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A cross-sectional, observational study was conducted to determine the relationship between sociodemographic variables and the development of cervical cancer through detection of detection of HPVE6 oncoprotein. A total of 47 endocervical swabs were collected from colposcopy clinic under the Department of Obstetrics & Gynaecology, Mymensingh Medical College, Mymensingh, Bangladesh, from January to December of 2015. Laboratory work was done in the Department of Microbiology of the same institution. E6 strip test is an immunochromatographic test based on detection of HPV-E6 oncoprotein in cervical swab samples. The swab specimen was treated with lysis solution and conditioning solution. Then the specimen solution was clarified by centrifugation. After that the sample solution was transferred into the detector mAb vial, wash solution vial, and finally, into developing solution vial. The test unit was then placed on a reading guide. Positive result was indicated by the appearance of purple colored test line. Out of 47 specimens, 21 (44.68%) were OncoE6 positive. Among those 21 positive cases, 19 (90.48%) were HPV-16 and 2 were (9.52%) HPV-18. Out of 11 histologically diagnosed CIN I cases, 1 (9.09%) case came out as positive. However, there were no positive cases by oncoE6 cervical swab test in CIN II and CINIII categories. Among histopathologically confirmed 22 cervical carcinoma cases, 20 (90.90%) came out as positive through this test. The results were compared with sociodemographic variables. OncoE6 is more common among ≥50 age group, and who got married before 18 years, and in multiparous women (P

Candida auris, Candida blankii, and Kodamaea ohmeri have been regarded as emerging fungal pathogens that can cause infections with high mortality. For genotyping of C. auris, a multilocus sequence typing (MLST) scheme based on four locus sequences has been reported, while there is no typing scheme for C. blankii and K. ohmeri. In the present study, the existing MLST scheme of C. auris was modified by adding more locus types deduced from sequence data available in the GenBank database. Furthermore, MLST schemes of C. blankii and K. ohmeri were developed using the four cognate loci (ITS, RPB1, RPB2, D1/D2) and similar sequence regions to those of C. auris. These MLST schemes were applied to identify the ST (sequence type) of clinical isolates of C. auris (n = 7), C. blankii (n = 9), and K. ohmeri (n = 6), derived from septicemia or otomycosis in Bangladesh in 2021. All the C. auris isolates were classified into a single ST (ST5) and clade I, having a Y132F substitution in ERG11p, which is associated with azole resistance. Similarly, all the C. blankii isolates belonged to a single type (ST1). In contrast, six K. ohmeri isolates were assigned to five types (ST1-ST5), suggesting its higher genetic diversity. These findings revealed the availability of MLST schemes for these three fungal species for understanding their clonal diversity among clinical isolates.

Background & objectives: Scrub typhus is a mite borne rickettsial illness, caused by the bacterium Orientia tsutsugamushi, which is endemic to Asia pacific region. Due to wide spectrum of non-specific manifestations and inaccessibility of accurate diagnostic tools, it remains underdiagnosed in many countries of Southeast Asia including Bangladesh, resulting in severe life-threatening complications. Therefore, this study was aimed to diagnose scrub typhus through molecular detection of O. tsutsugamushi by ‘Nested Polymerase Chain Reaction (N-PCR)’ among febrile patients in Mymensingh, Bangladesh & to study the socio-demographic as well as clinical characteristics of the diagnosed cases. Methods: It was a cross-sectional type of study, conducted at department of Microbiology, Mymensingh Medical College between March 2018 and February 2019. Blood samples were taken from 453 febrile patients of suspected rickettsial illness, referred from both inpatient and outpatient facility of Department of Medicine and Department of Pediatrics, Mymensingh Medical college Hospital (MMCH). Then DNA was extracted from the whole blood, following Phenol-Chloroform extraction & ethanol precipitation method. Finally, N-PCR was performed on extracted DNA, targeting 47Kda antigen gene, to detect O. tsutsugamushi. Results: Out of 453, this study documented [78 (17.21%)] PCR positive scrub typhus cases, among which majority [42 (53.84%)] were female & maximum [26 (33.33%)] were in age group >15-30 years. Higher number of PCR positive patients [51 (65.39%)] were from rural areas. Among the scrub typhus cases, myalgia (48; 61.53%) was the most common manifestation, followed by headache (44; 56.41%) and cough (44; 56.41%). Eschar was present only in 14 (17.94%) cases and 8 (10.25 %) patients had skin rashes. Leukocytosis and leukopenia were documented in 13 (16.66%) and 5 (6.41%) cases respectively. Decreased Hb% was recorded in 14(17.9%) & 16 (20.5%) cases had thrombocytopenia. Conclusion: This study recorded a high number of scrub typhus cases in Mymensingh region with non-specific febrile manifestations, hindering early & accurate clinical diagnosis. Complications like - renal & hepatic impairment, CNS involvement, ARDS as well as hematological abnormalities were documented also. So, scrub typhus should be considered in the differential diagnosis of undifferentiated febrile illness in Bangladesh. Further molecular studies on scrub typhus might be done throughout the countries to create awareness among physicians & to evaluate actual disease burden. Mediscope 2022;9(1): .30-40

Aims: The study was carried out to understand the current status of used drugs and chemicals in fish hatcheries and farms in Feni district, Bangladesh. Methodology: Data were collected by pre-defined questionnaire interview, personal contact with farm and hatchery owners, and representatives of pharmaceutical companies by market survey. Results: Twelve different groups of chemicals were being used for disease treatment and fish health management. Traditionally used chemicals were Lime, Salt, Potash (KMnO4) and Melathion. Although Malachite green hazardous to human health, it was widely used in hatcheries. Geotox, JV Zeolite, Amoxy fish, Megavit Aqua, Square aqua premix, Orgavit, Pure Oxy, Vitamin gel, O2-Marine etc. were widely used new chemicals. Renamycin was the most widely (36% farmer) used antibiotic followed by Oxysentin 20%, Orgamycin15% and Otetra vet power 50. Conclusion: Nearly all farmers did not apply chemicals and drugs at proper doses because they thought the higher the doses applied the more and rapid will be the action. It was found that manufacturers and retailers of the products often neglected to provide farmers with necessary information regarding active ingredients and relevant instructions for safe and efficient use of aqua-drugs and chemicals. Recommended use of chemicals apparently brings good result but indiscriminate use of chemicals can be extremely detrimental to fish and our environment as well as to us and therefore, all of us should be aware of the proper use of chemicals.

Background: Urinary tract infection (UTI) is among the most common bacterial infections and posses significant healthcare burden. Escherichia coli is the most common cause of UTI accounting for about 70%% and a variable contribution from Proteus mirabilis, Pseudomonas aeruginosa and Klebsiella pneumoniae Patients are often treated as soon as bacteria are shown to be present by microbiological culture. Objective: To identify the prevalence of bacterial isolates specimens from suspected patients of urinary tract infection in both outpatient department and in patient department. Methods: This study was carried out in the department of Microbiology, Mymensingh Medical College during the period from July 2016 to June 2017. Urine specimens were collected and isolation and identification of major uropathogens (Escherichiacoli Klehsiella pneumonias, Proteusmirabilis, and Pseudomonas aeruginosa) were done by standard microbiological procedure a biochemical tests. The antibiotic sensitivity pattern of the isolate according to age and sex. Results: Out of 250 urine specimens, 200 specimens were isolated and identified by culture and different biochemical methods which were supported by microscopical examination and at the same time PCR could detect species specific genes in 201 specimens directly from urine of suspected UTI patient Escherichia coli was responsible as a leading causative pathogen in both outpatient department and in patient department with a higher prevalence of 71.8% for outpatient department. On the other hand prevalence of Proteus mirabilis was lowest and it was 1.8 % in outpatient population. Culture positivity of urine specimens was higher in female in both out patient population and inpatient population. Culture positivity of in patient population among the male (45.5%) was slighty higher than that of outpatient population (34.5%). The predominant age group suffered from UTI in case of outpatient population was >15-30 but for the in patient ..............

Background: Rickettsial diseases are neglected, re-emerging vector borne zoonosis & increasingly considered as one of the most important causes of pyrexia of unknown origin (PUO). They are grossly underdiagnosed due to wide range of non-specific symptoms, low index of clinical suspicion, lack of widely available specific diagnostic tools, leading to significant morbidity & mortality. Appropriate diagnosis in early stages is therefore necessary to prevent fatal complications associated with this disease. Objective: Present study was attempted to assess the burden of rickettsial illness by Weil-Felix agglutination test, among the suspected febrile patients, visiting a tertiary care hospital as well as to analyze the demographic profile & clinical manifestations of the seropositive cases. Methods: This was a cross-sectional study, conducted at department of microbiology, Mymensingh Medical College from March 2018 to February 2019. A total of 453 febrile patients of suspected rickettsial illness, irrespective of age and sex, were enrolled in this study. Serum sample from all the enrolled cases were then analyzed for rickettsial antibodies by Weil-Felix slide agglutination test. Results: Out of 453 cases, a total of 260 (57.39%) showed significant agglutination by Weil-Felix test, of which 101 (38.84%) were reactive to OX2 (spotted fever group rickettsiae), 65 (25%) were reactive to OXK (Scrub typhus) & 13 (5%) showed significant titers to OX19 (typhus fever). Remaining 81 (31.15%) sera were reactive to more than one antigens (mixed reactivity). Seropositivity was higher among female subjects (142; 54.61%) & age group >15-30 accounted for highest number of cases (95; 36.53%). Positive cases showed diverse clinical manifestations like headache (55.76%), myalgia (50.76%), skin rash (10.38%), eschar (9.23%), oliguria (7.3%), jaundice (10.76%), splenomegaly (6.81%), hepatomegaly (7.30%) etc. Conclusion: Rickettsial diseases should be considered as an important etiology of PUO & early diagnosis should be done to initiate proper treatment to prevent fatal complications. Though it lacks sensitivity & specificity, in a resource constraint area like Bangladesh, Weil-Felix test still serves as the cheapest initial diagnostic tool for rickettsial illness to guide the physician for further approaches. Mediscope 2021;8(2): 112-121

Bangladesh is the second-worst-affected country in South Asia by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The aim of this study is to examine genome sequences from Bangladesh from January 2021 to June 2021 in order to monitor the SARS-CoV-2 VOC and the clades or lineages that are prevalent in the country. Within the study timeframe, at least eight Nextstrain clades were found: 20A, 20B, 20C, 20H (Beta, V2), 20I (Alpha, V1), 20 J (Gamma, V3), 21A (Delta), 21D (Eta), and six GISAID clades: four main (G, GH, GR, GRY) and two minors (GV, O) with an introduction of VOC B.1.1.7/Alpha, B.1.351/Beta and B.1.617.2/Delta. The introduction and recent occurrence of VOCs with substantial alterations in the receptor binding site of spike protein (K417 N, K417T, L452R, T478K, E484K, S494P, N501Y) are of particular importance. Specifically, VOC B.1.617.2/Delta has surpassed all prior VOCs in Bangladesh, posing a challenge to the existing disease management.

The reproductive biology of the silver hatchet chela, Chela cachius, was addressed in the present study. A total of 1200 specimens were caught by fine-meshed seine nets from a large perennial water body in Bangladesh Agricultural University Campus, Mymensingh. The gonadosomatic index and the histological examination suggested that the spawning seasons of C. cachius were from February to May and from July to September. Based on histological examination, nine stages of oocyte development were determined; namely, early perinucleolus, late perinucleolus, yolk vesicle, primary yolk, secondary yolk, tertiary yolk, migratory nucleus, premature and mature stage. The absence of postovulatory follicles and hydrated eggs and the presence of two modes of eggs in the mature ovaries indicated that C. cachius was a single spawner, and its spawning frequency or strategy was a synchronous type. The average fecundity was 1708±838.86 having a standard length of 49±2.89 mm in the first season (February to May) and 1997.33±889.92, whereas the standard length was 46.66±1.53 mm in the second season (from July to September). The findings of the present study might be helpful for induced breeding of the species for commercial purposes as well as for management of the natural population (banning/restriction of fishing during spawning season) of C. cachius.

Brucellosis is a major Bacterial Zoonotic disease worldwide. More than 500,000 new cases are reported globally every year with the annual incidence rates varying widely from 500 per 1000,000 population among different region of the world. This cross sectional descriptive study was carried out in the department of microbiology, Mymensingh medical college, Mymensingh, Bangladesh from 1st January to 31 December 2017, on total 600 patients of PUO with or without occupational exposure. Blood was taken as sample, serum was separated and screening test was done by Brucella specific latex agglutination test from all collected samples. A Titer of ≥ 1:160 was taken as positive. ICT, PCR and real time PCR were done from all screening positive samples. Among the study population 65.83% (395/600) were male and 34.17% (205/600) were female. The sero prevalence of Human Brucellosis was found 13.33% (40/300) and 5% (15/300), respectively in risk and non risk group of population. Out of 55 Brucella specific latex agglutination test positive samples 27.27% (15/55) were ICT positive, 5.45% (3/55) were PCR positive and 3.64% (2/55) were real time PCR positive. No ICT, PCR or Real time PCR cases were found from sero negative samples. Among the ICT positive cases 86.67% (13/15) from risk group and 13.33% (2/15) from non risk group of study population. Among the 3 PCR positive cases 13.33% (2/15) were from ICT positive cases and 2.5 % (1/40) from ICT negative cases. All PCR and Real time PCR positive cases were found in risk group of study population. No reliable data for Human Brucellosis is available in our country. However the present study revealed that a considerable number of Human Brucellosis is present in risk group as well as non risk group of population in both rural and urban area in Mymensingh district of Bangladesh. In our country we use only Brucella specific latex agglutination test for diagnosis of human Brucellosis. It is a non specific test and gives many false positive results. So it is necessary to introduce newer tests with higher sensitivity and specificity which will help to diagnose the disease rapidly and more accurately. Bangladesh J Med Microbiol 2020; 14 (2): 19-24

An experiment was conducted at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh during January to June 2016 to observe the effect of water, nutrient and weed management practices on the yield and quality of aromatic Boro rice (cv. BRRI dhan50). The experiment consisted of three water managements viz. conventional flood irrigation, AWD (Alternate Wetting and Drying) and SRI (System of Rice Intensification); two nutrient managements viz. recommended dose of inorganic fertilizers (Urea, TSP, MoP, Gypsum, ZnSO4 @ 250, 120, 120, 100, 10 Kg ha-1, respectively) and 25% less than recommended dose of inorganic fertilizer + poultry manure @ 2.5 t ha-1; and three weed managements viz. weedy check (control), two hand weeding at 20 and 40 DAT, and pre-emergence herbicide (Rifit 33EC) followed by post emergence herbicide (Fast klin 10WP) application. The highest number of effective tillers hill-1, grains panicle-1,grain yield and protein (%) in grain were obtained in SRI water management which was followed by AWD and conventional flood irrigation. Between the two nutrient management practices, application of 25% less than recommended dose of inorganic fertilizer + poultry manure @ 2.5 t ha-1 produced higher number of effective tillers hill-1,grains panicle-1,1000-grain weight, grain yield and protein (%) in grain than in organic fertilizer. Among the weed management practices, application of pre-emergence herbicide (Rifit 33EC) followed by post-emergence herbicide (Fast Klin 10WP) produced the highest number of effective tillers hill-1,grains panicle-1,1000-grain weight, grain yield and protein (%) in grain followed by two weedings at 20 and 40 DAT while the lowest grain yield was obtained in weedy check. The highest number of effective tillers hill-1,grains panicle-1, grain yield and protein (%) in grain was found in SRI water management combined with 25% less than recommended dose of inorganic fertilizer + poultry manure @ 2.5 t ha-1 and application of pre-emergence herbicide followed by post-emergence herbicide. So, it may be concluded that, to get the highest grain yield in aromatic Boro rice, SRI method along with application of 25% less than recommended dose of inorganic fertilizer + poultry manure @ 2.5 t ha-1 and applying pre-emergence herbicide (Rifit 33EC) followed by post emergence herbicide (Fast Klin 10WP) could be recommended. Bangladesh Agron. J. 2019, 22(1): 57-69

Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.

Genetic characterization may provide useful insights into severe acute respiratory coronavirus 2 (SARS CoV 2) circulating in Bangladesh. Here we analyzed the SARS Cov 2 positive 41 nasopharyngeal samples collected in lysis buffer obtained at different regional national laboratories of Bangladesh during July – December 2020. Full length spike gene was amplified and SARS CoV 2 was confirmed upon Sanger sequencing. Multiple ClustalW alignment and phylogenetic study of 15 strains showed that genetically diverse SARS CoV 2 is circulating in the country where 80 documented and 55 novel substitutions have been observed in different regions of spike glycoprotein. Major mutations and/or deletions was identified at conserved amino acid positions that are functionally linked to host transition, antigenic drift, host surface receptor binding or antibody recognition sites, and viral oligomerization interfaces that may have significant effects on pathogenic capacity and epidemiological signatures.

Leptospira was detected in 48.9% of blood samples from 182 febrile patients in north-central Bangladesh in 2019. Most Leptospira were classified as L. wolffii (93%) on the basis of phylogenetic analysis of 16S ribosomal RNA genes, while others were assigned to L. borgpetersenii and L. meyeri.

Enterococcus faecalis is one of the major causes of urinary tract infection, showing acquired resistance to various classes of antimicrobials. The objective of this study was to determine the prevalence of drug resistance and its genetic determinants for E. faecalis clinical isolates in north-central Bangladesh. Among a total of 210 E. faecalis isolates, isolated from urine, the resistance rates to erythromycin, levofloxacin, and gentamicin (high level) were 85.2, 45.7, and 11.4%, respectively, while no isolates were resistant to ampicillin, vancomycin and teicoplanin. The most prevalent resistance gene was erm(B) (97%), and any of the four genes encoding aminoglycoside modifying enzyme (AME) were detected in 99 isolates (47%). The AME gene aac(6&prime, )-Ie-aph(2&rdquo, )-Ia was detected in 46 isolates (21.9%) and was diverse in terms of IS256-flanking patterns, which were associated with resistance level to gentamicin. Tetracycline resistance was ascribable to tet(M) (61%) and tet(L) (38%), and mutations in the quinolone resistance-determining region of both GyrA and ParC were identified in 44% of isolates. Five isolates (2.4%) exhibited non-susceptibility to linezolide (MIC, 4 &mu, g/mL), and harbored the oxazolidinone resistance gene optrA, which was located in a novel genetic cluster containing the phenicol exporter gene fexA. The optrA-positive isolates belonged to ST59, ST902, and ST917 (CC59), while common lineages of other multiple drug-resistant isolates were ST6, ST28, CC16, and CC116. The present study first revealed the prevalence of drug resistance determinants of E. faecalis and their genetic profiles in Bangladesh.

The changes of pine wood structure were evaluated based on Congo red (CR) adsorption in this study. Cellulose free –OH group act as electron acceptor and CR amino or azo group as electron donor that interacts each other to form H–bonds. This interaction of CR with cellulose is considered in this study to analyze the structural changes of pine wood. Pine wood samples were treated with different concentrated NaOH solution at 130 °C for 30 min. CR adsorption of treated samples were assayed in terms of absorbance decrease of CR solution measured by spectrophotometer. Field emission scanning electron microscopy (FE-SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) were used to evaluate the microstructural changes of treated samples. Finally enzymatic saccharification was carried out using commercial cellulase enzyme. Treatment of pine wood with alkali degrades the intra and/or intermolecular H– bonds of cellulose leading to an exposure of free –OH groups. These free –OH groups bind with CR molecule while in contact with CR solution. Structural change of pine wood caused by different NaOH (0 to 20%) treatment at 130 °C for 30 min was evaluated in terms of CR adsorption. Scanning electron microscopy and Fourier transform infrared spectroscopy studies showed that 10% NaOH treated sample exposed more cellulose fibers compared to other treatments leading to more CR binding. The cellulose crystalline index was increased with increasing NaOH–treatments and lowered by the 20% NaOH–treatment due to degradation of cellusose fibres. Moreover, after 72 h, reducing sugar yield was 76.5% and 70.7% using enzyme loading of 15FP U/g and 30CB U/g from 10% and 20% NaOH treated pine wood samples, respectively. Reducing sugar yield was decreased from samples while treating more than 10% NaOH solution. 10% NaOH treatment can be considered as an effective concentration for pine wood treatment at 130 °C for 30 min. These results suggest that CR approach is supposed to be helpful for selecting the treatment condition.

Widal test is the most widely used laboratory investigation for diagnosis of typhoid. However, the test interpretation remains controversial in the context of endemic regions such as Bangladesh, as agglutination occurs at varied titrations among a large percentage of healthy population. Paired Widal tests are often not feasible; hence single unpaired test has to be used for screening, diagnosis and treatment. We aimed to assess the normal range of baseline titre for Anti TO, TH, AO, AH, BO agglutinins among healthy population in an endemic country with a view to guide the researchers and the clinicians, facilitating further investigation on updating cut off points of single Widal test for screening and diagnosis of typhoid fever in the context of Bangladesh. A cross-sectional study was carried out in Mymensingh Medical College, Bangladesh on 2925 male immigration applicants. A single blood sample was collected for Widal test and interpreted using standard guidelines. The highest baseline titer for Anti TO, TH, AO, AH, BO agglutinins among 95% of the healthy participants was found to be 1:80 for each respectively. A titre of 1: 40 was observed for BH antigen. In case of singular Widal test, baseline values for the normal range was found to be 1:20 - 1:80 for all the antigens (TO, TH, AO, AH, BO, BH), except BH, for which it was 1:20-1:40. Further studies, inclusive of other sociodemographic groups and positive controls are required to determine the updated cut off values.

This experiment was designed with three experimental treatments namely T1 (natural feed), T2 (feeding with 10% body weight) and T3 (feeding with 5% body weight) for ten weeks. In the content of 33.8% of crude protein (CP), 11.2% of crude fiber (CF), 6% of fat and 10.2% of ash content feed were used as an experimental diet in this experiment. The stocking densities were 280 fish decimal-1 in three treatments where the mean initial weight of fry was 20 ± 0.2 g in all treatments combined and at the end of the experiment the mean final weight was found as 58.9 ± 2.86 g, 134.4 ± 3.62 g and 142.5 ± 4.23 g for T1, T2, and T3 respectively. Mean initial length was 10.2 ± 0.01 cm in three treatments and final length was found as 14.58 ± 1.60 cm, 18.74 ± 1.23 cm and 20.16 ± 2.08 cm in T1, T2 and T3 respectively. The mean weight gains 38.9 ± 1.53 g, 114.4 ± 3.05 g and 122.5 ± 1.5 g, mean length gain 4.38 ± 0.24 cm, 8.54 ± 0.65 cm and 9.96 ± 0.59 cm, mean SGR 1.76%, 3.5% and 3.82% were recorded in T1, T2 and T3, respectively. The highest weight gain, length gain and SGR were found in T3 and the lowest was found in T1. The survival rate was 82%, 88% and 94% in T1, T2 and T3, respectively. FCR values were found as 3.49 ± 0.5 and 2.51 ± 0.4 in T2 and T3. The result demonstrated that feeding with 5% body weight had a better effect on the growth and survival rate of monosex (male) O. niloticus.

Introduction: Sandfly breeds in soil but is selective to identify soil favourable for their breeding. Soil covered by vegetation, marshy land, orchards and settlements shows high sandfly breeding in an endemic region. Besides,the presence of inorganic constituents of the soil was found to affect sandfly breeding. Objective: To identify soil pattern in Kala-azar endemic areas suitable for sandfly breeding, and the relationship of soil’s physical and chemical properties with their breeding which may help in taking feasible measure to control the vector of Kala-azar or Visceral Leishmaniasis (VL). Materials and Methods: The cross-sectional type of descriptive study was conducted in the Kala-azar endemic areas of Trishal and Fulbaria of Mymensingh, Madhupur of Tangail and Chatmohor of Pabna district, Bangladesh during the period of July 2015 to December 2015. From each site, 250 gm soil was collected and packed in a plastic container. All the samples were taken in the laboratory and were kept as it is for one week to configure the moisture and soil temperature maintaining the lab room temp at 28±2ºC and relative humidity at 75.0%±2.0. Soil samples were analysed for physical and chemical properties at the Soil Science Department of Sher-e-Bangla Agricultural University, Dhaka. Results: Total 48 soil samples were collected from Trishal, Fulbaria, Madhupur, Chatmohor and each sample was analysed for physical property (sand, silt, clay, porosity, water content), chemical constituents (pH, C, N, Ca, Mg, K, P, Fe). The mean from each district’s soil constituents (sand, silt, clay, porosity, water content) ranged from 17.36%-18.83%, 44.10%-45.46%, 35.70%-38.06% 41.98%-47.24% respectively and among the chemical constituents, pH ranged from 7.46-7.98, Carbon 0.92-0.98 Cmolkg-1, Nitrogen 0.174-0.184 Cmolkg-1, Calcium 4.83-6.21 Cmolkg-1, Magnesium 1.97-2.46 Cmolkg-1, Potassium as K2O 1.37-1.79 Cmolkg-1, Phosphorus as P2O5 12.60-13.78 Cmolkg-1, Iron as Fe2O3 9.54-10.06 Cmolkg-1 respectively. Conclusion: Physical and chemical characteristics of soil by area of endemicity have been postulated to afford suitable environment for sandfly breeding. This information of the breeding sites of phlebotomine sandflies could help to plan environmental intervention measures that would impede the breeding of these insects. Journal of Armed Forces Medical College Bangladesh Vol.13(1) 2017: 3-7

Chikungunya viruses from the 2017 outbreak in Dhaka, Bangladesh, were analysed phylogenetically. E1 sequences from 21 strains belonged to the Indian Ocean clade of the East/Central/South African (ECSA) genotype, forming a novel cluster with latest South Asian strains. They lacked the A226V substitution. Keywords: Bangladesh, chikungunya virus, Dhaka, genotype, molecular epidemiology

Scrub typhus is a mite-borne rickettsial disease caused by Orientia tsutsugamushi, which is endemic in Asia Pacific region. In this study, infection rate and molecular epidemiologic traits of O. tsutsugamushi was investigated in Mymensingh, located in north-central Bangladesh. Among the blood samples from 453 febrile patients who visited Mymensingh medical college hospital in 2018, the 47 kDa protein gene of O. tsutsugamushi was detected in 78 samples (17.2%) by nested PCR. Phylogenetic analysis of the O. tsutsugamushi 56 kDa protein gene (18 samples) revealed a predominance of Karp-related genotype (89%), while the remaining belonged to Gilliam genotype. Samples of the Karp-related genotype mostly clustered with those of China, Taiwan, Thailand and India, etc., in emergent subgroups clades 2 and 4, which were distinct from clade 1, including prototype Karp strains. Among the 18 samples, three variable domains (VD) of 56 kDa type-specific antigen had different types of sequence diversity; VDI contained two or three repeats of eight amino acid units, while VDII and VDIII had amino acid substitution, deletion or insertion. The present study documented a potentially high prevalence of genetically diverse O. tsutsugamushi in north-central Bangladesh. Keywords: 56 kDa type-specific antigen, Bangladesh, Orientia tsutsugamushi, scrub typhus, Karp-related genotype

Predominance of genotype G3P[8] rotavirus was revealed for children and adults with diarrhoea in north-central Bangladesh for a 1-year period from September 2018. The G3P[8] rotaviruses were phylogenetically close to recent Indian strains, having antigenic variation in VP7 and VP4 compared with old Bangladeshi strains. Keywords: Antigenic drift, Bangladesh, G3P[8], phylogenetic analysis, rotavirus

Leptospiral 16S rRNA genes were detected in 13 blood samples from 74 febrile patients in north-central Bangladesh, and their sequences phylogenetically clustered with those of Leptospira interrogans or Leptospira wolffii. Genetic diversity in O-antigen polymerase (wzy) was found in an L. interrogans sample. Keywords: Bangladesh, Leptospira interrogans, Leptospira wolffii, 16S rRNA, wzy

Bangladesh is an endemic region of dengue fever and experienced an unprecedented large outbreak with more than 100,000 confirmed cases in 2019. To understand the prevalence of dengue antibody in patients and molecular epidemiological characteristics of dengue virus (DENV) in this outbreak, a total of 179 blood samples were collected from patients in 10 districts (seven divisions) covering nearly the whole country from August to December 2019. DENV NS-1 was detected in 162 samples, among which DENV-specific IgM was positive in 119 samples (73.5%), including 60.5% samples also positive for DENV-specific IgG. Sequencing of the partial C-prM gene and its phylogenetic analysis revealed predominance of DENV type 3 genotype I, accounting for 93% of samples examined. DENV-3 genotype III was identified in two samples from separate districts, and only one DENV-2 cosmopolitan genotype was found in the capital city, Dhaka. These findings suggest the predominance of DENV-3 genotype I and occurrence of DENV-3 genotype III, associated with increased incidence of recent secondary infection in Bangladesh in 2019.

Human rotavirus B (RVB), a rare cause of diarrhea in several Asian countries, has been reported to be genetically highly conserved. However, 14 RVB strains with two distinct RNA electropherotypes E1 and E2 (11 and 3 strains, respectively) were detected in adult patients with diarrhea, in Mymensingh in the north-central Bangladesh in 2014. In this study, VP7 gene sequences of all the 14 strains and nearly full-length sequences of all the 11 RNA segments of four RVB (two strains each representing E1 and E2 types) were determined and analyzed phylogenetically. For all the gene segments, sequence identities among strains with the same RNA pattern were higher (99%-100%) than those between strains with different RNA patterns (94-98%). Although all the gene segments of RVB strains were grouped into Indian-Bangladeshi lineage, VP1-3, VP6, VP7, NSP1, NSP2 and NSP5 genes of strains with E1 and E2 types were assigned to distinct sublineages S1 and S2, respectively. E1-strains clustered with Bangladeshi RVB strains reported previously (e.g., Bang117), while E2-strains with those from India (e.g., NIV-1048101), Myanmar, and Nepal. In contrast, VP4, NSP3 and NSP4 genes of both E1 and E2 RVB strains were classified into sublineage S2. These findings indicated that two genetically distinct RVB strains were simultaneously circulating in Mymensingh, Bangladesh. RVB strains with E1 electropherotype were suggested to be reassortants acquiring three gene segments (VP4, NSP3 and NSP4 genes) from the foreign RVB in the genetic background of indigenous Bangladeshi RVB represented by the strain Bang117.

Mechanical intervention in rice (Oryza sativa L.) postharvest operation especially harvesting, threshing and carrying is increasing due to shifting labour from agriculture to non-agricultural sector. It was hypothesized that mechanical intervention in rice postharvest operation will increase the postharvest losses. A two-year study (2008-2010) was conducted during Aus, Aman and Boro seasons in six locations of sadar upazila at Gazipur district to test the hypothesis. The widely used varieties of BR11, BR23, BR26, BR27, BRRI dhan28, BRRI dhan29 were used to assess the losses during harvesting to drying. In the study areas, farmer’s common practices (harvesting paddy by sickle; transportation by head, shoulder and power tiller operated trolley; threshing by open drum and close drum thresher; cleaning by traditional cleaning device kula and winnower and sun drying) were used to assess the postharvest losses. The average postharvest losses from harvesting to drying recorded 10% in three rice growing seasons. Losses due to mechanical threshing and traditional sun drying were 3.16% and 3.14% respectively. Power tiller operated trolley showed the lowest carrying loss compared to shoulder and head carrying methods. Both kula and winnower were observed as the most appropriate method of grain cleaning. Mechanical intervention in threshing increased the losses, whereas decreased in transportation and winnowing. These data might be used for policy makers to assess the national food grain loss and for researchers to design and development new technology to reduce the postharvest loss. The study should be continued to other regions for consistent results.Bangladesh Rice j. 2016, 20(1): 23-32

Introduction: Parasitic diseases and Tuberculosis were shown to be the risk factor for each other. Co-infection of visceral leishmaniasis and pulmonary tuberculosis are increasing public health problem now a days especially in developing countries. More than 81% of cases and deaths from TB are in developing countries and is aggravated by concurrency with parasitic diseases. Objective: To find out the occurrence of Leishmaniasis amongst Tuberculosis (TB) patients of Kala-azar endemic areas admitted to Surya Kanto (SK) Hospital, Mymensingh. Materials and Methods: This descriptive cross-sectional study was conducted at Infectious and Tropical Disease Department of Mymensingh Medical College Hospital, a tertiary referral hospital from January 2014 to Decmber 2016. A total 176 TB patients reported from Kala-azar endemic areas admitted were included. For confirmation of diagnosis all cases of TB were sent for Gene expert before that relevant tests like CBC (Complete Blood Count), X-ray chest, Mantoux test, Smear tests were done. After having confirmed all the TB cases were investigated for Kala-azar. Venous blood was collected for buffy coat and serum for ELISA. All 176 patients’ blood were tested with ICT(rK39) for VL. There after splenic aspiration were done with full aseptic preparation for only those who were ICT positive. Smears were prepared and viewed under microscope with 10x 100 magnification. After that all these cases were tested by ELISA. Results: A total of 176 TB patients were selected in this study of which 120(68.1%) were male and male-female ratio was 2.1: 1, the mean age was 43.06 years. Among patients 87.49% were within 16 to 60 years of age that means within productive age of life are infected more with TB. In terms of education 79.10%(139) patients were below Secondary level, that revealed the illiterate and or less literate people were affected more by TB. Maximum patient’s family 132(74.99%) had monthly income up to 10,000.00 BDT (125 US$)i.e. the poorer people of the area. Out of 176 patients Smear positive TB cases were 170(97.41%) but By Gene Xpert all 176 patients were found positive. The blood sample of 176 patients were tested with ICT rK39 and 12(6.81%) patients were found positive for leishmaniasis who suffered from TB. In splenic smear test 12 patients smear were examined of which 11(91.66%) were positive but by ELISA all 12(100%) were found positive. Conclusion: Visceral leishmaniasis and tuberculosis co-infection have drawn attention to the clinical aspect. In both diseases infection may remain dormant asymptomatic which may be related to immune suppression and may lead to active disease. This study has been able to find out leishmaniasis amongst tuberculosis patients from kala-azar endemic areas of Bangladesh. Journal of Armed Forces Medical College Bangladesh Vol.12(2) 2016: 3-8

Background : Rotavirus infects almost all children by the age of five. More than 180,000 annual deaths due to rotavirus, occurs in Bangladesh. Aims : This study aimed to determine the incidence of rotavirus infection in children by a modified polyacrylamide gel electrophoresis (PAGE) in stool samples. Materials and Methods : In this descriptive type cross sectional study, a total of 400 stool samples were examined for the presence of rotavirus by a modified PAGE analysis of viral genome. Stool culture was done for common enteric pathogens. The study was carried out from November 2012 to July 2013 in the department of Microbiology, Mymensingh Medical College, Mymensingh. Results : PAGE results were found in 365 of 400 (91%) specimens. Maximum incidence of rotavirus infection was seen in age group of 6 months - 24 months (67.25%). All 151 rotavirus positive cases did not show infection with bacterial pathogens. Conclusion : The modified PAGE technique for the detection of viral RNA was found to be rapid, simple, reliable and less expensive technique. Bangladesh Journal of Medical Science Vol.15(2) 2016 p.154-159

Antimicrobial susceptibility and coagulase typing of Staphylococcus aureus isolates, with particular emphasis to Methicillin Resistant S. aureus (MRSA), were studied among strains isolated from various types of specimens collected at Mymensingh. A newly developed panel of anti-sera against different coagulase enzymes was used for coagulase typing. The study included 79 strains of S. aureus and of those, 40 were identified as MRSA on the basis of resistance to oxacillin (1 gm) discs. The rate of resistance of S. aureus to different antibiotics observed: penicillin (88.61%), oxacillin (48.10%), cephradine (44.30%), gentamicin (27.85%), erythromycin (34.18%), fusidic acid (25.0%) and rifampicin (20.0%). None of the isolates showed vancomycin resistance. Both MRSA and non-MRSA strains were found belonging to Coagulase type VI. Drug resistance pattern and coagulase type of MRSA strains indicated a homogenous epidemiologic origin that needs further exploration including strains from different geographic locations.Bangladesh J Med Microbiol 2007; 01 (02): 56-60

Antimicrobial resistance has been coming up as one of the challenging business for treating domiciliary and nosocomial infections. The present study compared rate of resistance towards different commonly used antibiotics for common bacterial pathogens isolated during 2001 to 2003. Regarding Escherichia coli, mentionable increase (p

Extended spectrum beta lactamases (ESBLs) produced by Gram negative bacteria are mainly mediated by three important genes, namely TEM, SHV and CTX-M. In this study, we used a multiplex PCR to determine the prevalence of CTX-M and its subgroups CTX-M-3, CTX-M-14, among the members of Enterobacteriaceae family and in Pseudomonas spp that were isolated from different clinical samples in a tertiary care hospital in Bangladesh. A total of 300 culture positive clinical isolates were selected for the study. Out of these, 216 from urine, 45 from wound swab, 39 from pus aspirates. The ESBL status was determined by double disc diffusion test (DDDT) as recommended by Clinical Laboratory Standard Institute 2010 (CLSI) and by multiplex PCR for TEM, SHV and CTX-M, CTX-M-3, CTX-M-14 genes. Out of 300 isolates tested, 71.3% were positive for ESBL production by DDDT. The rate of positivity for TEM, SHV and CTX-M genes in 107 randomely selected isolates was 83.2%. Among these, 56.2% (50/89) was positive for CTX-M. Among the CTX-M positive isolates, CTX-M-3 and CTX-M- 14 were 78.0% (39/50) and 80.0% (40/50) respectively. Our study demonstrated that CTX-M variants were common in Enterobacteriaceae and Pseudomonas spp prevalent in the hospital of Bangladesh.Ibrahim Med. Coll. J. 2015; 9(1): 26-30

Background: Urinary tract infection (UTI) is among the most common bacterial infections and possess significant healthcare burden. Hence a study was necessary to apply PCR technology directly to clinical specimens to allow early and accurate identification of pathogens of UTI. Objective: Diagnosis of major uropathogens by different laboratory diagnostic procedures including polymerase chain reaction (PCR) directly from urine specimens from suspected patients of urinary tract infection. Methods: This study was carried out in the department of Microbiology, Mymensingh Medical College during the period from July 2016 to June 2017. Urine specimens were collected and isolation and identification of major uropathogens (Escherichiacoli Klehsiella pneumonias, Proteusmirabilis, and Pseudomonas aeruginosa) were done by standard microbiological procedure anbiochemical tests. PCR was performed by using standard protocol with species specific primer for detection offim H gene for Escherichia coli, fimK gene for Klehsiella paeunomiae, UreC for Proteus mirabilis and ETA for Pseudomonas aeruginasa. Results: Out of 250 urine specimens, 200 specimens were isolated and identified by culture and different biochemical methods which were supported by microscopical examination and at the same time PCR could detect species specific genes in 201 specimens directly from urine of suspected UTI patient Escherichia coli was responsible as a leading causative pathogen in both outpatient department and in patient department. Urine specimens was higher in female in both out patient population and inpatient population. Culture positivity of in patient population among the male (45.5%) was slighty higher than that of outpatient population (34.5%). The predominant age group suffered from UTI in case of outpatient population was >15-30 but for the in patient population, the age group was 60 years and above. 90 culture positive in patient population, 43 (95.5%) were from the gynae unit, 23 (92%) were from surgery unit, 8 (72.7%) were from the medicine unit, 12 (85.7%) were from orthopaedic unit and 4 (80%) were from paediatric unit. On the other hand Pseudomonas aeruginosa Profeus mirabilis and Klebsiella pneumonia were more prevalent in in-patient department and it was 21.1%, 5.6% and 5.5% respectively, Among the 50 culture negative urine specimens, 14 (28%) showed PCR positive for Escherichia coli, Klehsiella pneumonia and Pseudomonas aeruginosa. Conclusion: This study revealed that, the prevalence of UTI is high n MMCH Single pathogen base uniplex PCR was found superior than standard culture and less time consuming. Because uniplex PCR could detect many (28%) culture negative cases.

From July 2015 to December 2016, the presence of rickettsial pathogens was investigated for 414 patients with unknown fever in eight places in all the divisions of Bangladesh. Rickettsia felis was identified in blood samples from all the regions (overall detection rate, 19.6%), suggesting nationwide prevalence of R. felis infections.

Spread of Gram-negative bacteria producing extended-spectrum beta-lactamases (ESBLs) and carbapenemases constitutes a growing challenge in control of bacterial infections. In this study, prevalence and genetic characteristics of