No abstract

Antimicrobial resistance is a global problem. Surveillance is one of the effective tools to address this multifaceted problem. In Bangladesh a countrywide antimicrobial resistance surveillance is ongoing since 2016-2020. The main objective of the surveillance is to know the sensitivity pattern of some common bacteria which will eventually help to formulate a standard treatment guideline for the clinician and to know the gravity of the AMR problem in Bangladesh. It is a case based surveillance conducted by Institute of Epidemiology, Disease Control & Research (IEDCR) in nine sentinel sites where five types of clinical cases were selected according to case definition, tested in the microbiological department of the sites and ten types of bacteria were identified from six types of preselected specimens and their sensitivity test were done. All the laboratory works were done following the same standard operative procedure supplied by the AMR surveillance Reference laboratory at IEDCR. Total 19,263 samples were processed during the period of March 2017- March 2020 among which wound swab yielded highest growth (57%). E.coli was the highest (1717) isolated organism among the ten priority pathogens which showed highest sensitivity (91%) to Imipenem. Imipenem also showed higher sensitivity to other organisms like K. pneumoniae (77%), Salmonella species (100%), P. aeruginosa (53%) and Acb complex (29%). Third generation cephalosporin like ceftriaxone was found less than 50% sensitive to E.coli (37%) and K.pneumoniae (28%) although Salmonella spp. showed higher sensitivity (97%) to it. ACB complex, mostly isolated from ICU patients showed alarming resistance to all of the antibiotics and was less than 50% sensitive to even the highest sensitive antibiotic Imipenem (29%). Salmonella spp. isolated from blood showed higher susceptibility to most of the antibiotics except ciprofloxacin (7%). The result of the surveillance representing whole country is surely alarming as most of the bacteria are highly resistant to the commonly used as well some of the reserve group of antibiotics. So concerted effort should be taken from all concerned to curb the problem immediately.

No abstract

In a try to understand the pathogenesis, evolution, and epidemiology of the SARS-CoV-2 virus, scientists from all over the world are tracking its genomic changes in real-time. Genomic studies can be helpful in understanding the disease dynamics. We have downloaded 324 complete and near-complete SARS-CoV-2 genomes submitted in the GISAID database from Bangladesh which were isolated between 30 March to 7 September 2020. We then compared these genomes with the Wuhan reference sequence and found 4160 mutation events including 2253 missense single nucleotide variations, 38 deletions, and 10 insertions. The C>T nucleotide change was most prevalent possibly due to selective mutation pressure to reduce CpG sites to evade CpG targeted host immune response. The most frequent mutation that occurred in 98% of the isolates was 3037C>T which is a synonymous change that almost always accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp), and 23403A>G (D614G in spike protein). The P323L was reported to increase mutation rate and D614G is associated with increased viral replication and currently the most prevalent variant circulating all over the world. We identified multiple missense mutations in B-cell and T-cell predicted epitope regions and/or PCR target regions (including R203K and G204R that occurred in 86% of the isolates) that may impact immunogenicity and/or RT-PCR based diagnosis. Our analysis revealed 5 large deletion events in ORF7a and ORF8 gene products that may be associated with less severity of the disease and increased viral clearance. Our phylogeny analysis identified most of the isolates belonged to the Nextstrain clade 20B (86%) and GISAID clade GR (88%). Most of our isolates shared common ancestors either directly with European countries or jointly with middle eastern countries as well as Australia and India. Interestingly, the 19B clade (GISAID S clade) was unique to Chittagong which was originally prevalent in China. This reveals possible multiple introductions of the virus in Bangladesh via different routes. Hence more genome sequencing and analysis with related clinical data are needed to interpret the functional significance and better predict the disease dynamics that may be helpful for policymakers to control the COVID-19 pandemic in Bangladesh.

No abstract