Munawar Sultana

Complete Genome Sequence of Foot-and-Mouth Disease Virus Serotype O Isolated from Bangladesh

ABSTRACT Foot-and-mouth disease (FMD) is a highly infectious enzootic disease caused by FMD virus. The complete genome sequence of a circulatory FMD virus (FMDV) serotype O isolated from Natore, Bangladesh, is reported here. Genomic analysis revealed antigenic heterogeneity within the VP1 region, a fragment deletion, and insertions at the 5′ untranslated region (UTR) and 3A region compared to the genome of the available vaccine strain.

Serological Cross-Reactivity of Environmental Isolates of Enterobacter, Escherichia, Stenotrophomonas, and Aerococcus with Shigella spp.-Specific Antisera

Using protocols designed for the isolation of Shigella from environmental freshwater samples from different regions of Bangladesh, 11 bacterial strains giving rise to Shigella-like colonies on selective agar plates and showing serological cross-reaction with Shigella-specific antisera were isolated. Phylogenetic analyses revealed that three of the isolates were most closely related to Escherichia coli, four to Enterobacter sp., two to Stenotrophomonas, and two isolates belonged to the Gram-positive genus Aerococcus. The isolates cross-reacted with six different serotypes of Shigella and were, in each case, highly type-specific. Two of the isolates belonging to the Enterobacter and Escherichia genera gave extremely strong cross-reactivity with Shigella dysenteriae and Shigella boydii antisera, respectively. The Aerococcus isolates gave relatively weak but significant cross-reactions with S. dysenteriae. Western blot analysis revealed that a number of antigens from the isolates cross-react with Shigella spp. The results indicate that important Shigella spp. surface antigens are shared by a number of environmental bacteria, which have implications for the use of serological methods in attempts for the detection and recovery of Shigella from aquatic environments.

Prevalence and Characterization of Multidrug-Resistant Zoonotic Enterobacter spp. in Poultry of Bangladesh

Poultry and poultry products are major contributors of zoonotic pathogens. Limited data are available on Enterobacter spp. as a potent zoonotic pathogen in poultry. The present study is a first endeavor on the emergence of multidrug-resistant zoonotic Enterobacter spp. and its prevalence arising from poultry in Bangladesh. Cloacal swabs from poultry samples of five different farms at Savar, Dhaka, Bangladesh were collected and from 106 isolates, 18 presumptive Enterobacter spp. were obtained. Antibiogram using 19 used antibiotics belonging to 15 major groups revealed that all of the 18 isolates were completely resistant to penicillin and rifampicin, but differed in their drug resistance pattern against ampicillin (94.4%), clindamycin (94.4%), erythromycin (94.4%), vancomycin (88.9%), sulfonamides (72.2%), imipenem (66.6%), streptomycin (55.6%), nitrofurantoin (33.3%), doxycycline (33.3%), tetracyclines (33.3%), cefepime (11.1%), and gentamicin (5.6%). All Enterobacter spp. were found to be plasmid free, implying that multidrug-resistant properties are chromosomal borne. The vanA and sulI were detected by polymerase chain reaction assay in 17 and 13 isolates, respectively. Amplified ribosomal DNA restriction analysis and randomly amplified polymorphic DNA distributed the 18 multidrug-resistant Enterobacter spp. into three genotypes. Phylogenetic analysis of the representatives of the three genotypes using partial 16S rRNA gene sequence (approximately 900 bp) showed that the genotypically diverse groups belonged to Enterobacter hormaechei, E. cloacae, and E. cancerogenus, respectively. The clinical significance of the close relative Enterobacter spp. is indicative of their zoonotic potential. Therefore, urgent intervention is required to limit the emergence and spread of these bacteria in poultry feed as well as prudent use of antibiotics among poultry farmers in Bangladesh.

Evidence of interspecies O antigen gene cluster transfer between Shigella boydii 15 and Escherichia fergusonii.

An environmental bacterial isolate, Iso10, previously found to show serological cross‐reactivity with type‐specific Shigella boydii 15 antisera was subjected to further molecular and serological analyses that revealed interspecies transfer of the O antigen gene cluster. Western blot analysis of Iso10 cell surface extracts and purified lipopolysaccharides demonstrated strong cross‐reactivity with S. boydii 15‐specific monovalent antisera and a lipopolysaccharide gel banding profile similar to that of S. boydii 15. Biochemical and phylogenetic analyses identified the Iso10 isolate as Escherichia fergusonii. O antigen gene cluster analyses of Iso10, carried out by restriction fragment length analysis of the amplified ~10‐kb O antigen‐encoding gene cluster, revealed a profile highly similar to that of S. boydii 15, confirming the presence of the S. boydii 15 somatic antigen in Iso10. To the best of our knowledge, this is the first report of interspecies transfer of O antigen‐encoding genes between S. boydii and E. fergusonii, and it has implications for our understanding of the role of lateral gene transfer in the emergence of novel Shigella serotypes.

Complete Genome Sequence of Foot-and-Mouth Disease Virus Type A Circulating in Bangladesh

ABSTRACT The complete genome sequence of a foot-and-and mouth disease virus (FMDV) type A strain (BAN/GA/Sa-197/2013), isolated from Gazipur in Bangladesh, revealed an 84-nucleotide insertion within the 5′-untranslated region (UTR), a lengthened poly(C) tract, and amino acid substitutions at the VP1 region compared to the available genome sequence of the vaccine strain (GenBank accession no. HM854025).

Serological Cross-Reaction Between O-Antigens of Shigella dysenteriae Type 4 and an Environmental Escherichia albertii Isolate

An environmental freshwater bacterial isolate, DM104, appearing as Shigella-like colonies on selective agar plates was found to show strong and specific serological cross-reactivity with Shigella dysenteriae type 4. Biochemical identification according to the analytical profile index, molecular serotyping by restriction of the amplified O-antigen gene cluster (rfb-RFLP), together with phylogenetic analysis of the 16S rRNA gene and multi-locus sequence analysis, identified the isolate as Escherichia albertii. rfb-RFLP of DM104, revealed a profile different from that of S. dysenteriae type 4. However, western blot analysis of extracted lipopolysaccharides demonstrated strong cross-reactivity with S. dysenteriae type 4 using specific monovalent antisera and a lipopolysaccharide gel banding profile similar to that of S. dysenteriae type 4. The observed O-antigen cross-reaction between an E. albertii isolate and S. dysenteriae extends our knowledge of the extent of O-antigen cross-reaction within the Escherichia/Shigella group of organisms, and offers the possibility of using DM104 and similar cross-reacting strains as shigellosis vaccine candidates.

Recovery and Characterization of Environmental Variants of Shigella flexneri from Surface Water in Bangladesh

Little is known about the distribution, survival, and transmission of Shigella in environmental surface waters. To gain more insight into the environmental biology of Shigella we isolated five bacterial strains serotyped as Shigella flexneri 2b from a freshwater lake in Bangladesh using a modified nutrient broth supplemented with nucleic acid bases. The biochemical properties of the isolates, including inability to ferment lactose and a negative lysine decarboxylase test, indicated common physiological characteristics with Shigella, but differed significantly from that of standard clinical strains. The isolates possessed the ipaH virulence gene and a megaplasmid, but lacked other Shigella-related virulence marker genes. Genetic fingerprinting and sequence analysis of housekeeping genes confirmed the strains as S. flexneri isolates. An apparent clonal origin of strains recovered with a one-year interval indicates a strong environmental selection pressure on Shigella for persistence in the freshwater environment. The lack of a complete set of virulence genes as well as uncommon biochemical properties suggest that these strains might represent a group of non-invasive and atypical environmental Shigella variants, with the potential for further elucidation of the survival mechanism, diversity, and emergence of virulent Shigella in tropical freshwater environments.

Iron Cycling Potentials of Arsenic Contaminated Groundwater in Bangladesh as Revealed by Enrichment Cultivation

ABSTRACT The activities of iron-oxidizing and reducing microorganisms impact the fate of arsenic in groundwater. Phylogenetic information cannot exclusively be used to infer the potential for iron oxidation or reduction in aquifers. Therefore, we complemented a previous cultivation-independent microbial community survey covering 22 arsenic contaminated drinking water wells in Bangladesh, with the characterization of enrichments of microaerophilic iron oxidizers and anaerobic iron reducers, conducted on the same water samples. All investigated samples revealed a potential for microbial iron oxidation and reduction. Microbial communities were phylogenetically diverse within and between enrichments as was also observed in the previous cultivation-independent analysis of the water samples from which these enrichments were derived. Enrichment uncovered a larger diversity in iron-cycling microorganisms than previously indicated. The iron-reducing enrichments revealed the presence of several 16S ribosomal RNA (16S rRNA) gene sequences most closely related to Acetobacterium, Clostridium, Bacillus, Rhizobiales, Desulfovibrio, Bacteroides, and Spirochaetes, in addition to well-known dissimilatory iron-reducing Geobacter and Geothrix species. Although a large diversity of Geobacteraceae was observed, they comprised only a small part of the iron-reducing consortia. Iron-oxidizing gradient tube enrichments were dominated by Comamonadaceae and Rhodocyclaceae instead of Gallionellaceae. Forty-five percent of these enrichments also revealed the presence of the gene encoding arsenite oxidase, which converts arsenite to less toxic and less mobile arsenate. Their potential for ferric (oxyhydr)oxides precipitation and arsenic immobilization makes these iron-oxidizing enrichments of interest for rational bioaugmentation of arsenite contaminated groundwater.

Re-emergence of circulatory foot-and-mouth disease virus serotypes Asia1 in Bangladesh and VP1 protein heterogeneity with vaccine strain IND 63/72

Foot‐and‐mouth disease virus (FMDV) serotypes O, A and Asia1 are responsible for significant number of disease outbreaks in Bangladesh; however serotype Asia1 has not been reported in circulation since 1996. The present investigation reports the detection of serotype FMDV Asia1 from local farms in 2012 and 2013 outbreaks. The farms were located in Jessore and Gazipur districts, and one of these farms was under vaccine control programme. Phylogenetic analysis of the complete VP1 gene revealed that FMDV Asia1 is under genetic lineage C having close similarity to the Asia1 sequences of Indian origin. The circulatory genotype Asia1 showed VP1 protein sequence heterogeneity of eight amino acid substitutions within the G‐H loop with the vaccine strain [IND 63/72 (AY304994)] used in vaccination programme. ELISA assay revealed that, of seven, only one local field serum sample (cattle vaccinated 38 days earlier) was positive at a titre level of >2·4 (log10) but failed to protect the cattle from infection occurred by the virus. This investigation focused that the eight amino acid substitution in VP1 protein at G‐H loop of the locally circulated FMDV serotype Asia1 strain may be a reason for current vaccination failure.

Antigenic heterogeneity of capsid protein VP1 in foot-and-mouth disease virus (FMDV) serotype Asia 1.

Foot and mouth disease virus (FMDV), with its seven serotypes, is a highly contagious virus infecting mainly cloven-hoofed animals. The serotype Asia1 occurs mainly in Asian regions. An in-silico approach was taken to reveal the antigenic heterogeneities within the capsid protein VP1 of Asia1. A total of 47 VP1 sequences of Asia1 isolates from different countries of South Asian regions were selected, retrieved from database, and were aligned. The structure of VP1 protein was modeled using a homology modeling approach. Several antigenic sites were identified and mapped onto the three-dimensional protein structure. Variations at these antigenic sites were analyzed by calculating the protein variability index and finding mutation combinations. The data suggested that vaccine escape mutants have derived from only few mutations at several antigenic sites. Five antigenic peptides have been identified as the least variable epitopes, with just fewer amino acid substitutions. Only a limited number of serotype Asia1 antigenic variants were found to be circulated within the South Asian region. This emphasizes a possibility of formulating synthetic vaccines for controlling foot-and-mouth disease by Asia1 serotypes.