The newly designed primer MK1F/R could be a better alternative for PCR based diagnosis of VL using less invasive sample, peripheral blood instead of bone marrow or spleen aspirates.

Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor-intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface (GUI) tool named BioCluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering (HC) and the Improved Hierarchical Clustering (IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1–47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/.

25Streptococcus mutans, considered as principal causative agent of dental caries, maintains 26 a biofilm lifestyle in the dental plaque. The oral cavity harbors numerous S. mutans strains, which 27 displayed remarkable genotypic and phenotypic diversity. This study evaluated the genotypic and 28 phenotypic diversity of 209 S. mutans strains isolated from 336 patients with dental caries and 29 compared with the universal reference strain UA159. Our study has revealed a high degree of 30 genotypic and phenotypic variability among the clinical strains. We observed significant 31 differences in colony morphology, generation time, biofilm formation, bacteriocin and acid 32 production while growing in culture medium. All the clinical isolates were able to lower pH while 33 growing in THY broth. In consistent with phenotypic variations, we also observed tremendous 34 level of genotypic variation by AP-PCR and gene specific PCR. AP-PCR analysis suggested that 35 most of the patients with dental caries have distinct type of S. mutans strains. Genes related to 36 various two component systems were highly conserved among the strains, however, bacteriocin 37 encoding genes such as nlmAB, nlmC were absent in half of the clinical isolates. In sum, our study 38 highlights the genotypic and phenotypic diversity of S. mutans clinical isolates and indicates the 39 presence of diverse mechanism to initiate and establish the biofilm lifestyle which leads to tooth 40 decay. 41 42 43 44 45 46 48The initiation and successful development of dental caries is caused by multiple bacterial 49 and host factors, such as the composition and biochemical activity of the biofilm organisms, 50 dietary habit, genetic constitution and behavior of the host, tooth architecture and exposure to 51 fluoride (1-4). The mutans streptococci, specifically S. mutans, are considered to be the primary 52 causative agents of dental caries, commonly known as tooth decay (5, 6). In addition, several recent 53 studies have reported the associations of certain sub-groups of S. mutans with cardiovascular 54 disease (7-11). The ability to form biofilm on tooth surface, production of organic acid from 55 various carbohydrates (acidogenicity), ability to survive at low pH (acidurance), outstanding 56 ability to outcompete other bacteria by the production of bacteriocin and their adaptability to 57 rapidly changing environment can be attributed as the major virulence factors (12-18). 58Development of natural competence, which is coordinately regulated with the bacteriocin 59 production, is another vital attribute that provides genetic diversity to S. mutans for niche 60 adaptation and colonization (19-21). 61Strains belong to the species, S. mutans, are generally classified into four (c, e, f, and k) 62 serological groups based on the composition of cell-surface rhamose-glucose polysaccharides (22, 63 23). Strains belonged to serotype c are the most abundant in the oral cavity (70-80%), followed 64 by serotype e (20%) and serotype f or k (2-5%) (1, 24). However, serot...

Background: Streptococcus mutans, considered as principal causative agent of dental caries, maintains a biofilm lifestyle in the dental plaque. The oral cavity harbors numerous S. mutans strains which displayed remarkable genotypic and phenotypic diversity. This study evaluated the genotypic and phenotypic diversity of S. mutans strains isolated from patients with dental caries and compared with the universal reference strain UA159.Methods: Selective cultivation on mitis-salivaries-bacitracin agar and species-specific polymerase chain reaction (PCR) was carried out to isolate and identify the 209 S. mutans isolates from 336 patients with dental caries. Arbitrarily primed polymerase chain reaction (AP-PCR), PCR amplification of specific gene, acid production, biofilm formation capacity, and deferred antagonism bacteriocin assay were performed to evaluate the genotypic and phenotypic variation. All statistical analysis was performed using the SPSS software version 20 (SPSS, Chicago, IL, USA).Results: Our study revealed a high degree of genotypic and phenotypic variability among the clinical strains. We observed significant differences in colony morphology, generation time, biofilm formation, bacteriocin and acid production while growing in culture medium. All the clinical isolates were able to lower pH while growing in Todd-Hewitt broth. Consistent with phenotypic variations, we also observed genotypic variation by AP-PCR and gene specific PCR. AP-PCR analysis suggested that most of the patients with dental caries have distinct type of S. mutans strains. Genes related to various two component systems were highly conserved among the isolated strains, however, bacteriocin encoding genes such as nlmAB, nlmC were absent in nearly half of the clinical isolates.Conclusions: Our study highlights the genotypic and phenotypic diversity of S. mutans clinical isolates and indicates the presence of diverse mechanism to initiate and establish the biofilm lifestyle which leads to tooth decay.

Background and Objectives: The oral cavity harbors numerous Streptococcus mutans strains which display remarkable genotypic and phenotypic diversity. This study evaluated the genotypic and phenotypic diversity of 209 S. mutans strains isolated from 336 patients with dental caries and compared with the universal reference strain, UA159. Materials and Methods: Selective cultivation on mitis-salivaries-bacitracin agar and species-specific polymerase chain re- action (PCR) was carried out to isolate and identify the 209 S. mutans isolates from 336 patients with dental caries. Arbitrari- ly primed polymerase chain reaction (AP-PCR), PCR amplification of specific gene, acid production and biofilm formation capacity were performed to evaluate the genotypic and phenotypic variation. Student’s t-test and Chi-square test were used for analysis of variables and a probability (P) of <0.05 was considered as significant. Results: Our study revealed a high degree of genotypic and phenotypic variability among the clinical strains. We observed significant differences in colony morphology, generation time, biofilm formation, and acid production while growing in cul- ture medium. All the clinical isolates were able to lower pH while growing in Todd-Hewitt broth. Consistent with phenotypic variations, we also observed genotypic variation by AP-PCR and gene specific PCR. AP-PCR analysis suggested that most of the patients with dental caries have distinct type of S. mutans strains. Genes related to various two component systems were highly conserved among the isolated strains, however, bacteriocin encoding genes such as nlmAB, nlmC were absent in nearly half of the clinical isolates. Conclusion: Our results support that S. mutans clinical isolates have wide genotypic diversity and show variation in growth kinetics, acid production, acid tolerance and biofilm formation capacity and indicates the presence of diverse mechanism to initiate and establish the biofilm lifestyle which leads to tooth decay.