Search

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

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

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

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

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

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

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

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

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

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

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

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

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.

High prevalence of Rickettsia felis in patients with fever of unknown origin was revealed in the north-central Bangladesh from 2012 to 2013. Subsequently, in this study, prevalence of R. felis in cats and cat fleas (Ctenocephalides felis), together with febrile patients, was studied by PCR detection of 17 kDa antigen gene and DNA sequencing. R. felis was detected in 28% (28/100) and 21% (14/68) of cat blood and cat flea samples, respectively, whereas 42% (21/50) of patients were positive for R. felis. R. felis-positive cat fleas were detected at significantly higher rate on R. felis-positive cats. The results suggested a potential role of cats and cat fleas for transmission of R. felis to humans in Bangladesh.

Dengue virus (DENV) that caused an outbreak in Dhaka, Bangladesh during 2018 was analysed phylogenetically. DENV samples were classified into type 2-Cosmopolitan genotype (54%) and type 3-genotype I (46%), indicating co-circulation of two DENV types and resurgence of type 3 associated with genotype replacement. Keywords: Bangladesh, dengue virus, Dhaka, resurgence, type 3

Escherichia coli ( E. coli ) is an important group of pathogens associated with diarrhea among children. Despite the fact that diarrhaegenic Escherichia coli (DEC) has been identified as a major etiologic agent of childhood diarrhea, only a few studies have been performed in Bangladesh to identify these organisms. The objective of this study was to determine the frequency and antimicrobial susceptibility of DEC obtained from patients with acute diarrhea. To detect DEC in patients with acute diarrhea, a total of 300 stool specimens were tested by multiplex polymerase chain reaction (PCR). The antimicrobial susceptibility of DEC were tested by Kirby-Bauer disc diffusion technique as per recommendation of CLSI (Clinical and Laboratory Standards Institute), 2010. Out of 300 stool specimens collected from patients with acute diarrhea, the DEC was detected in 18% (54/300) cases. The dominating strain was Enterotoxigenic E. coli ( ETEC) (13%, 39/300), followed by Enteroaggregative E. coli (EAEC) (5%, 15/300) and no Enterohemorrhagic E. coli (EHEC), Enteroinvasive E. coli ( EIEC) and Enteropathogenic E. coli ( EPEC) could be detected. Detected ETEC were 100% sensitive to Ceftriaxone, Nitrofurantioin, Amikacin, 94% sensitive to Nalidixic acid, 89% sensitive to Gentamycin, 83% sensitive to Ciprofloxacin, 79% sensitive to Cephalexin, 39% sensitive to Amoxycillin, 46% sensitive to Tetracyclin and 31% sensitive to Cotrimoxazole. Detected EAEC were 100% sensitive to Ceftriaxone, Nitrofurantioin, Amikacin, Nalidixic acid, 90% sensitive to Gentamycin and Ciprofloxacin, 85% sensitive to Cephalexin, 41% sensitive to Amoxycillin, 49% sensitive to Tetracycline and 31% sensitive to Cotrimoxazole. Both ETEC and EAEC isolates exhibited decreased susceptibility for Amoxycillin, Tetracycline and Cotrimoxazole. Our results revealed that ETEC and EAEC, had significant association with acute diarrhea and should be considered as potential pathogens. Guidelines for appropriate use of antibiotics in tertiary care hospitals need updating. DOI: http://dx.doi.org/10.3329/cbmj.v2i2.16698 Community Based Medical Journal 2013 July: Vol.02 No 02: 46-51

Enterococci are part of the normal intestinal flora of humans and animals but have also emerged as important pathogens responsible for serious infections in hospital and community acquired infections. The aim of this study was to investigate the prevalence of Enterococcus with their antimicrobialsusceptibility pattern from patients ofMymensingh Medical College Hospital, Bangladesh during the period from July 2015 to June 2016.Samples were collected and identification of enterococcus was done by standard microbiological procedure and biochemical tests.Multiplex PCR was performed by using species specific primers for Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium),vanA, vanB, vanC1, vanC2/C3 genes for vancomycin resistance.A total of 105 enterococci were isolated from 1201 different clinical specimens (from urine (931), pus (175) and wound swab (95) respectively) from July, 2015 to June, 2016.The prevalence of enterococci was 12.34% in urine, 17.17% in pus and 1.58% in wound samples. Out of 105 enterococci,80 (77.14%) were Enterococcus faecalis,1 (0.95%) was E. gallinaramand 24 (22.86%) were other species. All the species were highly resistant to aminoglycosides (Gentamicin) (75.24%) and ciprofloxacin (73.33%). Regarding antibiotic sensitivity, all the enterococci were (100%) sensitive to linezolidand vancomycin followed by nitrofurantoin 93 (88.57%) and imipenem 89 (84.76%). No vancomycin resistant enterococci were identified by disk-diffusion method. But by PCR, vanB was found in 1/80 (1.25%) of the E. faecalis isolates and 01 (100%) of the E. gallinarum.vanC1 was detected in 1 (100%) ofE. gallinarum isolates. The vanA and vanC2/C3 gene was not found in any isolates. For the first time, one isolate of E. gallinarum has been found harboringthe vanB gene in our hospital.The presence of multidrug resistant enterococci should be considered as danger alarm for serious enterococcal infections and further study in large scale is needed.

Rotavirus A (RVA) is a dominant causative agent of acute gastroenteritis in children worldwide. G2P[4] is one of the most common genotypes among human rotavirus (HRV) strains, and has been persistently prevalent in South Asia including Bangladesh. In the present study, whole genome sequences of a total of 16 G2P[4] HRV strains (8 strains each in 2010 and 2013) detected in Mymensingh, north-central Bangladesh were determined. These strains had typical DS-1-like genotype constellation. Most of gene segments from DS-1 genogroup exhibited high level sequence identities to each other (>98%), while slight diversity was observed for VP1, VP3, and NSP4 genes. By phylogenetic analysis, individual RNA segments were classified into one (V) or two-three lineages (V–VI or V–VII). In terms of lineages (sublineages) of 11 gene segments, the 16 Bangladeshi strains could be further classified into four clades (A-D) containing 8 lineage constellations, revealing the presence of three clades (A-C) with three lineage constellations in 2010, and a single clade (D) with four constellations in 2013. Therefore, co-existence of multiple G2P[4] HRV strains with different lineage constellations, and change in clades for the study period were demonstrated. Although amino acids in the antigenic regions on VP7 and VP4 were mostly identical to those of global G2P[4] strains after 2000, VP4 of clade D RVAs in 2013 had alanine and proline at positions 88 and 114, respectively, which are novel substitutions compared with recent global G2P[4] strains. Replacement of lineage constellations associated with unique amino acid changes in the antigenic region in VP4 suggested continuous genetic evolutionary state for emerging new G2P[4] rotavirus strains in Bangladesh.

Visceral leishmaniasis (VL) or kala-azar is a neglected tropical disease caused by the intracellular protozoan Leishmania donovani and is transmitted by an infected female sand fly vector. The sand fly inoculates the promastigote form of the parasite to the human host through the dermis during a blood meal. This extracellular form is rapidly taken up, principally by the host macrophage, where it undergoes metamorphosis to an amastigote. After rupture of the macrophage, the amastigote circulates in the blood and other body tissues. These amastigotes are again taken up by another sand fly during its next blood meal and again transform in the fly gut to its infective promastigote form to infect the next victim. After a variable incubation period there develops a spectrum of clinical manifestations like fever, weight loss, anaemia, and splenomegaly. These clinical manifestations are associated with immune suppression (CMI) leading to parasite survival accompanied by induction of IL-10 and/or IL-4 in tissues, hypergammaglobulinemia, and an increased amount of IL-4 in the blood of VL patients.

Puerperal infection is a common complication during postnatal period in developing countries. Bacterial species, drug resistance, and genetic characteristics were investigated for a total of 470 isolates from puerperal infections in Bangladesh for a 2-year period (2010-2012). The most common species was Escherichia coli (n=98), followed by Enterococcus faecalis (n=54), Staphylococcus haemolyticus (n=33), Proteus mirabilis (n=32), Staphylococcus aureus (n=27), Klebsiella pneumoniae (n=22), and Enterobacter cloacae (n=21). S. aureus and Acinetobacter baumannii were isolated at a higher frequency from wound infections after cesarean section, while E. coli, E. cloacae, and K. pneumoniae were isolated from community-acquired endometritis and urinary tract infections. Resistance to third-generation cephalosporins was frequent for Enterobacteriacae, and was mainly mediated by blaCTX-M-1 group beta-lactamases. The CTX-M gene in E. coli from the four phylogroups was identified as blaCTX-M-15, and phylogroup B2 isolates with blaCTX-M-15 were classified into ST131 with O25b allele, harboring aac(6')-Ib-cr and various virulence factors. Carbapenemase genes blaNDM-1 and blaNDM-7 were identified in one isolate each of phylogroup A E. coli. Methicillin-resistant S. aureus isolates had type IV or V SCCmec, including isolates of ST361 (CC672), which is related to an emerging ST672 clone in the Indian subcontinent. This study revealed the recent epidemiological status of aerobic bacteria causing puerperal infections in Bangladesh, providing useful information to improve clinical practice and infection control.

Rotaviruses with the P[8] VP4 genotype are a major cause of acute infantile diarrhea. The P[8] genotype is classified into two genetically distinct subtypes, P[8]a and P[8]b. Most of the P[8] strains belong to subtype P[8]a, whilst P[8]b strains are rare. To date, the whole genomes of a few P[8]a strains have been analyzed, whilst there are no reports on full genomic analysis of the P[8]b strains. To determine the genetic makeup of the rare P[8]b strains and their overall genetic relatedness to the P[8]a strains, the present study analyzed the full genomes of a human G9P[8]b strain, MMC38, and a G1P[8]b strain, MMC71, detected in Bangladesh in 2005. By nucleotide sequence identities and phylogenetic analyses, strains MMC38 and MMC71 exhibited a human rotavirus Wa-like genotype constellation. Except for the VP4 gene, all the genes of strains MMC38 and MMC71 were closely related to cognate genes of the contemporary and more recent human Wa-like G1P[8]a, G9P[8]a, G11P[8]a, G11P[25], G12P[6] and G12P[8]a strains, including those from Bangladesh. Therefore, strains MMC38 and MMC71 possessed the genetically distinct P[8]b VP4 gene on a common human Wa-like genetic backbone, pointing towards their possible origin from reassortment events between common human Wa-like strains and unidentified rotavirus strains possessing the rare P[8]b-like VP4 gene. Since strains with this stable Wa-like genetic backbone can spread rapidly, and it is not certain as to whether the current rotavirus vaccines will be equally efficacious against the P[8]b strains as the P[8]a strains, proper detection of P[8]b strains and their whole genomic analyses might be of public health significance. To our knowledge, the present study is the first report on full genomic analysis of the rare P[8]b rotavirus strains.

Methicillin resistance in staphylococci is conferred by the acquisition in its chromosome of the mecA gene, which is located on a mobile genetic element called staphylococcal cassette chromosome mec (SCCmec). Genetic type of SCCmec is defined by combination of mec gene complex class and cassette chromosome recombinase gene (ccr) allotype. In this study, we analyzed genetic diversity of the SCCmec in 11 Staphylococcus haemolyticus strains and a Staphylococcus sciuri strain, which were recently isolated from clinical specimens in Bangladesh. Among these strains, only two S. haemolyticus strains were proved to have the known types of SCCmec, that is, SCCmec V (class C2 mec-ccrC) and VII (class C1 mec-ccrC). Five S. haemolyticus strains were assigned two unique mec-ccr gene complexes combination; that is, class C1 mec-ccrA4B4 (four isolates) and class A mec-ccrC (one isolate). In the remaining four S. haemolyticus strains with class C1 mec, no known ccr allotypes could be detected. A single S. sciuri strain with class A mec complex carried a ccrA gene belonging to a novel allotype designated ccrA7, together with ccrB3. The ccrA7 gene in the S. sciuri strain showed 61.7%-82.7% sequence identity to the ccrA gene sequences published so far, and 75.3% identity to ccrA3, which is a component of the type 3 ccr complex (ccrA3-ccrB3) in methicillin-resistant Staphylococcus aureus. The results of the present study indicated that mec gene complex and ccr genes in coagulase-negative staphylococci are highly divergent, and distinct from those of common methicillin-resistant S. aureus. Identification of the novel ccrA7 allotype combined with ccrB3 suggested an occurrence of recombination between different ccr complexes in nature.

An unusual human rotavirus strain B219 was detected in a stool specimen from a 65-year old patient with diarrhea in Bangladesh during April 2002. Cloning and sequence analysis of five genes of the B219 strain indicated that this virus is genetically closely related to the ADRV-N strain, which caused an adult diarrhea outbreak in China, but distinct from groups A, B, and C rotaviruses known to cause diarrheal diseases in humans. Accordingly, rotavirus strains B219 and ADRV-N were considered to belong to a novel group of human rotavirus, and the ADRV-N-like novel human rotaviruses were suggested to be distributed to a geographically wider area.