Genetic characterization of methicillin-resistant / susceptible Staphylococcus aureus (MRSA/MSSA) and Staphylococcus argenteus clinical isolates in Bangladesh: Dominance of ST6-MRSA-IV/t304 and detection of cfr/fexA in ST8-MSSA/t008

Objectives

Coagulase-positive staphylococcus (CoPS), represented by Staphylococcus aureus, is a major cause of infections in humans. This study aimed to investigate molecular epidemiological characteristics, antimicrobial resistance, and their trends of CoPS in Bangladesh.

Methods

Clinical isolates of CoPS were collected from two medical institutions in Bangladesh for a 2-year period and analyzed for their species, genotypes, virulence factors, antimicrobial susceptibility, and resistance determinants.

Results

172 CoPS isolates collected were identified as S. aureus or S. argenteus (170 and two, respectively). Methicillin-resistant S. aureus (MRSA) accounted for 36% (n = 61), having Staphylococcal cassette chromosome mec (SCCmec)-IV (82%) or V (18%). Panton-Valentine leukocidin (PVL) genes were detected at higher rate in methicillin-susceptible S. aureus (MSSA) (62%) than MRSA (26%). MRSA comprised 11 STs, including a dominant type ST6 (46%) associated with mostly SCCmec-IVa/spa-t304, and one isolate had genetic features of the USA300 clone (ST8/SCCmec-IVa/coa-IIIa/spa-t008/ACME-I/ΦSa2USA). STs of CC1, CC88, and CC398 were common in MSSA, with CC88 showing the highest PVL-positive rate. One MSSA isolate (ST8/spa-t008) harbored fexA and cfr showing susceptibility to linezolid. S. argenteus was methicillin-susceptible and belonged to ST2250/coa-XId.

Conclusions

Genetic characteristics of current MRSA/MSSA in Bangladesh were revealed, with first identification of S. argenteus at low prevalence.

The Prevalence, Risk Factors, and Antimicrobial Resistance Determinants of Helicobacter pylori Detected in Dyspeptic Patients in North-Central Bangladesh

Chronic infection of Helicobacter pylori represents a key factor in the etiology of gastrointestinal diseases, with high endemicity in South Asia. The present study aimed to determine the prevalence of H. pylori among dyspeptic patients in north-central Bangladesh (Mymensingh) and analyze risk factors of infection and antimicrobial resistance (AMR) determinants in the pathogen. Endoscopic gastrointestinal biopsy samples were collected from dyspeptic patients for a one-year period from March 2022 and were checked for the presence of H. pylori via the rapid urease test and PCR and further analyzed for the status of virulence factors vacA/cagA and genetic determinants related to AMR via PCR with direct sequencing or RFLP. Among a total of 221 samples collected, 80 (36%) were positive for H. pylori, with the vacA+/cagA+ genotype being detected in almost half of them. H. pylori was most prevalent in the age group of 41-50-year-olds, with it being more common in males and rural residents with a lower economic status and using nonfiltered water, though the rates of these factors were not significantly different from those of the H. pylori-negative group. Relatively higher frequency was noted for the A2147G mutation in 23S rRNA, related to clarithromycin resistance (18%, 7/39). Amino acid substitutions in PBP-1A (T556S) and GyrA (N87K and D91N) and a 200 bp deletion in rdxA were detected in samples from some patients with recurrence after treatment with amoxicillin, levofloxacin, and metronidazole, respectively. The present study describes the epidemiological features of H. pylori infection in the area outside the capital in Bangladesh, revealing the spread of AMR-associated mutations.

Genetic Characterization of the Dengue Virus Type 3 Genotype I Prevailing in Dhaka, Bangladesh, 2021

Background: In Bangladesh, dengue has been prevalent since its resurgence in 2018, and the dominant causative virus in 2019 was considered dengue virus serotype 3 (DENV-3). However, limited information is available for DENV serotype/genotype circulating after 2020. Materials and Methods: Viral RNA was extracted from NS1 antigen-positive blood samples of febrile patients in Dhaka, in 2021. DENV gene was detected by semi-nested RT-PCR, and sequences of envelope (E) gene and C-prM gene were determined by direct sequencing of RT-PCR products for genetic analysis. Results: Among 172 NS1-positive samples collected, 91 samples were assigned to DENV-3 and DENV-2 (88 and 3 samples, respectively) by RT-PCR targeting the C-prM gene. Phylogenetic analysis of the E gene for the 17 representative DENV-3 samples showed that all the viruses belonged to genotype I, forming a cluster (B-cluster) with those of DENV-3 reported in Bangladesh in 2017. Analysis of the deduced amino acid sequences of E protein revealed 16 amino acid substitutions, including two novel ones (G221W, L285P), and a substitution T223I that was specifically found in DENV-3 B-cluster. Conclusion: This study showed the persistent predominance of DENV-3 genotype I in Bangladesh having unique genetic traits in the E gene. (Approval number: MMC/IRB/2022/468).

Detection of Oncogenic Human Papillomavirus (HPV-16 and HPV-18) from Bacterial Vaginosis Positive Patient Attending at Tertiary Care Hospital in Mymensingh

Cervical cancer is the fourth most common cancer in women in the world and is the second leading malignancy among Bangladeshi women. Persistent infection with high risk human papillomavirus (HPV) is an important cause of development of cervical intraepithelial neoplasia (CIN) followed by cancer. Bacterial vaginosis (BV), a common treatable vaginal infection which can disrupt the balanced vaginal ecosystem and its innate protective mechanisms against infection, can play an essential role in the acquisition and persistence of high risk human papillomavirus (HR-HPV) infection. This cross sectional study was conducted to detect the HR-HPV (HPV-16 and HPV-18) infection among bacterial vaginosis positive patient in the Department of Microbiology, Mymensingh Medical College (MMC), Bangladesh, from March 2018 to February 2019. A total of 300 endocervical swabs and high vaginal swabs were collected from the VIA (Visual inspection with acetic acid) outdoor clinic of Obstetrics and Gynaecology Department of Mymensingh Medical college Hospital. HPV DNA was tested among all 300 cases by nested PCR. Typing of HPV 16 and HPV 18 was done among HPV DNA positive cases with BV and intermediate flora by multiplex PCR. BV was diagnosed according to Nugent criteria by using the gram stained smear of high vaginal swab. A total of 57/300 (19.0%) samples were positive for HPV DNA by nested PCR. Of the total 300 cases 78(26.0%) had BV, 38(13.0%) had intermediate flora and 184(61.0%) had normal vaginal flora. HPV DNA was more positive in patients having intermediate flora 08/38 (21.05%) followed by the patients having normal vaginal flora 37/184 (20.11%) and BV 12/78 (15.38%). Among the 12 BV patients who were also HPV DNA positive (83.33%) were belong to high risk HPV (type 16 and 18) group and among them 08(66.67%) were HPV-16 and 02(16.67%) were HPV-18. But among 08 HPV DNA positive intermediate flora containing patients only 01(12.5%) were belong to HR-HPV (type 16 and no type 18 was detected).

Clonal Diversity of Candida auris, Candida blankii, and Kodamaea ohmeri Isolated from Septicemia and Otomycosis in Bangladesh as Determined by Multilocus Sequence Typing

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.

Prevalence of Virulence Genes in Acinetobacter baumannii Isolated from Clinical Samples in Mymensingh Medical College Hospital, Bangladesh

Acinetobacter baumannii is an opportunistic bacterial pathogen that is the most important cause of hospital-acquired infections. The objective of this study was to evaluate the predominance and determination of virulence encoding genes in A. baumannii isolates. During this cross-sectional study period from February 2019 to March 2020 of 380 clinical samples including endotracheal aspirates (70), wound swab or pus (175), urine (70) and blood (65) analysed in inpatients admitted to the hospital in different unit like ICU, Surgery and Burn unit of Mymensingh Medical College Hospital. Out of 380 studied samples, 130(34.21%) strains were yielded growth. Among 130 isolates, Acinetobacter spp. was 49(37.69%). Totally, 39(79.59%) were Acinetobacter baumannii which was detected by molecular technique PCR. Further more, the determination of virulence genes csgA and fimH detected by PCR. Among two studied virulence genes, csgA (38.46%) was the most prevalent virulent genes associated with disease severity and co-morbidity of the patient in A. baumannii infections.

Distribution and Pattern of Anti-Tubercular Drug Resistance in Patients with Pulmonary Tuberculosis in Mymensingh Region of Bangladesh

Globally, the emergence of multidrug-resistant strains of Mycobacterium tuberculosis is an increasing problem that adversely affects patient care and public health. This cross sectional descriptive study was carried out in the Department of Microbiology, Mymensingh Medical College from January 2010 to December 2010 to isolate M. tuberculosis from smear-positive sputum samples by Lowenstein-Jensen (L-J) media and investigate the drug resistance pattern. Among 101 smear-positive cases 80(79.20%) yielded growth of Mycobacteria, 5(4.95%) were contaminated and 16(15.84%) showed no growth. Among 80 isolates 76(95.0%) were M. tuberculosis and the remaining 4(5.0%) were Non-tuberculous Mycobacteria (NTM). Out of 76 M. tuberculosis 27(35.52%) were resistant to at least one drug, 4(5.26%) to Isoniazid (INH), 1(1.32%) to Rifampicin (RMP), 8(10.53%) to Streptomycin (SM) and 0(0.0%) to Ethambutol (EMB) and multi-drug resistant tuberculosis (MDR-TB) was 9(11.84%). The present study creates the impression that fairly high rate of anti-tuberculosis drug resistance among the tuberculosis cases and also high MDR-TB (Resistant to both Rifampicin and Isoniazide). The emergence of MDR-TB poses significant trouble to TB control activities throughout the world. The complexity of MDR-TB operation makes it essential to produce new skills to design, plan, application and monitor interventions for the management of MDR-TB. More surveillance and immediate remedial interventions should be performed to combat the trouble of MDR-TB to the general population.

Prevalence and Antifungal Susceptibility of Clinically Relevant Candida Species, Identification of Candida auris and Kodamaea ohmeri in Bangladesh

Candida species are major fungal pathogens in humans. The aim of this study was to determine the prevalence of individual Candida species and their susceptibility to antifungal drugs among clinical isolates in a tertiary care hospital in Bangladesh. During a 10-month period in 2021, high vaginal swabs (HVSs), blood, and aural swabs were collected from 360 patients. From these specimens, Candida spp. was isolated from cultures on Sabouraud dextrose agar media, and phenotypic and genetic analyses were performed. A total of 109 isolates were recovered, and C. albicans accounted for 37%, being derived mostly from HVSs. Among non-albicans Candida (NAC), C. parapsilosis was the most frequent, followed by C. ciferrii, C. tropicalis, and C. glabrata. Three isolates from blood and two isolates from aural discharge were genetically identified as C. auris and Kodamaea ohmeri, respectively. NAC isolates were more resistant to fluconazole (overall rate, 29%) than C. albicans (10%). Candida isolates from blood showed 95% susceptibility to voriconazole and less susceptibility to fluconazole (67%). Two or three amino acid substitutions were detected in the ERG11 of two fluconazole-resistant C. albicans isolates. The present study is the first to reveal the prevalence of Candida species and their antifungal susceptibility in Bangladesh.

Study of Human Brucellosis among Patients with Pyrexia of Unknown Origin by Antibody Detection

This study was performed to determine the seropositivity of human brucellosis among the patients suffering from pyrexia of unidentified origin. This cross-sectional study was performed at department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh from September 2018 to August 2019; among the patients of pyrexia of unknown origin visited inpatient and outpatient facility of department of Medicine and department of Paediatrics, Mymensingh Medical College Hospital (MMCH) in Mymensingh division of Bangladesh. A total of 400 serum samples were screened by Brucella-specific latex agglutination test to determine seropositivity. Seven percent (7.0%) (28/400) serum samples were found to be seropositive for brucellosis by detecting Brucella-specific antibody at a titer ≥1:160. Therefore, Brucella-specific latex agglutination test may be recommended as a screening test for human brucellosis in developing and underdeveloped countries.

Molecular Detection of MBL Encoding Genes in Acinetobacter baumannii strains Isolated from Various Samples at a Tertiary Care Hospital in Mymensingh

MBL producing Acinetobacter baumannii is a major threat for therapeutic treatment of hospital acquired infections. The aim of this study was to determine the prevalence of metallo-β-lactamase genes VIM, IMP & SIM genes amongst isolated A. baumannii. This cross sectional study conducted in the department of Microbiology Mymensingh Medical College from March 2019 to February 2020. 49 Acinetobacter spp. were isolated from different clinical samples including endotracheal aspirates, wound swab/pus, urine and blood. Among 380 clinical samples 130 organisms were isolated growth was 34.21%. Out of 130 isolated strains, 49(37.69%) were Acinetobacter spp identified by standard bacteriological method and resistance to different antibiotics was assessed with Kirby- Bauer Disc diffusion method. Among 49 Acinetobacter spp, 39(79.59%) were Acinetobacter baumannii which was identified by molecular method PCR directing OXA-51 like gene. Multiplex PCR was done to determine MBL genes existence VIM, IMP & SIM. Ceftriaxone (79.48%) showing higher resistance and colistin (12.82%) showing lower resistance. All the strains were sensitive to tigecycline. The distribution of MBLs genes such as VIM 20(51.28%), IMP 5(12.82%) and SIM 0 (0%). This study showed that high level of antibiotic resistance and VIM was the most prevalent MBL genes among A. baumannii highlighting the need for indigenous antibiotic usage plan & infection control measures to prevent the spread of these resistance genes.

Concurrent Infection of Orientia Tsutsugamushi with Rickettsia spp. Including Rickettsia felis in North Central Bangladesh

Rickettsial diseases are one of the leading causes of treatable acute febrile illness in Asia pacific region. This cross-sectional descriptive study was conducted at Department of Microbiology, Mymensingh Medical College to diagnose scrub typhus by rapid Immunochromatographic Test (ICT) and Nested PCR followed by molecular identification of possible Rickettsial coinfection among suspected febrile patients in Mymensingh, Bangladesh from March 2019 to February 2020. Among the enrolled 402 patients, 89 samples (22.13%) were seropositive by Immunochromatographic Test (ICT) and 65 samples (16.16%) were positive for O. tsutsugamushi DNA by Nested PCR, targeting 47KDa gene. Therefore, 113/402 (28.10%) samples were positive for scrub typhus by PCR and/or ICT. All the scrub typhus positive samples were further subjected to Nested PCR targeting 17 KDa gene for identification of Rickettsial co-infection and 13/113 (11.50%) were documented as positive. Then 13 Rickettsial co-infected samples were undertaken to automate sequencing and all were genetically confirmed as Rickettsia felis. Findings of the study may help clinicians to expand their list of differential diagnoses for undifferentiated fever and detection of Rickettsial co-infection may guide them to prescribe effective antimicrobials.

Socio-demographic and Clinico-epidemiological Study of Scrub Typhus in A Tertiary Care Hospital of Mymensingh, Bangladesh

Scrub typhus is one of the leading causes of undifferentiated treatable febrile illness in Asia pacific region. It is grossly under diagnosed in many tropical countries of South Asia including Bangladesh, due to wide range of non-specific clinical presentations, low index of suspicion among clinicians, limited awareness and lack of accurate diagnostic facilities. This cross sectional observational study was conducted at department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh from March 2019 to February 2020 enrolling 113 diagnosed cases of scrub typhus by Immunochromatographic test (ICT) and / or Nested PCR to characterize the socio-demographic and clinico-epidemiological features of scrub typhus in Mymensingh area. Majority of the scrub typhus cases came from rural areas (63.83%) and there was a slight female predominance (52.21%). The young (32.74%) and the young-adult age group (28.31%) were mostly affected. Most of the scrub typhus cases were housewives (30.98%), followed by farmers (23.89%) and students (21.23%). All the enrolled cases presented with fever. Other findings were myalgia (76.10%), headache (56.63%), cough (30.97%), vomiting (12.38%) and Respiratory distress (9.73%). Typical eschar of scrub typhus was present only in 9(7.96%) cases and 4(3.53%) patients had rashes on their skin. Few cases (3.53%) had jaundice and 15.96% cases were anaemic. Oliguria (7.96%) and neck rigidity (1.76%) were also documented. Most of the Nested PCR positive scrub typhus cases were documented during late rainy season and beginning of winter months. Findings of the study may offer increased awareness about high burden of scrub typhus as well as heightened suspicion among clinicians for early diagnosis, timely treatment and prevention of complications.

Coexistence of ESBL and MBL-mediated resistance in Acinetobacter baumannii in a Tertiary Care Hospital, Bangladesh

Antimicrobial resistance mediated by extended-spectrum beta-lactamases (ESBL), AmpC beta-lactamase and metallo-beta-lactamase (MBL) producing Acinetobacter species is an emerging problem worldwide. In this cross-sectional study total 341 specimens were collected over a period of one year from January 2017 to January 2018. Specimens were collected from ICU and Surgery unit of Mymensingh Medical College Hospital, Mymensingh, Bangladesh. Specimens were collected from ICU and Surgery Unit of Mymensingh Medical College Hospital, Mymensingh, Bangladesh. Samples were processed for culture by standard conventional methods and susceptibility testing and determined by Kirby Bauer disc diffusion method. Antibiotic discs and their strength were according to the CLSI 2017 guideline. Molecular study was done to detect the species by OXA-51 gene and drug resistance genes (IMP, VIM, NDM, TEM, SHV, CTX, SPM, SIM and GIM). Species identification was done by OXA-51 gene which is intrinsic to Acinetobacter baumannii. Among the 46 isolates, 36(78.26%) were positive for Oxa-51 gene, 16(34.8%) for TEM gene, 9(19.6%) for VIM gene, 3(6.5%) for NDM gene and 1(2.2%) for IMP gene. This study gives an alarming sign towards high prevalence of cephalosporin and carbapenem resistance due to production of extended spectrum beta-lactamases and metallo-betalactamases, respectively. Early detection, proper antibiotic policies, and compliance towards infection control practices are the best defenses against these organisms.

Detection of Quinolone Resistance Pattern and Presence of qnr Genes in Human Salmonella Isolates at Mymensingh, Bangladesh

Among the quinolones, fluoroquinolones are broad spectrum antimicrobial agents used for treating many clinical infections including Salmonellosis. Although high level of resistance to fluoroquinolones remains low in Salmonella but reduced susceptibility is increasing worldwide. Plasmid-mediated quinolone resistance (PMQR) of qnr type (qnrA, B and S) has been identified now a day in several enterobacterial species including Salmonella spp. This cross-sectional study was held at department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh from March 2019 to February 2020. This study was conducted to determine the current quinolone resistance pattern and to detect the presence of qnrA, qnrB and qnrS genes among Salmonella isolates. Antimicrobial susceptibility test of 36 Salmonella isolates were done by disc diffusion method. MIC of ciprofloxacin was detected by agar dilution method. Then amplification with specific primers of qnrA, qnrB and qnrS genes were performed for all Salmonella isolates. The present study observed 80.5% resistance to nalidixic acid, 33.3% to ciprofloxacin and 19.4% to ofloxacin by disc diffusion method. qnr A gene was detected in 2(5.5%) isolates, where as qnrS was detected in 5 (13.8%) isolates. None of the isolates was positive for qnrB gene. All the qnrA positive isolates showed resistance to Ciprofloxacin (MIC=128μg/ml) and Ofloxacin. In conclusion, presence of qnr genes in the study isolates is alarming, because, rapid dissemination might occur due to conjugative plasmid mediated horizontal transfer.

Rapid Serologic and Molecular Diagnosis of Scrub Typhus among Suspected Febrile Patients Visiting Mymensingh Medical College Hospital

Scrub typhus, caused by the bacterium- Orientia tsutsugamushi is one of the leading causes of undifferentiated treatable febrile illness in Asia pacific region. It is grossly under diagnosed in many tropical countries of South Asia including Bangladesh, due to wide range of non-specific clinical presentations, low index of suspicion among clinicians, limited awareness and lack of accurate diagnostic facilities. This cross-sectional descriptive study was conducted at Department of Microbiology, Mymensingh Medical College to diagnose scrub typhus by rapid Immunochromatographic test (ICT) as well as molecular detection of O. tsutsugamushi by Nested PCR and automated nucleotide sequencing among suspected febrile patients in Mymensingh, Bangladesh during 2019-20. Blood samples were collected from 402 febrile patients of suspected Rickettsial illness, referred from inpatient and outpatient departments of Medicine and Pediatrics, Mymensingh Medical College Hospital (MMCH). Among the enrolled 402 patients, 89 samples (22.13%) were seropositive by Immunochromatographic test (ICT) and 65 samples (16.16%) were positive for O. tsutsugamushi DNA by Nested PCR, targeting 47KDa gene. Therefore, 113/402 (28.10%) samples were positive for scrub typhus by PCR and/ or ICT. Highest number of patients was detected positive by nested PCR during the first 5-10 days of fever but only 2 cases were positive after 20 days. In case of ICT, highest positivity for only IgM (8.13%) and both antibodies (2.43%) were documented in first 5-10 days of fever, but IgG positivity was highest (41.66) in >20 days of fever. From 65 PCR positive samples, automated nucleotide sequencing was performed on 20 randomly selected samples and all were genetically confirmed to be O. tsutsugamushi.

Seropositivity of Human Brucellosis among Patients with Pyrexia of Unknown Origin on Both Risk and Non-Risk Group of Individuals and Molecular Detection by Real-time PCR

Brucellosis is a zoonotic disease that is one of the important infectious causes of Pyrexia of Unknown Origin (PUO). The objective of the present study was to determine the seropositivity and molecular detection of human brucellosis among the patients with pyrexia of unknown origin on both risk and non-risk group of individuals in greater Mymensingh. A total of 400 blood samples were randomly collected from pyretic patients started from September 2018 to August 2019. Questionnaires were used to collect data on both risk and non-risk group of individuals. All samples were initially screened for anti-Brucella antibodies using the Brucella-specific latex agglutination test. For accurate investigation, seropositive as well as seronegative serum samples were tested by BCSP31 Brucella genus-specific TaqMan real-time PCR. Overall 32(8%) cases were positive out of 400 samples by Brucella-specific latex agglutination test and/or BCSP31 Brucella genus-specific real-time PCR. Brucella-specific latex agglutination test documented 7% (28/400) positivity for brucellosis. 22(5.5%) samples found Brucella genus-specific real-time PCR positive out of 400 samples. Most real-time PCR positive cases were found from sero-positive samples of risk group population (15/32). Sero-negative but real-time PCR positive cases also found only from risk group population (4/32). There were 10 seropositive cases where real-time PCR was negative. In addition to Brucella-specific latex agglutination test as a screening test, Brucella genus-specific real-time PCR was performed for confirmation and also to avoid unjustified costs, drug toxicity, and masking of other potentially dangerous diseases.

Early and Rapid Detection of Typhoid Fever by Nested PCR in Blood

Typhoid fever caused by Salmonella typhi is one of the major health problems in developing countries including Bangladesh. Still now blood culture is gold standard method for diagnosing typhoid fever, but this method is laborious, requires several days and detection rate is low. Failure of early laboratory diagnosis often leads to increased morbidity and mortality. This study was intended to apply a nested PCR in blood for early diagnosis of typhoid fever. In this cross sectional study blood samples were collected from 200 suspected typhoid fever patients attending Mymensingh Medical College Hospital, Bangladesh. Nested Polymerase Chain Reaction (n PCR) of flagellin gene was done in all the blood samples. At the same time all blood samples were subjected to culture by lytic centrifugation method. Culture positive isolates were identified as S. typhi by biochemical tests. Among the 200 blood samples, 57 (28.5%) were positive for S. typhi on nested PCR where as blood culture was positive for S. typhi in 16 (8%) samples. Among the 57 PCR positive samples, only 15 (26.3%) samples were culture positive for S. typhi and rest 42 (73.7%) were culture negative. So, in culture negative cases PCR can be used as a rapid diagnostic test for diagnosing typhoid fever. Considering time requirement, PCR takes one day, whereas blood culture takes 3 or more days to confirm diagnosis.

Detection of Biocide Resistance Genes (qacE and qacΔE1) in Pseudomonas spp Isolated from Patients with CSOM at Mymensingh Medical College Hospital, Bangladesh

Biocides, including disinfectants and antiseptics, are used for a variety of topical and hard surface applications in health care facilities. Biocides play a significant role for preventing and controlling nosocomial infections. However, failures in the antimicrobial activities of biocides have been reported. The resistance mechanism to disinfectants is usually determined by genes which are related to resistance to quaternary ammonium compounds, namely, qacE, qacΔE1 that are found in Gram-negative bacteria. The aim of this study is to detect the prevalence of Biocides resistance genes, qacE and qacΔE1, in clinical isolates of Pseudomonas spp. It was carried out from March 2017 to July 2018 in the department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh. Samples were collected from Outpatient of ENT department, MMCH. In this study, 300 clinical samples of CSOM cases were tested by the PCR method. The present study shows detection of biocide resistance genes (qacE, qacΔE1) among 87 isolated Pseudomonas spp by uniplex PCR. Among 72 clinical isolates of Pseudomonas aeruginosa 67(93.05%) had the gene qacEΔ1 and 25(34.72%) had the gene qacE. In addition other 15 Pseudomonas spp 3(20%) isolates had the qacEΔ1 gene and 2(13.33%) isolates had the qacE gene. In this study there is a marked difference in detection of the qacEΔ1 gene between the MDR and non MDR P. aeruginosa isolates. The qacEΔ1 was identified in 50 of 54(92.59%) MDR isolates and 7 of 18(38.89%) non MDR strains respectively. While gene qacE was detect 25(46.29%) MDR isolates and did not show any qacEΔ1gene in non MDR isolates. This study shows that the genes, qacE, qacΔE1 are widespread among Pseudomonas aeruginosa, they are higher in MDR strains than non MDR strains.

Prevalence of ESBL Encoding Genes in Acinetobacter baumannii Strains Isolated from Various Samples of a Tertiary Care Hospital in Mymensingh

The aim of this study was to find the prevalence of ESBL genes among A. baumannii isolates. In this cross sectional study, 49 Acinetobacter spp. were isolated from various clinical samples from March 2019 to February 2020 conducted in the department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh. Clinical samples including endotracheal aspirates, wound swab/pus, urine and blood. A total of 380 samples were analyzed. Growth was obtained in 34.21% of the samples yielding 130 organisms. Out of 130 organisms, 49(37.69%) were Acinetobacter spp. Among 49 Acinetobacter spp, 39(79.59%) were Acinetobacter baumannii which was identified by PCR targeting OXA-51 like gene. Amplification of the ESBL encoding genes, namely CTX-M, TEM, SHV done by molecular technique PCR. The most antibacterial resistance was against ceftriaxone (79.48%) and lower resistance only showed in colistin (12.82%). All the isolates were sensitive to tigecycline. The distribution of ESBLs genes such as TEM 20(51.28%), CTX-M 16(41.02%) and SHV 0(0%). The high resistance to most of the antibiotics among the studied strains and also a high prevalence of TEM gene in A. baumannii strains found in our study gives alarming sign towards the treatment complexity of these strains.

Clinical Features of Covid-19 Infection: a Study of SARS-CoV-2 Positive Patients from Mymensingh Region, in Bangladesh

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to almost every country on the globe and it is considered by World Health Organization as a pandemic. SARS-CoV-2 causes the Coronavirus disease 2019 (COVID-19). Many of country are reporting the symptomatic characteristics of their cases to give better observations into the various clinical presentations of SARS-CoV-2 infection. However, the symptomatic literature is limited in Bangladesh. The aim of the study is to analyze the symptomatic characteristics of patients having the SARS-CoV-2 positive by real time reverse transcription polymerase chain reaction (rRT -PCR) test. Here, the data of 146 patients who were positive for the SARS-CoV-2 virus and were residents of different districts of Mymensingh region were analyzed. Patients' demographics, symptoms, history of co-morbidities condition like DM, HTN, Hypothyroid etc, travel and contact were collected from MMC Daily Reported data from April 1, 2020 to April 30, 2020. Among the total 3184 patients' nasopharyngeal samples, we have got 146 (4.58%) positive for SARS-CoV-2. Of the 146 positive patients most of the patients were male 95(65%), the majority 80(54.8%) were the 21 to 40year age group. Most of the patients 61(41.78%) were residents of Mymensingh include Mymensingh Sadar, Valuka, Trishal and Ishhorganj. Among the patients 94(64.4%) were symptomatic and 52(35.6%) were asymptomatic. The symptomatic patients presented mostly were with fever 45(30.82%), cough 33(22.6%) and breathlessness 9(6.16%). The majority of patients 54(36.9%) had a history of contact with SARS-CoV-2 patients and 16(11%) had a travel history within 14 days of their rRT-PCR test positive. The only 3(2%) patients had history of comorbidities condition like DM, HTN, Hypothyroid etc. The number of SARS-CoV-2 cases is rapidly increasing in our country. The education of the population about the most common symptoms of the virus infection is needed mostly; therefore, individuals may able to recognize these symptoms. So, that people might get themselves tested.

Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020

In Bangladesh, coronavirus disease 2019 (COVID-19) has been highly prevalent during late 2020, with nearly 500 000 confirmed cases. In the present study, the spike (S) protein of severe acute respiratory coronavirus 2 (SARS-CoV-2) circulating in Bangladesh was genetically investigated to elucidate the diversity of mutations and their prevalence. The nucleotide sequence of the S protein gene was determined for 15 SARS-CoV-2 samples collected from eight divisions in Bangladesh, and analysed for mutations compared with the reference strain (hCoV-19/Wuhan/WIV04/2019). All the SARS-CoV-2 S genes were assigned to B.1 lineage in G clade, and individual S proteins had 1-25 mutations causing amino acid substitution/deletion. A total of 133 mutations were detected in 15 samples, with D614G being present in all the samples; 53 were novel mutations as of January 2021. On the receptor-binding domain, 21 substitutions including ten novel mutations were identified. Other novel mutations were located on the N-terminal domain (S1 subunit) and dispersed sites in the S2 subunit, including two substitutions that remove potential N-glycosylation sites. A P681R substitution adjacent to the furin cleavage site was detected in one sample. All the mutations detected were located on positions that are functionally linked to host transition, antigenic drift, host surface receptor binding or antibody recognition sites, and viral oligomerization interfaces, which presumably related to viral transmission and pathogenic capacity.

Detection of Antimicrobial Resistance Pattern and ESBL Production among Clinical Isolates of Salmonella Species in Mymensingh, Bangladesh

The occurrence of antimicrobial resistance in Salmonella enterica serovars (both typhoidal and non-typhoidal Salmonellae) is a major public health problem especially in developing countries, which have been associated with treatment failures. Therefore, the study was undertaken to determine the current antimicrobial resistance pattern and extended spectrum β-lactamase (ESBL) production among clinical isolates of Salmonella spp. during 2019-2020 in Mymensingh, Bangladesh. In this cross sectional study, 36 Salmonella enterica isolates were obtained from blood and stool culture of suspected 200 enteric fever and 100 gastroenteritis patients attending at Mymensingh Medical College Hospital, Mymensingh, Bangladesh. Isolated Salmonella species were identified by biochemical tests and Polymerase Chain Reaction (PCR). Disk diffusion test was performed by modified Kirby Bauer method. Minimum Inhibitory Concentration (MIC) of ceftriaxone was detected by agar dilution method. Double disk synergy test was used as a screening test for ESBL production. PCR was done for detection of blaTEM, blaSHV and blaCTX-MU genes. The isolates showed 25% resistance to Ceftriaxone and 58.3% to Azithromycin. The highest sensitivity rates were 88.9% to Meropenem and 83.3% to Amikacin. Whereas 6(16.7%) isolates were Multi Drug Resistant (MDR). Eight (8) isolates were confirmed as ESBL producer by DDST. The marked increase in MIC was observed between 8->512μg/ml to ceftriaxone. blaTEM, blaSHV and blaCTX-MU genes were detected in 3, 5 and 8 isolates respectively. In conclusion, the current study observed, higher level of resistance to ceftriaxone and azithromycin. At the same times 22.2% isolates showed ESBL production, which is a cause for concern as it may lead to treatment failure. On the other hand the study also showed the re-emergence of chloramphenicol and Sulfamethoxazole-Trimethoprim sensitivity.

Molecular Detection of Human Coronavirus from North Central Part of Bangladesh Depending on ORF1ab and N Gene

The Coronavirus disease 2019 (COVID-19) resulted severe respiratory illness such as pneumonia and lung dysfunctions that was first identified at Wuhan, the capital of Hubeiin China during the end of December 2019. The etiological cause of COVID-19 has been confirmed as a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was similar with the zoonotic virus SARS-CoV (2002). Now a days for early diagnosis of COVID-19 the nucleic acid based test like RT PCR (real time reverse transcription polymerase chain reaction) is most consistent and used all over the world. In this study among 11,280 cases 825(7.31%) were positive by molecular RT PCR method on June 2020 at Microbiology department of Mymensingh Medical College and the samples are collected from different areas of Northern part of Bangladesh. Among this positive cases 588(71%) N gene, 10 ORF1ab (2%) and 227(27%) both N and ORF gene showed significant curve which is specific for COVID-19 positive patients. Because N and ORF gene of this virus inhibit immune system of human body especially interferon. Out of SARS-CoV-2 positive cases maximum number of N gene were found in male patients and above 40 years old aged group. So, Molecular diagnosis of this pandemic virus especially by N and ORF gene might be helpful to reduce the spread of SARS-CoV-2 as well as early treatment for saving many lives.

Molecular Detection of Human Brucellosis among Patients with Pyrexia of Unknown Origin

This study describes the molecular detection of human brucellosis among patients with pyrexia of unknown origin. It was a cross-sectional descriptive study and was carried out in the Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh. Non-probability purposive type of sampling technique was used. Blood samples were collected from 400 pyretic patients from September 2018 to August 2019. BCSP31 Brucella genus-specific TaqMan real-time PCR and SYBR Green real-time PCR were undertaken for molecular detection. Out of 400 samples, 22 (5.5%) samples found BCSP31 Brucella genus-specific real-time PCR positive. The study revealed that a considerable number of brucellosis is present in rural areas among risk as well as non-risk group study population having definite male predominancy, most prone to develop among >40-80 years age group. Brucella genus and species-specific real-time PCR might be performed for confirmation and also to avoid unjustified costs, drug toxicity, and un-masking of other potentially dangerous diseases.

Detection of 2019-Novel Coronavirus (2019-nCoV) by rRT-PCR at Mymensingh Medical College, Mymensingh, Bangladesh

The coronavirus disease (COVID-19) is highly pathogenic viral infection caused by SARS-CoV-2. Currently, COVID-19 has caused global health concern. WHO has declared COVID-19 as a pandemic disease on March 11, 2020 and characterized by fever, dry cough, fatigue, myalgia and chest pain with pneumonia in severe cases. The virus has spread to at least 213 countries and more than 9093827 confirmed cases and 471490 deaths have been recorded. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. There are some newly developed and promising methods for detection of SARS-CoV-2, in order to facilitate the development of novel approaches for early diagnosis. Nucleic acid based tests currently offer the most sensitive and early detection and confirmation for SARS-CoV-2 infection. Among them Real-time reverse transcription polymerase chain reaction (rRT-PCR) is the most popular and the "gold standard" testing method for the detection of SARS-CoV-2. The present study was carried out to detect 2019-Novel Coronavirus (2019-nCoV) by rRT-PCR method at Mymensingh Medical College, Mymensingh, Bangladesh from 1st April, 2020 to 31st May, 2020. A total of 14356 samples were tested from four districts of Mymensingh division namely, Mymensingh, Jamalpur, Sherpur, Netrokona and some parts of Sunamganj for rRT-PCR. Among them 1086 (7.5%) patients were positive for SARS-CoV-2. Out of 1086 positive cases 716(65.9%) were male and 370(34.1%) were female with a Mean±SD age 34.1±12 years. Maximum positivity was found in Mymensingh district followed by Netrokona, Jamalpur, Sherpur and Sunamganj respectively. This is the first base line study for genetic detection of 2019-nCoV in Mymensingh division which may reflect the total scenario of Bangladesh situation. We hope this paper will help the researcher to increase the availability, accuracy, and speed of widespread COVID-19 testing throughout the world in this crisis moment.

Isolation of Acinetobacter species from Clinical Specimens with Detection of Their Antimicrobial Susceptibility Pattern from a Tertiary Care Hospital, Bangladesh

Acinetobacter species are important opportunistic and nosocomial pathogens capable of causing both community and health care-associated infections. The aim of this study was to determine the prevalence of Acinetobacter species and determination of the antibiotic susceptibility patterns of Acinetobacter. A total of 341 specimens were collected over a period of one year from January 2017 to January 2018 from ICU and Surgery unit of Mymensingh Medical College Hospital, Mymensingh, Bangladesh. Antimicrobial susceptibility testing of all Acinetobacter isolates was done using Kirby Bauer's disc diffusion technique as per recommendations of Clinical Laboratory Standards Institute (CLSI). MIC of commonly used Imipenem and newly introduced Tigecycline by agar dilution method was done and was compared it with disc diffusion method. From total 341 specimens, 119(34.8%) pathogen were isolated. Among 119 isolates total 46(38.6%) Acinetobacter were isolated. Maximum number of Acinetobacter was isolated from respiratory samples- endotracheal secretions. Regarding antimicrobial resistance, 42(91.3%), 33(71.7%), 20(43.5%), 28(60.9%) and 1(2.2%) were resistant to Piperacillin-Tazobactam, Doxycycline, Imipenem, Colistin and Tigecycline. Regarding, MIC of Imipenem, 41.3% was resistant, 32.6% was intermediate and 26.1% was sensitive. Regarding MIC of Tigecycline none was resistant, 39.1% was intermediate and 60.9% was sensitive. Acinetobacter species is emerging as a predominant healthcare associated multidrug resistant pathogen. The findings of this study will help our clinicians to apply appropriate antibiotics for treatment of patients.

Molecular characterization of Orientia tsutsugamushi causing scrub typhus among febrile patients in north-central Bangladesh

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.

Distribution of HPV-16 and HPV-18 from the Patients Attending At Mymensingh Medical College Hospital by Newly Developed Oncoprotein Detection Assay

Cervical cancer is one of cause of death in women in many developing countries. Persistent infection with Human Papilloma Virus (HPV), primarily high risk types 16 and 18, is recognized as a causal and essential factor for the development of cervical cancer. The objective of this cross sectional observational study is to detect the distribution of HPV-16 and HPV-18 among Onco E6 positive cases. Following universal safety precautions a total of 180 endocervical swabs were collected from Colposcopy clinic of Obstetrics and Gynaecology Department of Mymensingh Medical College Hospital (MMCH), Mymensingh, Bangladesh from January 2016 to December 2016. Laboratory work was done in the department of Microbiology, Mymensingh Medical College. E6 strip test is an immunochromatographic test based on the detection of HPV-E6 oncoprotein in cervical swab samples. Onco E6 cervical test was done on 180cases. Among them 60% were VIA positive and 120% were VIA negative. From this VIA positive cases 12(16.25%) were On E6 cervical test positive and from VIA negative cases 3(2.5%) were positive by this On E6 cervical test. From this 12 Onco E6 cervical test positive cases 10(%) were HPV-16 and 2(%) were HPV-18 and from VIA negative cases 3 were only HPV-16 by this test. Histopathological test done on 35 suspected cases and out of 08 cervical carcinoma cases 07 were positive by this Onco E6 cervical test which was also HPV-16 type. It may be concluded that HPV-16 is most prevalent type to cause cervical cancer and by this newly developed protein detection assay will be helpful to reduce over treatment and save many lives.

Molecular Diagnosis of Human Papilloma Virus by PCR

Cervical cancer is a major world health problem and the fourth most leading cause of death in women around the world. High risk HPV DNA has been shown to be present in 99.7% of cervical cancers worldwide. So detection of HPV DNA by PCR may help in early detection and management of cervical cancer. This cross sectional observational study was done to detect L1 antigen gene of HPV from cervical swab by nested PCR. Following universal safety precautions a total of 141 endocervical swabs were collected from Colposcopy clinic of Obstetrics and Gynaecology department of MMCH from January 2015 to December 2015. Laboratory work was done in the department of Microbiology, Mymensingh Medical College (MMC), Mymensingh, Bangladesh HPV DNA was tested among 141 VIA positive women aged between 20-70 years by nested PCR method. DNA was extracted by phenol-chloroform extraction method. Two pairs of consensus primers MY09-MY11 and GP5-GP6 were used in a nested PCR assay. Histopathological examination was done on 66 samples in the Department of Pathology, MMC, Mymensingh, Bangladesh. A total of 36.9% (52/141) cases were positive for HPV DNA by nested PCR. On Histopathological diagnosis PCR was positive in 42.9% chronic cervicitis, 21.2% CIN cases and 90.9% cervical carcinoma cases. Based on the findings of the study, it may be concluded that the HPV DNA testing has opened the door for an alternative surveillance mechanism to routine cytological screening. Detection of HPV may play an important role in diagnosis and clinical prognosis of precancerous lesions. So PCR may be done for all VIA positive cases for screening of cervical cancer.

Electrophoretic Patterns of Human Rotavirus Strain Prevailing Among Children

Rotavirus gastroenteritis is a major cause of severe dehydrating diarrhea in children worldwide. Group A rotavirus causes approximately 40% of hospitalization for diarrhea among under 5 years children. Polyacrylamide gel electrophoresis (PAGE) and silver staining was applied to detect rotavirus dsRNA from acute diarrheic stool of 776 hospitalized children below five years. The study was conducted in Mymensingh district, Bangladesh from January 2013 to December 2014. Among 776 stool specimens tested 368(47.4%) were positive by PAGE. Among 368 positive 341(92.5%) showed clearly stained electrophoretic patterns of viral RNA which enabled their classification into different electropherotypes. The rate of infection was highest in children of 7-12 months of age and infection rate was more in winter. RNA profiles of the analyzed specimens, 164/341 (48%) were long and 177/341 (52%) were short patterns. Mixed electropherotypes (2%) among 368 were also detected. Electropherotyping technique could be an applied excellent method for studying genomic variation, tracing mixed infections, detecting atypical rotaviruses.

Molecular Epidemiological Characterization of Methicillin-Susceptible and -Resistant Staphylococcus aureus Isolated from Skin and Soft Tissue Infections in Bangladesh

Genetic background and molecular characteristics of Staphylococcus aureus collected from patients with skin and soft tissue infections were studied in the North-Central region of Bangladesh from 2015 to 2016. Among 430 clinical isolates, methicillin-resistant S. aureus (MRSA) accounted for 31% having SCCmec type IV (73%) and V (14%), and belonged mostly to coagulase (coa) genotypes IIa, IIIa, IVb, and XIa, while dominant coa type in methicillin-susceptible S. aureus (MSSA) was IIIa, followed by Va, IIa, and VIa. Panton-Valentine Leukocidin genes (pvl) were detected at higher rate in MSSA (54%) than in MRSA (24%). Based on multilocus sequence typing, pvl-positive MRSA isolates were classified into clonal complex 88 (CC88) (ST88, ST2884, ST4345), CC6 (ST6, ST4350), and CC1 (ST1, ST772), while pvl-negative MRSA into CC5, CC22, CC80, CC121, and CC672. The pvl-negative ST80 MRSA isolates had SCCmec-IVa (agr-III/coa-XIc, etd/edinB-positive, fusB-negative), indicating that they belong to the novel CC80 clade related to the European community-acquired MRSA clone. Among MSSA, genotypes ST121/spa-t645/coa-Va and ST2884 (CC88)/spa-t2393/coa-IIIa were identified in both pvl-positive and negative isolates, and all the ST772 isolates harbored pvl. All the ST121 isolates had a variant of elastin-binding protein gene (ebpS-v) with internal 180-nucleotide deletion. The present study suggested that CC88 (ST88, ST2884) and ST772 are the putative dominant lineages of pvl-positive MRSA/MSSA, while novel CC80 clade is one of the main pvl-negative MRSA lineages distributed endemically in Bangladesh.

Prevalence of Intestinal Parasites in Raw Vegetables Consumed by Inhabitants of Mymensingh City

Uncooked vegetables are an important part of a healthy diet in different parts of the world. The present descriptive cross sectional type of study was carried out to determine the parasitological contamination of vegetables sold at markets of Mymensingh city of Bangladesh. Parasitological examinations were performed in material derived from 200 specimens of 10 different vegetables to detect intestinal parasites in the department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh from July 2015 to July 2016. Each sample was washed with 5 liter distilled water, then washing fluid was centrifuged and resulting sediment was collected for iodine and normal saline wet mount slide preparation to detect human pathogenic intestinal parasites by microscopic examination. Out of 200 vegetable samples, 123(61.5%) were contaminated with different species of parasites. The vegetables red amaranth had the highest contamination rate of 18/20 (90%) followed by jute leaf 17/20 (85%), coriander leaf 15/20 (75%), onion 14/20 (70%), lady's finger 14/20 (70%), radish 13/20 (65%), green pepper 12/20 (60%), carrot 12/20 (60%), cucumber 5/20 (25%), tomato 3/20 (15%). Among the contaminating parasites Ascaris lumbricoides (egg) 36.5% was the most prevalent followed by Strongyloides stercoralis (larva) 35.5%, Entamoeba histolytica ( trophozoite and different cystic stages) 8.5%, Hook worm (egg and larva) 6.5% , Balantidium coli (trophozoite) 4.0%, Enterobius vermicularis (egg) 3.5%, Trichuris trichiura (egg) 1.5%, Giardia lamblia (cyst) 1.0%. To our knowledge, it was the first base line study pursued in Bangladesh. Contamination of raw vegetables from markets with pathogenic parasites would increase the risk of disease to the population that consumes or works with these products. So improperly washed raw eaten vegetables should be considered a potential risk for contracting parasites, particularly helminthes in Mymensingh city.

Comparative yielding of BACTEC MGIT 960 and GeneXpert MTB/RIF Assay for Rapid Diagnosis of Drug Resistance Tuberculosis from Sputum Specimen

Among communicable disease, tuberculosis is the second leading cause of death worldwide, killing nearly two million people each year. Several diagnostic techniques are currently used to detect mycobacteria in respiratory specimens. Therefore an alternative, rapid and most effective method is required for diagnosis of pulmonary tuberculosis which is relatively more sensitive and specific. A total of 107 sputum samples of suspected TB patients were enrolled attending the National Tuberculosis Reference Laboratory (NTRL), Mohakhali, Dhaka, Bangladesh from July 2014 to July 2015. Liquid culture of 107 sputum samples, yielded 76.63% culture positive and 1.86% contamination was observed. Antibiotic susceptibility test was done for 82 culture positive sputum samples among which 28.04% cases were resistant to both Rifampicin and Isoniazid. GeneXpert assay detected 85.04% M. tuberculosis among which 25.23% were found to be Rifampicin Resistance.

OncoE6 Positivity among VIA Positive Suspected Cases from Colposcopy Clinic of Mymensingh Medical College Hospital, Mymensingh

Cervical cancer is a major world health problem for women. It is the fourth most leading cause of death in women around the world. High risk HPV DNA has been shown to be present in 99.7% of cervical cancers worldwide. Oncoprotein E6 and E7 play an important role in the development of cervical cancer which can be detected by OncoE6 cervical test. This Cross sectional observational study was performed to detect E6 Oncoprotein from cervical swab by OncoE6 cervical test. Following universal safety precautions a total of 47 endocervical swabs were collected from Colposcopy clinic of Obstetrics and Gynaecology department of Mymensingh Medical College Hospital (MMCH), Mymensingh, Bangladesh from January 2015 to December 2015. Laboratory work was done in the department of Microbiology, Mymensingh medical college. E6 strip test is an immunochromatographic test based on the 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 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 by OncoE6 cervical test. Among 21 positive cases 19(90.48%) were HPV-16 and 2 were (9.52%) HPV-18. Histopathologically out of 22 cervical carcinoma cases 20(90.90%) were positive by this test. Based on the findings of the present study, it may be concluded that screening with HPV E6 may minimize the overtreatment as well as the colposcopy referral. So it can be used as primary screening to aid colposcopy and to identify real disease. HPV based screening may help to control cervical cancer in Bangladesh. As HPV is a sexually transmitted infection; so, male screening method should be established.

Nationwide prevalence of Rickettsia felis infections in patients with febrile illness in Bangladesh

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.

Detection of Human Papilloma virus by Molecular method from Patients Attending at Colposcopy Clinic of Mymensingh Medical College Hospital, Mymensingh

Cervical cancer is the second most common cancer in women worldwide. Human papillomavirus (HPV) is considered as the main cause of invasive cervical cancer and cervical intra-epithelial neoplasia. High risk HPV DNA has been shown to be present in 99.7% of cervical cancers. So HPV DNA testing for screening of cervical cancers may play a potential role in early detection and management of cervical cancer. With above background a cross sectional study was undertaken to estimate the prevalence and to identify the associated risk factors of human Papillomavirus infection among Visual Inspection with Acetic acid (VIA) positive women attending at colposcopy clinic of Mymensingh Medical College Hospital (MMCH), Mymensingh, Bangladesh from July 2013 to December 2014. One hundred and forty three cervical swabs for nested PCR were collected from the patients attending colposcopy clinic of MMCH, for detecting target gene of L1 region of the HPV genome. Among the 143 VIA positive patient nested PCR showed 49.6% (71/143) positive. Biopsy of 54 colposcopy positive women revealed that 16 (29.6%) cases were chronic cervicitis, 33 (61.1%) cases were mild dysplasia (C1NI), 01 (1.9%) were having moderate dysplasia (C1NII) and 04(7.4%) patients were diagnosed as invasive squamous cell carcinoma. So, high grade cervical lesions were 100% positive by nested PCR for HPV.

Molecular-Characterization of Methicillin-Resistance Staphylococcus aureus (MRSA) from Different Tertiary Care Hospitals in Bangladesh

Infections caused by Staphylococcus aureus were treated by methicillin, but about 95% of S. aureus has been resistance to methicillin, both in the community and hospitals and are increasing day by day. MRSA produces altered penicillin binding protein, PBP2a, due to the expression of mecA gene. Some strains of both the MRSA and MSSA carry PVL gene. This cross sectional observational study was conducted to detect the molecular-characterization of methicillin resistant Staphylococcus aureus (MRSA) and carried out in the Department of Microbiology, Mymensingh Medical College from July 2014 to December 2015. Clinical samples for this study were wound swab, pus, exudates from diabetic ulcer and burn ulcer, aural swab, blood and urine which were collected from three tertiary care hospitals such as from MMCH, BIRDEM hospital and SSMCH. Standard microbiological procedure & biochemical tests were carried out to detect S. aureus. Oxacillin disk diffusion method (ODDM) was done by Kirby-Bauer disk diffusion method. Out of a total 109 culture positive samples 69 isolates of S. aureus were selected for the study. Among the 69 isolates 33, 27 and 09 were from MMCH, BIRDEM hospital and SSMCH respectively. Among the 69 isolates, 17(24.6%) and 52(75.3%) were distinguished as MRSA and MSSA respectively by ODDM. In contrast, detection of presence and absence of mecA gene by PCR identified 20(28.9%) and 49(71.01%) isolates as MRSA and MSSA respectively. Multiplex PCR was performed by standard protocol with specific primers for detection of 16S rRNA gene for Staphylococcus, nuc gene for Staphylococcus aureus, mecA gene for MRSA, PVL gene as a virulence factor and ACME-arc gene for worldwide spreading USA 300 MRSA clone. The PVL gene were detected in 3 out of 20 MRSA (15%) and 19 out of 49 MSSA (38.7%) and the ACME- arc gene was not found in any isolates. All of the S. aureus (MRSA and MSSA) isolates were sensitive to Vancomycin and Gentamicin. All MRSA isolates (100%) showed resistance to Penicillin and Oxacillin. Of the MRSA isolates about 88.2% were resistance to Ceftazidime, 64.7% were resistance to Erythromycin and Ciprofloxacin, 11.7% were resistance to Tetracycline. Among the MSSA isolates 94.2% were resistance to Penicillin and 9.6% resistance to Ciprofloxacin. The MSSA were less resistance for non-beta lactam drugs than MRSA.

Antimicrobial Susceptibility Pattern of Methicillin-Resistance Staphylococcus aureus from Different Tertiary Care Hospitals Including Mymensingh Medical College Hospital

The aim of this study was to detect antimicrobial susceptibilities and the presence of drug resistance genes of MRSA from tertiary care hospitals. This study was carried out in the Department of Microbiology, Mymensingh Medical College during the period from Jan, 2015 to Dec, 2015. Clinical samples, including wound swab, pus, exudates from diabetic ulcer and burn ulcer, aural swab, blood and urine were collected. Standard microbiological procedure & biochemical tests were carried out to detect S. aureus. Oxacillin disk diffusion test was done by Kirby-Bauer disk diffusion method. Total 69 isolates of S. aureus were selected for the study. The isolates were collected from three different tertiary care hospitals, of which 33, 27 and 9 were from Mymensingh Medical College Hospital (MMCH), BIRDEM hospital and Sir Salimullah Medical College Hospital (SSMCH) respectively. Among the 69 isolates, 17(24.6%) and 52(75.3%) were distinguished as MRSA and MSSA respectively by ODDM (Oxacillin disk diffusion method). In contrast, detection of presence and absence of mecA gene by PCR identified 20 (28.9%) and 49 (71.01%) isolates as MRSA and MSSA respectively. All of the S. aureus (MRSA and MSSA) isolates were sensitive to vancomycin and gentamicin. All MRSA isolates (100%) showed resistance to Penicillin and Oxacillin. Among the MRSA isolates about 88.2% were resistance to Ceftazidime, 64.7% were resistance to Erythromycin and Ciprofloxacin, 11.7% were resistance to Tetracycline. Among the MSSA isolates about 94.2% were resistance to Penicillin and 9.6% resistance to Ciprofloxacin. The MSSA were less resistance for non-beta lactam drugs than MRSA. Regarding drug resistance genes, the blaZ genes were present in 47 out of 49(95.8%) MSSA and in 18 out of 18 (100%) MRSA. The erythromycin resistance gene ermB was found in 8.69% isolates, of which highest 20% in MRSA and 4.08% in MSSA. The ermA was not found in any isolates. Among tetracycline resistance genes, tetK were detected in 10.1% and tetL were found in 2.8% of MRSA. The highest tetK genes were found in 20% of MRSA and in 6.1% of MSSA. Regarding, the gentamicin drug resistance, the aac(6')-Iaph(2'')-Ia gene was not found in any isolates. The relatively high proportion of MRSA and the associated antibiotic resistance seen in this study emphasizes the need for country based surveillance to characterize and monitor MRSA and to develop strategies that will improve MRSA treatment and control.

Pattern of Dermatophytes in Patients Attend in Mymensingh Medical College Hospital

Dermatophytosis is a common fungal disease which involves the keratinized tissue. This is an attempt to observe the spectrum of dermatophytes among the clinically suspected cases of dermatophytosis attending the outpatient department of Dermatology and Venereology, Mymensingh Medical College Hospital, Mymensingh during the period of July 2013 to December 2014. Two hundred thirty (230) clinically suspected cases of dermatophytosis were subjected in this study. Sixty three cases (27.39%) were positive for fungus in direct microscopy while 53(23.04%) were culture positive. Among the clinical types tinea unguium was the most common followed by tinea corporis. Dermatophytosis was more common in the age group of 21-30 years. The male to female ratio was 1.53:1. Trichophyton rubrum 44(83.04%) was found common etiological dermatophyte species followed by Trichophyton mentagrophytes 5(9.43%) and Epidermophyton floccosum 4(7.55%).

PCR-based detection of Leishmania DNA in skin samples of post kala-azar dermal leishmaniasis patients from an endemic area of Bangladesh

Post kala-azar dermal leishmaniasis (PKDL) is a sequel of visceral leishmaniasis (VL) and PKDL patients are an important reservoir for anthroponotic transmission of VL. Therefore, diagnosis and treatment of PKDL is important for the kala-azar elimination program in South Asia, including Bangladesh. While definitive diagnosis of PKDL is still based on microscopy, despite the low sensitivity of this method of diagnosis, PCR for identification of kinetoplast DNA (kDNA) from Leishmania parasites is expected to be a rapid and sensitive diagnostic method. We attempted PCR-based diagnosis from skin biopsy specimens and compared PCR to other available detection methods in order to determine the acceptability and feasibility of the PCR diagnostic method in an endemic area of VL in Bangladesh. Both skin biopsy specimens and blood samples were collected from 110 patients suspected to have PKDL from 6 subdistrict health complexes in Mymensingh, Bangladesh. Using microscopy, we identified 32 samples (29.1%) that were positive for Leishmania. Immunochromatography tests indicated that 85 samples (77.3%) were positive for Leishmania. In contrast, a total of 104 (94.5%) samples tested positive using nested PCR, while unaffected portions of skin from PKDL patients tested negative. Sequencing analysis of the PCR products indicated that the amplified portion had more than 98% nucleotide sequence identity to the Leishmania donovani reference strain, D10. These findings indicate that the PCR method using a skin biopsy is highly sensitive and useful for confirmatory diagnosis of PKDL.

Lifestyle pattern in selected slums in Mymensingh Municipal area

Lifestyle is composed of cultural and behavioural patterns and lifelong personal habits that developed through processes of socialization. Lifestyle may be health promotive or detrimental to health. Health requires the promotion of healthy lifestyle. Many current day health problems are associated with lifestyle changes. Because of rising urban population, the number of slum dwellers is rising. The mobility of people from rural to urban areas is the main reason of the growing slum population in cities. This Descriptive, cross-sectional study was directed to assess lifestyle pattern in four purposively selected slums in Mymensingh Municipal area. Non-Probability purposive type of sampling technique was used for selecting the study unit. Sample size was one hundred and twenty-three (123) families. Data were collected by interview with one of the adult family members, preferably with the head of the family, with mixed type of interviewer administered questionnaire. There were 494 family members with an average family size of 4.02, while mean age was 24.58 years with a standard deviation (SD) of 17.79 years. Male-female ratio was 103:100. Of 409 members over 5 years, 174(42.54%) did not have schooling and were illiterate. At least 105(33.02%) members were house-wives, and 99(81.15%) members were smokers. An overwhelming majority (79, 64.23%) families had monthly income between 2000 to 4999 taka. As many as 55(44.72%) families lived in kaccha house, while 40(32.52%) had to live in "Jhupree". In cent per cent families, tube well was the source of water for drinking and other household purposes. A highest majority 121(98.37%) of the families had latrine, while the remaining 2(1.63%) did not have any latrine, and defecate in open air. Of 121 families, 78(64.46%) families had sanitary latrine, while 43(37.54%) did not have sanitary latrine. It was revealed that 86(69.92%) families had cell-phone, while 65(52.85%) families had television, 10(8.13%) families had radio, and 5(4.06%) families had DVD/VCR for recreational facilities. As many as 75(60.98%) respondents had correct knowledge, while the rest 48(39.02%) had incorrect knowledge on hand washing. Of 75, at least 66(88.00%) respondents practiced hand washing, while 9(12.00%) respondents did not practice it. As many as 110(89.43%) members sought medical help for major and minor illness of their family members, whereas the rest 13(10.57%) families did not. Of 110, 62(56.36%) families paid visit to government Hospital, while 22(20.00%) visited to private clinic, 12(10.90%) to pharmacy, 10(9.10%) to qualified doctors and 4(3.64%) to the traditional healers. As many as 58(52.71%) respondents mentioned that they preferred as the facilities cater service free of cost, while 32(29.10%) preferred for better and effective treatment, 16(14.55%) for close to their residence and 4(7.27%) for their belief. Living condition of slum dwellers is considerably low due to low income and inadequate education. Moreover, poor physical environment with unsanitary excreta disposal method is commonplace in slum areas. Existing lifestyle of slum dwellers is unacceptable, and should be improved so that they can contribute to the national development.

Risk Factors of Neonatal Mortality in Bangladesh

Introduction: To address United Nations Millennium Develop­ment Goal 4 (MDG 4) on reducing childhood mortality by three-quarter by 2015, there is a need for better population-based data on the rates and causes of neonatal death. This study aims to identify the risk factors of neonatal mortality in Bangladesh.Methods: The study used data from the nationally representative 2007 Bangladesh Demographic and Health Survey. The survey gathered information regarding socioeconomic, demographic, environmental and maternal and child health care of 10,996 ever married women and 6,058 children. Both bivariate and multivariate statistical analyses were used to assess the relationship between neonatal mortality and contextual factors.Results: The prevalence of neonatal mortality was 37/1,000. The statistical analyses yielded quantitatively important and reliable estimates of neonatal death. The multivariate logistic regression analysis yielded significantly increased risk of neonatal mortality for children with mother who had no formal education, the Muslims, whose mother were adolescents age 15-19, first ranked birth and twin babies.       Conclusion: Emphasis should be given to improve female education in Bangladesh for a better chance of satisfying important factors that can improve infant survival: the quality of infant feeding, general care, household sanitation, and adequate use of preventive and curative health services.Key words: Maternal and child health; Female education; MDG 4; Neonatal mortalityDOI: http://dx.doi.org/10.3126/jnps.v32i1.4845  J. Nepal Paediatr. Soc. Vol.32(1) 2012 37-46

Non-culture diagnosis of Chlamydia trachomatis genital infection in sexually active women

Infections caused by Chlamydia trachomatis (CT) are one of the most prevalent of all sexually transmitted diseases (STD). This cross sectional study was carried out to diagnose genital CT infection on 108 (59 pregnant and 49 non-pregnant) women attending at Department of Gynaecology and Obstetrics, Mymensingh Medical College Hospital (MMCH) during the period from January 2009 to December 2009. This non- culture technique was based on detection of CT major outer membrane protein (MOMP) by Direct Fluorescence Antibody Test (DFAT) from endocervical swab. Chlamydial inclusion bodies (IB) were looked for using Iodine stain. CT antigens were detected in 45.3% (49/108) cases by DFAT; IBs were detected in 5.5% cases (06/108) by Iodine staining technique. Majority of CT positive cases (65%) were found in the younger age group (15 to 25 years). The CT infection was found 47.2 % (35/74) in symptomatic cases, 41.1% (14/34) in asymptomatic cases and 47.4% in pregnant group, 42.8% in non-pregnant group. Although high incidence of genital chlamydia infection is common both in pregnant, non-pregnant, symptomatic and asymptomatic women in Bangladesh an early and reliable diagnostic method for genital chlamydia infection in Bangladesh should be further explored.

Seroprevalence of human brucellosis among the population at risk in rural area

This study was performed to evaluate the seroprevalence of brucellosis among the risk group of population. A cross sectional study was carried out in the Department of Microbiology, Mymensingh Medical College in collaboration with the Department of Medicine under the Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, between the period from July 2007 to June 2008. A total of 210 samples were included in this study from risk group of population. A variety of serological tests have been applied for detection of antibodies against Brucella spp. Among the 210 subjects from risk group of population, 9(4.28%), 7(3.33%) and 7(3.33%) were positive for brucellosis by slide agglutination test, rose bengal plate agglutination test (RBPA) and standard tube agglutination test (STAT) respectively. Out of total specimen 10 positive and 29 negative serum as detected by slide agglutination, rose bengal plate agglutination test (RBPT) and STAT were also examined by Enzyme linked immunosorbent assay (ELISA) for detection of IgG. Among them, 10 were positive by ELISA IgG. Seroprevalence among occupational groups were 11.11% in veterinary personnel, 6.45% in dairy workers and 4.67% in animal farmers. This study indicated that brucellosis is not uncommon at rural area of Mymensingh region in Bangladesh. It was suggested to conduct community survey and to plan properly the measures of control and prevention.

Epidemiological study of risk factors of stroke and its immediate consequence

The study was a cross sectional study conducted among 48 stroke patients in Medicine & Neuromedicine department of Mymensingh Medical College & Hospital. The objective of the study was to reveal the risk factors and other relevant information & immediate outcome of stroke patients. The sample size was 48 who were selected purposively and study area was selected for easy access. Study period was from 15th May 2007 to 15th July 2007. Forty eight (48) respondents and their reliable attendants were interviewed by pre tested structured questionnaire. Among 48 stroke patients 60% were male& 40% were female. Occupations of the patients were 21% desk job, 15% laborious work, 37% housewife, 6% businessman &21% in other profession. Age group of respondents were 13% below 45 years of age, 25% were 45-55 years of age, 29% were 55-65 years of age & 33% were over 65 years of age. Among 48 stroke patients 62.5% had 1st attack & others had multiple attacks. Among all the stroke patients 37.5% performed physical exercise. Forty six percent (46%) patients have family history of Hypertension. 27% have no family history of Hypertension & 27% have no idea. Sixty six percent (66%) patients have suffering from Hypertension, 23% have no history of Hypertension & 10% have no idea. Sixty percent (60%) patients had habit of Smoking, 40% had no habit of Smoking. 21% patients have family history of Diabetes, 48% have no family history of Diabetes & 31% have no idea about family history of Diabetes. Complications among stroke patients are 51% have Hemiplegia, 10% have Paraplegia, 23% have Paresis, 10% have Aphasia & 6% have others complications.

Contraceptive prevalence: experience from rural areas of Mymensingh

Contraceptive prevalence although increased over the last decade but has not yet achieved the desired level. The present descriptive type of cross-sectional study aimed at exploring the status of Contraceptive prevalence rate (CPR) along with relevant issues in two rural areas in Mymensingh. A total 223 respondent was interviewed. Majority respondents were females and young aged 36 years or below. Around a half of the respondents were illiterate while more than half was earning less than 3000 taka a month. Majority women were married earlier than the legal age of marriage with 15.92 years. Around two third (63%) respondents were found using any contraceptives while female partners' shyness and male partners' disliking were reported as reasons for non-use. Increase in female literacy and involvement of family planning worker in motivational programme at individual level could help in improving the situation.

Style of lecturing of medical teacher--an evaluation by medical students of Mymensingh Medical College

It was a cross sectional descriptive type of study carried out among the 3rd year, 4th year and 5th year medical students of Mymensingh Medical College (MMC) with the objective of finding out the various lecture style followed by medical teachers of MMC and other relevant information regarding teaching tools used related to lecturing. The sample size was 134 who were selected purposively. The study was conducted in the month of June 2004. One thirty four (134) respondents were interviewed by pre tested questionnaire. From the study it was revealed that majority (66%) of these respondents were male and 34% were female and 57%, 28.5% and 14.5% were 3rd, 4th and 5th year students respectively. A good number of students (82.5%) expressed their opinion that lecture time was sufficient for their learning. Among the medical teachers the lecture methods followed were VIG (81%) OP (54%) EP (47.2%) EL (25.5%) AT (23%). Eighty Seven percent of the students gave their opinion that the best style of lecture was EP. Seventy and half percent students disliked the AT style followed by OP, which was 85.5%. Seventy two percent of the students were not satisfied with the teaching aids used by the teachers. OHP (90%) was the most commonly used teaching material. Most of the respondents (97.5%) expressed their opinion that SGT was the most suitable way for imparting information.

Pregnancy outcome in adolescent and adult - a case comparison study

This study outlined the consequences of adolescent pregnancy with comparison to adults in Mymensingh Medical College Hospital, Mymensingh. It was a case-comparison study. The study population was the mothers who admitted and delivered at the Obstetrics and Gynaecology ward of hospital during April-June 2003. Sample size was 220 mothers, out of which 110 were primigravidae adolescent mothers and 110 were adults. The study finding showed that adolescents were 2.105 times and 3.679 times more at risk than adults to suffer from anaemia and UTI during pregnancy. Among adolescents 74(67.3%) and in adults 39(35.5%) had obstetric complications during pregnancy and the adolescents were 3.742 times more at risk than the adults. PET and Eclampsia were more common in adolescent than adult mothers. 86(78.2%) adolescents and 36(32.7%) adult mothers had complications before delivery. Pre term labour, Premature rupture of membrane (PROM) and Intra-uterine foetal death (IUD) were more common in adolescents than adult mothers. Stillbirths were more in adolescent mothers 23(20.9%) and adults 11(10.0%). There was more low birth weight (LBW) newborns in adolescents 42(38.2%) than adults 18(16.4%). As a result the adolescents were 3.157 times more likely to give birth to low birth weight babies . The newborns of the adolescent mothers were nearly 2 times more at risk to develop asphyxia neonatorum (p< 0.030, odds ratio=1.806).