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The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease., (© 2021. The Author(s).)

It is crucial to explore knowledge, attitudes and perceptions (KAP) about rabies among the people in the community, the personnel dealing with animal bite management and suspected rabies patients, including humans and animals, to facilitate intervention in improving rabies elimination strategies. In 2016, we conducted an interactive face-to-face survey in three different districts of Bangladesh to understand the extent of KAP towards rabies in the community peoples (CPs), human healthcare professionals (HCPs) and veterinary practitioners (VPs). A set of prescribed questions was employed to measure what proportion of each group possessed sufficient knowledge, positive attitudes and adequate perceptions about rabies. A total of 1133 CPs, 211 HCPs and 168 VPs were interviewed by using a standard questionnaire comprising both closed and open-ended questions. Of the CPs, 49% identified the disease correctly (i.e. rabies is caused by an animal bite or a scratch). Only 29% of the CPs were aware that a wound should be washed immediately with soap and water after an animal bite or a scratch. However, only 49% of the CPs, 65% of the HCPs and 60% of the VPs felt that it is important to consult a physician and receive post-exposure vaccine as the first line of treatment following an animal exposure. Among the HCPs, 23% of the respondents did not possess sufficient knowledge about animal bites as categorised by the World Health Organization (WHO), and 12% of the respondents did not possess the knowledge on how to manage an animal bite properly. Out of 52% of the VPs who previously treated suspected rabid animals, only 29% had a history of taking rabies pre-exposure prophylaxis (PEP). Lack of formal education and rural subsistence were found to largely contribute to poor rabies KAP level among the CPs ( P  ≤ 0.01). There has been a high demand for proper training to be provided to HCPs and VPs for the effective management of an animal bite incidence in human and animals, respectively. Multi-sectoral collaboration through integrated One Health initiatives including community education, awareness programmes, facilitation of rabies PEP, and dog vaccination as well as its population control are critical in the way forward to control rabies in Bangladesh., (© 2021 The Authors.)

Background: As evidence is mounting regarding irrational and often unnecessary use of antibiotics during the COVID-19 pandemic a cross-sectional Point Prevalence Survey (PPS) (in accordance with WHO guideline) was conducted across COVID-19 dedicated wards in Dhaka Medical College and Hospital (DMCH)., Methodology: Antibiotic usage data were collected from 193 patients at different COVID-19 dedicated wards at DMCH on 11 June 2020. Comparisons in antibiotic usage were made between different groups using Pearson chi-square and Fisher's exact test., Result: Findings reveal all surveyed patients (100%) were receiving at least one antibiotic with 133 patients (68.91%) receiving multiple antibiotics. Overall, patients presenting with the severe disease received more antibiotics. Third-generation cephalosporins (i.e. ceftriaxone) (53.8%), meropenem (40.9%), moxifloxacin (29.5%), and doxycycline (25.4%) were the four most prescribed antibiotics among surveyed patients. Diabetes mellitus (DM) was independently associated with multiple antibiotic prescribing. Abnormal C-reactive protein (CRP) and serum d-dimer were linked with higher odds of multiple antibiotic prescribing among study patients., Conclusion: Prevalence of multiple antibiotic prescriptions was high among severely ill patients and those with abnormal CRP and d-dimer levels. Data regarding the quality of antibiotic prescribing were lacking., (© 2021 The Authors.)

Background: The assessment of antibody responses to severe acute respiratory syndrome coronavirus-2 is potentially confounded by exposures to flaviviruses. The aims of the present research were to determine whether anti-dengue antibodies affect the viral load and the detection of anti-coronavirus nucleocapsid (N)-protein antibodies in coronavirus infectious disease 2019 (COVID-19) in Bangladesh., Methods: Viral RNA was evaluated in swab specimens from 115 COVID-19 patients by real-time reverse transcription polymerase chain reaction (rT-PCR). The anti-N-protein antibodies, anti-dengue virus E-protein antibodies and the dengue non-structural protein-1 were determined in serum from 115 COVID-19 patients, 30 acute dengue fever pre-COVID-19 pandemic and nine normal controls by ELISA., Results: The concentrations of viral RNA in the nasopharyngeal; Ct median (95% CI); 22 (21.9-23.3) was significantly higher than viral RNA concentrations in oropharyngeal swabs; and 29 (27-30.5) p < 0.0001. Viral RNA concentrations were not correlated with-dengue IgG levels. The anti-nucleocapsid antibodies were IgA 27% positive and IgG 35% positive at days 1 to 8 post-onset of COVID-19 symptoms versus IgA 0% and IgG 0% in dengue patients, p < 0.0001. The levels of anti- nucleocapsid IgA or IgG versus the levels of anti-dengue IgM or IgG revealed no significant correlations., Conclusions: Viral RNA and anti-nucleocapsid antibodies were detected in COVID-19 patients from dengue-endemic regions of Bangladesh, independently of the dengue IgG levels.

Identification of risk factors is crucial to find ways to reduce rabies deaths. We investigated the hospital records of rabies deceased through contact tracing of the relatives of the victims using enhanced verbal autopsies (VA) to identify why the people had to die from rabies in recent years in Bangladesh. Patients whose deaths were confirmed by physicians based on the history of animal exposure and clinical signs were taken into account for VA. Socio-demographic profile of the deceased, animal exposure, nature of the wound, and history of post-exposure prophylaxis (PEP) data were obtained and analysed. The study found 256 cases in which the cause of death was attributed to rabies, most of the victims were male (71.88%), resided in the rural community (80.47%), dependent (49.22%), and children below the age of 15 years (47.27%). Dogs were the single most responsible (81.64%); however, cats (12.11%), jackals (3.91%) and mongoose (2.34%) were also found accountable for rabies incidence ( P < 0.05). Significantly, limbs were the most common (67.97%) site of exposure, and the shortest incubation period was identified in the case of bites to head and face ( P < 0.05). The majority (86.72%) of the deceased did not receive any PEP; whereas, 66.80% sought treatment from traditional healers. Among the deceased (13.28%, n = 34) who had received PEP, only 8.82% of them completed the full course of the vaccination regimen ( P < 0.01); however, none of them had history of taking rabies immunoglobulin (RIG). The study recommends extensive public health awareness programs in the rural community and establishing methods to improve healthcare-seeking behaviours, including receiving PEP instead of visiting traditional healers. Moreover, the availability and accessibility of PEP in the government hospital facilities are desirable, and laboratory-based surveillance with compatible rapid data reporting may be incorporated in the existing policy., Competing Interests: The authors declare no conflict of interest., (© 2020 The Author(s).)

We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2&#95;V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. The data from this analysis will contribute to advancing our understanding of the epidemiology of SARS-CoV-2 in Bangladesh as well as worldwide at the molecular level and will identify potential new targets for interventions., (Copyright © 2020 Akter et al.)

Background: Spread of malaria and antimalarial resistance through human movement present major threats to current goals to eliminate the disease. Bordering the Greater Mekong Subregion, southeast Bangladesh is a potentially important route of spread to India and beyond, but information on travel patterns in this area are lacking., Methods: Using a standardised short survey tool, 2090 patients with malaria were interviewed at 57 study sites in 2015-2016 about their demographics and travel patterns in the preceding 2 months., Results: Most travel was in the south of the study region between Cox's Bazar district (coastal region) to forested areas in Bandarban (31% by days and 45% by nights), forming a source-sink route. Less than 1% of travel reported was between the north and south forested areas of the study area. Farmers (21%) and students (19%) were the top two occupations recorded, with 67 and 47% reporting travel to the forest respectively. Males aged 25-49 years accounted for 43% of cases visiting forests but only 24% of the study population. Children did not travel. Women, forest dwellers and farmers did not travel beyond union boundaries. Military personnel travelled the furthest especially to remote forested areas., Conclusions: The approach demonstrated here provides a framework for identifying key traveller groups and their origins and destinations of travel in combination with knowledge of local epidemiology to inform malaria control and elimination efforts. Working with the NMEP, the findings were used to derive a set of policy recommendations to guide targeting of interventions for elimination.

Vaccinating dogs against rabies is an effective means of reducing human rabies. We subjected 1327 clinically diagnosed human rabies death and mass dog vaccination (MDV) data during 2006-2018 to quantify the impacts of MDV on human rabies incidence in Bangladesh and a subset of rabies death data (422) for clinico-epidemiological analysis. A positive and increasing trend of MDV (p = 0.01 and tau = 0.71) and a negative and declining trend (p < 0.001 and tau = -0.88) of human rabies cases (Correlation coefficient: -0.82) have been observed. Among 422 deaths, the majority (78%) of the victims sought treatment from traditional healers, and 12% received post-exposure prophylaxis (PEP). The mean incubation period of rabies in cases with exposure sites on the head & neck (35 days) was shorter than the upper limb (mean = 64 days, p = 0.02) and lower limb (mean = 89 days, p < 0.01). MDV has been found to be effective for reducing human rabies cases in Bangladesh. Creating awareness among the animal bite victims to stop reliance on traditional healers rather seeking PEP, addressing the role of traditional healers through awareness education programme with respect to the treatment of dog bites, ensuring availability of PEP, and continuing to scale up MDV may help to prevent human rabies deaths.

For countries aiming for malaria elimination, travel of infected individuals between endemic areas undermines local interventions. Quantifying parasite importation has therefore become a priority for national control programs. We analyzed epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data to measure the spatial spread of malaria parasites in southeast Bangladesh. We developed a genetic mixing index to estimate the likelihood of samples being local or imported from parasite genetic data and inferred the direction and intensity of parasite flow between locations using an epidemiological model integrating the travel survey and mobile phone calling data. Our approach indicates that, contrary to dogma, frequent mixing occurs in low transmission regions in the southwest, and elimination will require interventions in addition to reducing imported infections from forested regions. Unlike risk maps generated from clinical case counts alone, therefore, our approach distinguishes areas of frequent importation as well as high transmission., Competing Interests: HC, AW, IS, CJ, AM, DU, SZ, MH, MF, AG, AS, MR, AI, MK, MR, AS, SJ, MA, ED, SG, MK, MD, RV, OM, KE, DK, RM, CB No competing interests declared, (© 2019, Chang et al.)

The escalating dengue situation in Bangladesh has been emerging as a serious public health problem in terms of morbidity and mortality. Results of analysis of 40,476 cases of Bangladesh occurring during 2000-2017 indicated that 49.73% of the dengue cases occurred during the monsoon season (May-August) and 49.22% during the post-monsoon season (September-December). However, data also showed that, since 2014, these trends have been changing, and dengue cases have been reported during the pre-monsoon season. During 2015-2017, in the pre-monsoon season, the dengue cases were reported to be more than seven times higher compared to the previous 14 years. The findings closely correlate with those of the pre-monsoon Aedes vector survey which revealed the presence of high density of larva and pupa of the dengue vectors in the environment all the year round. In our study, climate changes, such as average rainfall, humidity, and temperature, after 2014, and rapid unplanned urbanization were the strong predictors of an imbalance in the existing ecology that has led to increase in dengue cases in 2016 and the emergence of the chikungunya virus for the first time in Bangladesh in 2017. Although 2018 dengue data are relevant but not included in this study due to study time frame, it is interesting to report an increase in the number of dengue cases in pre (2016) and post (2018, which is highest within 18 years) chikungunya outbreak, which favors the study hypothesis. Despite the efforts to control dengue, based primarily on the vector control and case management, the burden and costs of the disease and similar vector-borne diseases will continue to grow in future in our country. Developing a cost-effective vaccine against all the 4 strains of dengue remains a challenge. The CDC, in collaboration with other research organizations, may come forward to initiate and coordinate a large-scale randomized clinical trial of an effective dengue vaccine in Bangladesh.

Background: Adverse effects of antileishmanial drugs can affect patients' quality of life and adherence to therapy for visceral leishmaniasis (VL) and post-kala-azar dermal leishmaniasis (PKDL). In Bangladesh, there are 26 treatment centers that manage leishmaniasis cases coming from 100 endemic upazilas (subdistricts) of 26 districts (these include VL, PKDL, treatment failure, and relapse VL and cutaneous leishmaniasis cases). This study aimed to investigate the feasibility of using focused pharmacovigilance for VL (VLPV) in Bangladesh's National Kala-azar Elimination Programme for the early detection and prevention of expected and unexpected adverse drug reactions (ADRs)., Methods: This activity has been going on since December 2014. Activity area includes secondary public hospital or Upazila health complex (UHC) in hundred sub districts and Surya Kanta Kala-azar Research Center (SKKRC) in Mymensingh District, a specialized center for management of complicated VL and PKDL cases. Communicable Disease Control (CDC) of the Directorate General of Health Services (DGHS) assigned twenty five of hundred UHCs and SKKRC (total 26) as treatment centers depending on their suitable geographical location. This was implemented for better management of VL cases with Liposomal Amphotericin B (AmBisome®) to ensure patient convenience and proper utilization of this expensive donated drug. A VLPV expert committee and a UHC VLPV team were established, an operational manual and pharmacovigilance report forms were developed, training and refresher training of health personnel took place at UHCs and at the central level, collected information such as patient data including demographics, treatment history and response, adverse events were analyzed. This report includes information for the period from December 2014 to December 2016., Results: From December 2014 to December 2016, 1327 leishmaniasis patients were treated and 1066 (80%) were available for VLPV. Out of these, 57, 33, 9, and 1% were new VL, PKDL, VL relapse, and other cases, respectively. Liposomal amphotericin B was mostly used (82%) for case management, followed by miltefosine (20%) and paromomycin (3%). Out of the 1066 patients, 26% experienced ADRs. The most frequent ADR was fever (17%, 176/1066), followed by vomiting (5%, 51/1066). Thirteen serious adverse events (SAEs) (eight deaths and five unexpected SAEs) were observed. The expert committee assessed that three of the deaths and all unexpected SAEs were possibly related to treatment. Out of the five unexpected SAEs, four were miltefosine-induced ophthalmic complications and the other was an AmBisome®-induced avascular necrosis of the nasal alae. The Directorate General of the Drug Administration entered the ADRs into the World Health Organization Uppsala Monitoring Centre (WHO-UMC) VigiFlow database., Conclusions: This study found that VLPV through NKEP is feasible and should be continued as a routine activity into the public health system of Bangladesh to ensure patient safety against anti-leishmanial drugs.

Background: Careful monitoring for recrudescence of Wuchereria bancrofti infection is necessary in communities where mass drug administration (MDA) for the elimination of lymphatic filariasis (LF) as a public health problem has been stopped. During the post-MDA period, transmission assessment surveys (TAS) are recommended by the World Health Organization to monitor the presence of the parasite in humans. Molecular xenomonitoring (MX), a method by which parasite infection in the mosquito population is monitored, has also been proposed as a sensitive method to determine whether the parasite is still present in the human population. The aim of this study was to conduct an MX evaluation in two areas of Bangladesh, one previously endemic district that had stopped MDA (Panchagarh), and part of a non-endemic district (Gaibandha) that borders the district where transmission was most recently recorded., Methodology/principal Findings: Mosquitoes were systematically collected from 180 trap sites per district and mosquito pools were tested for W. bancrofti using real-time PCR. A total of 23,436 intact mosquitoes, representing 31 species, were collected from the two districts, of which 10,344 (41%) were Culex quinquefasciatus, the vector of W. bancrofti in Bangladesh. All of the 594 pools of Cx. quinquefasciatus tested by real-time PCR were negative for the presence of W. bancrofti DNA., Conclusions/significance: This study suggested the absence of W. bancrofti in these districts. MX could be a sensitive tool to confirm interruption of LF transmission in areas considered at higher risk of recrudescence, particularly in countries like Bangladesh where entomological and laboratory capacity to perform MX is available., Competing Interests: The authors have declared that no competing interests exist.

Background: Definitive diagnosis of visceral leishmaniasis (VL) by demonstrating parasites in tissue smears or by culture involves invasive procedures, technical expertise and adequate laboratory facilities. Endemic countries rely mainly on serological tests to diagnose VL. Currently, the immunochromatographic test incorporating the recombinant K39 antigen (rK39 ICT) is the reference test for rapid diagnosis of VL in the Indian subcontinent. The performance of serological tests using rK39 and other promastigote antigens can vary due to differences in antigen expression, the various hosts and environmental factors. To achieve elimination of VL, diagnostic accuracy will be necessary for active case detection especially in those who carry asymptomatic infections. We evaluated the performance of rK39 ICT, enzyme linked immunosorbent assay using mixed Leishmania promastigotes from different Leishmania species (p-ELISA) and indirect fluorescent antibody test (IFAT) utilizing whole promastigotes from the Leishmania donovani complex for sero-diagnosis of VL in Bangladesh., Methods: The sensitivity of each serological test was evaluated on 155 patients who were diagnosed to have VL by microscopy and/or by culture methods. Test specificities were calculated on 706 healthy blood donors, 91 diagnostic sera from patients with a febrile illness and sera from patients positive for malaria (n = 91) and Chagas disease (n = 91). All statistical calculations were at 95% confidence intervals., Results: The sensitivities of rK39 ICT, p-ELISA and IFAT were 100%, 86.5% and 92.3%, respectively. All three serological methods had a pooled sensitivity of 82.6%. The specificities of rK39 ICT, p-ELISA and IFAT from combined control groups were 100%, 93.1% and 99.9%, respectively. The respective positive and negative predictive values of the tests were both 100% for rK39 ICT, 66.3% and 97.8% for p-ELISA and 99.3% and 98.8% for IFAT. The p-ELISA showed cross reactivity with 36.3% of sera positive for malaria and 28.6% of sera positive for Chagas disease while rK39 ICT and IFAT showed no cross reactivity., Conclusion: This study confirms the efficiency of rK39 ICT for rapid diagnosis of VL. The p-ELISA using mixed promastigote antigens did not perform well as a serological test for VL in Bangladesh. Due to high sensitivity and specificity of whole promastigote antigen of L. donovani complex utilized in IFAT, this test can be considered in combination with rK39 ICT to confirm VL diagnosis when clinical diagnosis cannot distinguish between other diseases.