013. All these strains belonged to canSNP group A.Br.001/002 Sterne differing only in a few of 31 tandem-repeat (MLVA)-markers. Whole genome sequences were obtained from five of these strains and compared with genomic information of B. anthracis strains originating from various geographical locations. Characteristic signatures were detected defining two "Bangladesh" clusters potentially useful for rapid molecular epidemiology. From this data high-resolution PCR assays were developed and subsequently tested on additional isolates from Bangladesh and Central Europe. Remarkably, this comparative genomic analysis focusing on SNP-discovery revealed a close genetic relationship between these strains from Bangladesh and historic strains collected between 1991 and 2008 in The Netherlands and Germany, respectively. Possible explanations for these phylogenetic relationships are discussed.

Genotype Analysis of Bacillus anthracis Strains Circulating in Bangladesh.

In Bangladesh, anthrax, caused by the bacterium Bacillus anthracis, is considered an endemic disease affecting ruminants with sporadic zoonotic occurrences in humans. Due to the lack of knowledge about risks from an incorrect removal of infected carcasses, the disease is not properly monitored, and because of the socio-economic conditions, the situation is under-reported and under-diagnosed. For sensitive species, anthrax represents a fatal outcome with sudden death and sometimes bleeding from natural orifices. The most common source of infection for ruminants is ingestion of spores during grazing in contaminated pastures or through grass and water contaminated with anthrax spores. Domestic cattle, sheep and goats can also become infected through contaminated bone meal (used as feed) originating from anthrax-infected carcasses. The present investigation was conducted to isolate B. anthracis organisms from 169 samples (73 soil, 1 tissue, 4 bone and 91 bone meal samples) collected from 12 different districts of Bangladesh. The sampling was carried out from 2012 to 2015. Twelve samples resulted positive for B. anthracis. Biomolecular analyses were conducted starting from the Canonical Single Nucleotide Polymorphism (CanSNP) to analyze the phylogenetic origin of strains. The analysis of genotype, obtained through the Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) with the analysis of 15 Variable Number Tandem Repeats (VNTR), demonstrated four different genotypes: two of them were previously identified in the district of Sirajganj. The sub-genotyping, conducted with Single Nucleotide Repeats analysis, revealed the presence of eight subgenotypes. The data of the present study concluded that there was no observed correlation between imported cattle feed and anthrax occurrence in Bangladesh and that the remarkable genetic variations of B. anthracis were found in the soil of numerous outbreaks in this country.

Vibrio cholerae persisted in microcosm for 700 days inhibits motility but promotes biofilm formation in nutrient-poor lake water microcosms.

Toxigenic Vibrio cholerae, ubiquitous in aquatic environments, is responsible for cholera; humans can become infected after consuming food and/or water contaminated with the bacterium. The underlying basis of persistence of V. cholerae in the aquatic environment remains poorly understood despite decades of research. We recently described a "persister" phenotype of V. cholerae that survived in nutrient-poor "filter sterilized" lake water (FSLW) in excess of 700-days. Previous reports suggest that microorganisms can assume a growth advantage in stationary phase (GASP) phenotype in response to long-term survival during stationary phase of growth. Here we report a V. cholerae GASP phenotype (GASP-700D) that appeared to result from 700 day-old persister cells stored in glycerol broth at -80°C. The GASP-700D, compared to its wild-type N16961, was defective in motility, produced increased biofilm that was independent of vps (p<0.005) and resistant to oxidative stress when grown specifically in FSLW (p<0.005). We propose that V. cholerae GASP-700D represents cell populations that may better fit and adapt to stressful survival conditions while serving as a critical link in the cycle of cholera transmission.

High-frequency rugose exopolysaccharide production by Vibrio cholerae strains isolated in Haiti.

In October, 2010, epidemic cholera was reported for the first time in Haiti in over 100 years. Establishment of cholera endemicity in Haiti will be dependent in large part on the continued presence of toxigenic V. cholerae O1 in aquatic reservoirs. The rugose phenotype of V. cholerae, characterized by exopolysaccharide production that confers resistance to environmental stress, is a potential contributor to environmental persistence. Using a microbiologic medium promoting high-frequency conversion of smooth to rugose (S-R) phenotype, 80 (46.5%) of 172 V. cholerae strains isolated from clinical and environmental sources in Haiti were able to convert to a rugose phenotype. Toxigenic V. cholerae O1 strains isolated at the beginning of the epidemic (2010) were significantly less likely to shift to a rugose phenotype than clinical strains isolated in 2012/2013, or environmental strains. Frequency of rugose conversion was influenced by incubation temperature and time. Appearance of the biofilm produced by a Haitian clinical rugose strain (altered biotype El Tor HC16R) differed from that of a typical El Tor rugose strain (N16961R) by confocal microscopy. On whole-genome SNP analysis, there was no phylogenetic clustering of strains showing an ability to shift to a rugose phenotype. Our data confirm the ability of Haitian clinical (and environmental) strains to shift to a protective rugose phenotype, and suggest that factors such as temperature influence the frequency of transition to this phenotype.

Distribution of coliphages against four e. Coli virotypes in hospital originated sewage sample and a sewage treatment plant in bangladesh.

The distribution of coliphages infecting different Escherichia coli virotypes (EHEC, EIEC, EPEC, ETEC) and an avirulent strain (K-12) in sewage system of a hospital and a sewage treatment plant (STP) was investigated by culture-based agar overlay methods. Coliphages were found in all the samples except stool dumping site in the sewage system of the hospital and lagoon of the STP. Bacteriophage count (pfu/ml) infecting E. coli strains showed the following ascending pattern (EHEC < EIEC < EPEC < ETEC < E coli K-12) in all the collected samples except one. Phages capable of infecting avirulent E. coli K-12 strains were present in the highest number among all the examined locations. Phages specific for E. coli K-12 presented high diversity in plaque size on the bacterial lawn. Virulent E. coli specific coliphages rarely produced plaques with diameter of 1-2 mm or over. Conventional agar overlay method was found to be not satisfactory for phage community analysis from primary stool dumping site of the hospital, probably due to the presence of high concentration of antimicrobial substances. The gradual decrease seen in the five groups of coliphage quantity with the ongoing treatment process and then the absolute absence of coliphages in the outlet of the examined treatment plant is indicative of the usefulness of the treatment processes practiced there.

Molecular versus conventional methods: clinical evaluation of different methods for the diagnosis of tuberculosis in Bangladesh.

BACKGROUND: The diagnosis of tuberculosis (TB) in developing countries, such as Bangladesh, is based mainly on microscopic detection of acid-fast bacilli in smears from clinical specimens. On the other hand, the detection of TB by polymerase chain reaction (PCR) is quite new in Bangladesh. In this study, we compared the molecular method with the conventional diagnosis procedures, where Lowenstein-Jensen medium culture results have been used as the "gold standard." METHODS: A total of 135 sputum samples were collected from clinically suspected patients with pulmonary TB. A direct smear was made from each sputum specimen and stained by the Ziehl-Neelsen (Z-N) method. The sputum samples were then processed, and the pellet was used for both Z-N (concentration) and auramine O fluorescence staining or resuspended in phosphate buffered saline to inoculate Lowenstein-Jensen medium or processed for PCR detection of Mycobacterium tuberculosis. RESULTS: The direct smear staining yielded 44 (32.6%) sputum samples that were acid-fast positive, which increased after concentration, yielding 60 (44.4%) acid-fast-positive samples. Fluorescence microscopy using auramine O staining further increased the number of positive samples to 67 (49.6%). The biochemical tests showed 75 (55.6%) sputum samples to be culture positive, and the MB/BacT system increased the recovery up to 90 (66.7%) culture positives. On the other hand, PCR yielded 93 (68.9%) positive results, 20 (21.5%) of which were culture-negative sputum specimens. CONCLUSION: It is suggested that the Z-N direct microscopy on its own is the best method (with high specificity) for confirming the diagnosis of acid-fast bacilli. Although the PCR diagnosis of TB appears to be a rapid and sensitive method, the results should be interpreted with care in the clinical settings.