Reverse vaccinology & immunoinformatics approach to design a multiepitope vaccine (CV3Ag-antiMRSA) against methicillin resistant Staphylococcus aureus (MRSA) - a pathogen affecting both human and animal health.

Infections caused by drug resistant bacteria is a silent detrimental pandemic affecting the global health care profoundly. Methicillin resistant Staphylococcus aureus (MRSA) is a pathogen that causes serious infections in different settings (community, hospital & veterinary) whose treatment remains highly challenging due to its powerful characteristics (antibiotic resistance strategies, virulence factors). In this study, we used reverse vaccinology (RV) approach and designed an immunogenic multi epitope vaccine (CV3Ag-antiMRSA) targeting three potential antigen candidates viz., mecA encoding transpeptidase (PBP2a) protein responsible for conferring methicillin resistance and two virulence determinants - hlgA encoding gamma-hemolysin component A (a pore forming toxin) and isdB encoding iron regulated surface determinant B (heme transport component that allows S. aureus to scavenge iron from host hemoglobin and myoglobin). We employed an array of immunoinformatic tools/server to identify and use immunogenic epitopes (B cell and MHC class) to develop the chimeric subunit vaccine V4 (CV3Ag-antiMRSA) with immune modulating adjuvant and linkers. Based on different parameters, the vaccine construct V4 (CV3Ag-antiMRSA) was determined to be suitable vaccine (antigenic and non-allergen). Molecular docking and simulation of CV3Ag-antiMRSA with Toll Like Receptor (TLR2) predicted its immuno-stimulating potential. Finally, in silico cloning of CV3Ag-antiMRSA construct into pet28a and pet30 vector displayed its feasibility for the heterologous expression in the E. coli expression system. This vaccine candidate (CV3Ag-antiMRSA) designed based on the MRSA genomes obtained from both animal and human hosts can be experimentally validated and thereby contribute to vaccine development to impart protection to both animal and human health.Communicated by Ramaswamy H. Sarma.

Identification of a potential inhibitor for New Delhi metallo-ß-lactamase 1 (NDM-1) from FDA approved chemical library- a drug repurposing approach to combat carbapenem resistance.

Superbugs producing New Delhi metallo-ß-lactamase 1 (NDM-1) enzyme is a growing crisis, that is adversely affecting the global health care system. NDM-1 empowers the bacteria to inactivate entire arsenal of ß-lactam antibiotics including carbapenem (the last resort antibiotic) and remains ineffective to all the available ß lactamase inhibitors used in the clinics. Limited therapeutic option available for rapidly disseminating NDM-1 producing bacteria makes it imperative to identify a potential inhibitor for NDM-1 enzyme. With drug repurposing approach, in this study, we used virtual screening of available Food and Drug Administration (FDA) approved chemical library (ZINC12 database) and captured 'adapalene' (FDA drug) as a potent inhibitor candidate for NDM-1 enzyme. Active site docking with NDM-1, showed adapalene with binding energy -9.21 kcal/mol and interacting with key amino acid residues (Asp124, His122, His189, His250, Cys208) in the active site of NDM-1. Further, molecular dynamic simulation of NDM-1 docked with the adapalene at 100 ns displayed a stable conformation dynamic, with relative RMSD and RMSF in the acceptable range. Subsequently, in vitro enzyme assays using recombinant NDM-1 protein demonstrated inhibition of NDM-1 by adapalene. Further, the combination of adapalene plus meropenem (carbapenem antibiotic) showed synergistic effect against the NDM-1 producing carbapenem (meropenem) resistant clinical isolates (Escherichia coli and Klebsiella pneumoniae). Overall, our data indicated that adapalene can be a potential inhibitor candidate for NDM-1 enzyme that can contribute to the development of a suitable adjuvant to save the activity of carbapenem antibiotic against infections caused by NDM-1 positive gram-negative bacteria. Communicated by Ramaswamy H. Sarma.

Genetic characterization and comparative genomics of a multi drug resistant (MDR) Escherichia coli SCM-21 isolated from a subclinical case of bovine mastitis.

Escherichia coli is one of the major pathogens causing mastitis that adversely affects the dairy industry worldwide. This study employed whole genome sequence (WGS) approach to characterize the repertoire of antibiotic resistance genes (resistome), virulence genes (virulome), phylogenetic relationship and genome wide comparison of a multi drug resistant (MDR) E. coli(SCM-21) isolated from a case of subclinical bovine mastitis in Bangalore, India. The genome of E. coli SCM- 21 was found to be of 4.29 Mb size with 50.6% GC content, comprising a resistome of 22 genes encoding beta-lactamases (blaTEM,blaAmpC), polymyxin resistance (arnA) and various efflux pumps (acr, ade, emr,rob, mac, mar, rob), attributing to the bacteria's overall antibiotic resistance genetic profile. The virulome of E. coli SCM-21 consisted of genes encoding different traits [adhesion (ecp, fim, fde), biofilm formation (csg) and toxin production (ent, esp, fep, gsp)], necessary for manifestation of the infection. Phylogenetic relationship of E. coli SCM- 21 with other global E. coli strains (n = 4867) revealed its close genetic relatedness with E. coli strains originating from different hosts of varied geographical regions [human (Germany) bos taurus (USA, Belgium and Scotland) and chicken (China)]. Further, genome wide comparative analysis with E. coli (n = 6) from human and other animal origins showed synteny across the genomes. Overall findings of this study provided a comprehensive insight of the hidden genetic determinants/power of E. coli SCM-21 that might be responsible for manifestation of mastitis and failure of antibiotic treatment. Aforesaid strain forms a reservoir of antibiotic resistance genes (ARGs) and can integrate to one health micro biosphere.

Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India.

We report here the draft genome sequence of a multidrug-resistant Escherichia coli strain (NIVEDI-P44) isolated from a chicken fecal sample. The estimated genome size is 4.76 Mb, with a G+C content of 50.65%. The genome harbors multiple antibiotic resistance genes, blaDHA-1, mph(A), strA, strB, dfrA14, sul-2, tet(A), and qnrS1.

Epigenetic response in mice mastitis: Role of histone H3 acetylation and microRNA(s) in the regulation of host inflammatory gene expression during Staphylococcus aureus infection.

BACKGROUND: There is renewed interest towards understanding the host-pathogen interaction in the light of epigenetic modifications. Although epithelial tissue is the major site for host-pathogen interactions, there is handful of studies to show how epithelial cells respond to pathogens. Bacterial infection in the mammary gland parenchyma induces local and subsequently systemic inflammation that results in a complex disease called mastitis. Globally Staphylococcus aureus is the single largest mastitis pathogen and the infection can ultimately result in either subclinical or chronic and sometimes lifelong infection. RESULTS: In the present report we have addressed the differential inflammatory response in mice mammary tissue during intramammary infection and the altered epigenetic context induced by two closely related strains of S. aureus, isolated from field samples. Immunohistochemical and immunoblotting analysis showed strain specific hyperacetylation at histone H3K9 and H3K14 residues. Global gene expression analysis in S. aureus infected mice mammary tissue revealed a selective set of upregulated genes that significantly correlated with the promoter specific, histone H3K14 acetylation. Furthermore, we have identified several differentially expressed known miRNAs and 3 novel miRNAs in S. aureus infected mice mammary tissue by small RNA sequencing. By employing these gene expression data, an attempt has been made to delineate the gene regulatory networks in the strain specific inflammatory response. Apparently, one of the isolates of S. aureus activated the NF-κB signaling leading to drastic inflammatory response and induction of immune surveillance, which could possibly lead to rapid clearance of the pathogen. The other strain repressed most of the inflammatory response, which might help in its sustenance in the host tissue. CONCLUSION: Taken together, our studies shed substantial lights to understand the mechanisms of strain specific differential inflammatory response to S. aureus infection during mastitis. In a broader perspective this study also paves the way to understand how certain bacteria can evade the immune surveillance and cause sustained infection while others are rapidly cleared from the host body.

Histone H3K14 and H4K8 hyperacetylation is associated with Escherichia coli-induced mastitis in mice.

Mastitis is a multietiological complex disease, defined as inflammation of parenchyma of mammary glands. Bacterial infection is the predominant cause of mastitis, though fungal, viral and mycoplasma infections also have been reported. Based on the severity of the disease, mastitis can be classified into subclinical, clinical and chronic forms. Bacterial pathogens from fresh cow milk were isolated and classified by standard microbiological tests and multiplex PCR. Epidemiological studies have shown that Escherichia coli is the second largest mastitis pathogen after Staphylococcus aureus in India. Based on Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR profile and presence of virulence genes, a field isolate of E. coli was used for intramammary inoculation in lactating mice. Histopathological examination of hematoxylin and eosin stained sections showed severe infiltration of polymorphonuclear neutrophils, mononuclear inflammatory cells in the alveolar lumen and also in interstitial space, and necrosis of alveolar epithelial cells after 24 h. Western blot and immunohistochemical analysis of mice mammary tissues showed significant hyperacetylation at histone H3K14 residue of both mammary epithelial cells and migrated inflammatory cells. Quantitative real-time PCR and genome-wide gene expression profile in E. coli infected mice mammary tissue revealed differential expression of genes related to inflammation, immunity, antimicrobial peptide expression, acute phase response and oxidative stress response. Expression of milk proteins was also suppressed. ChIP assay from paraffinized tissues showed selective enrichment of acetylated histone H3K14 and H4K8 at the promoters of overexpressed genes. These data suggest that E. coli infection in mice mammary tissue leads to histone hyperacetylation at the promoter of immune genes, which is a pre-requisite for the expression of inflammatory genes in order to mount a drastic immune response.