Molecular characterization and in silico analysis of naturally occurring TEM beta-lactamase variants among pathogenic Enterobacteriaceae infecting Indian patients

Contribution of genetic factors towards cefotaxime and ciprofloxacin resistance development among Extended spectrum beta-lactamase producing-Quinolone resistant pathogenic Enterobacteriaceae

β-lactams and quinolones are widely utilised to treat pathogenic Enterobacterial isolates worldwide. Due to improper use of these antibiotics, both ESBL producing and quinolone resistant (ESBL-QR) pathogenic bacteria have emerged. Nature of contribution of beta-lactamase (bla)/quinolone resistant (QR) genes, efflux pumps (AcrAB-TolC) over-expression and outer membrane proteins (OMPs) /porin loss/reduction and their combinations towards development of this phenotype were explored in this study. Kirby-Bauer disc diffusion method was used for phenotypic characterization of these bacteria and minimum inhibitory concentration of cefotaxime and ciprofloxacin was determined by broth micro dilution assay. Presence of bla, QR, gyrA/B genes was examined by PCR; acrB upregulation by real-time quantitative PCR and porin loss/reduction by SDS-PAGE. Based on antibiogram, phenotypic categorization of 715 non-duplicate clinical isolates was: ESBL+QR+ (n = 265), ESBL+QR- (n = 6), ESBL-QR+ (n = 346) and ESBL-QR-(n = 11). Increased OmpF/K35 and OmpC/K36 reduction, acrB up-regulation, prevalence of bla, QR genes and gyrA/B mutation was observed among the groups in following order: ESBL+QR+> ESBL-QR+> ESBL+QR-> ESBL-QR-. Presence of bla gene alone or combined porin loss and efflux pump upregulation or their combination contributed most for development of a highest level of cefotaxime resistance of ESBL+QR+ isolates. Similarly, combined presence of QR genes, porin loss/reduction, efflux pump upregulation and gyrA/B mutation contributed towards highest ciprofloxacin resistance development of these isolates.

Identification of Arg32Ser, His92Tyr and Leu147Phe novel mutations in chromosomally mediated β-lactamase SHV and in silico characterization to understand their substrate activity imparting resistance

The emergence of β-lactam resistance is yearning for clinical significance in Enterobacteriaceae, which are categorized under global priority pathogen lists by the World Health Organization. Likewise, the prevalence of numerous β-lactamase enzymes, mutational propensity in such bacteria, and their role in accelerating resistance is still a major concern. Thus, the present work intends to characterize the β-lactamase producing bacteria isolated from acute diarrheal patients to understand their chromosomally acquired resistance pattern through molecular characterization and in silico approaches. The current study highlights the first identified Escherichia fergusonii and Escherichia marmotae species and their β-lactamase encoding genes, blaOKP-A, blaNDM and blaOXA from the unexplored Enterobacteriaceae family from North East India. First-ever reported point mutations such as Arg32Ser, His92Tyr, and Leu147Phe were observed in BlaSHV protein of two Klebsiella pneumoniae isolates S-35 and S-46. In molecular docking, non-catalytic site H-bond interactions of Arg 218, Ala 223, Asn 128, Ser 126, Gln 95, Asp 100, Tyr 101, Ser 102, Ala 274 with a low binding affinity towards BlaSHV was found. This correlates with the high imipenem, ceftazidime, cefuroxime, ceftriaxone, and cefpodoxime resistance in Klebsiella pneumoniae S-35 with the complementary effect of mutations Arg32Ser and Leu147Phe. Besides, the role of His92Tyr mutation in controlling the resistance in Klebsiella pneumoniae S-46 is also illustrated. Thus, our study highlights the novel mutations of β-lactamase and its clinical importance with altered resistance profiles. This could be useful to design better therapeutics and to readjust antibiotic treatment regimes against them and control to grow more resistance under selective pressure.Communicated by Ramaswamy H. Sarma.

New N-Alkylated Heterocyclic Compounds as Prospective NDM1 Inhibitors: Investigation of In Vitro and In Silico Properties

A new family of pyrazole-based compounds (1–15) was synthesized and characterized using different physicochemical analyses, such as FTIR, UV-Visible, ¹H, ¹³C NMR, and ESI/LC-MS. The compounds were evaluated for their in vitro antifungal and antibacterial activities against several fungal and bacterial strains. The results indicate that some compounds showed excellent antibacterial activity against E. coli, S. aureus, C. freundii, and L. monocytogenes strains. In contrast, none of the compounds had antifungal activity. Molecular electrostatic potential (MEP) map analyses and inductive and mesomeric effect studies were performed to study the relationship between the chemical structure of our compounds and the biological activity. In addition, molecular docking and virtual screening studies were carried out to rationalize the antibacterial findings to characterize the modes of binding of the most active compounds to the active pockets of NDM1 proteins.

In vitro antibacterial activity of MGDG-palmitoyl from Oscillatoria acuminata NTAPC05 against extended-spectrum β-lactamase producers

Extended-spectrum β-lactamase (ESBL)-producing bacteria pose a big challenge in clinical practices, warranting a new therapeutic strategy. In this study, methanol extract of the marine cyanobacterium Oscillatoria acuminata NTAPC05 was fractionated under bioassay guidance and the fractions were tested against three well-characterized ESBL-producing bacteria Escherichia coli U655, Stenotrophomonas maltophilia B929 and Enterobacter asburiae B938. Out of the four HPLC fractions, fraction 2 showed bactericidal activity against all the three ESBL producers much more efficiently (MIC 100 μg ml^-1) than the fourth-generation cephalosporin (MIC >125 μg ml^-1). The active fraction was subjected to time-kill test at concentrations of 1/2 × MIC, 1 × MIC and 2 × MIC, and the results substantiated the bactericidal property of the fraction against the ESBL producers. Spectral analysis revealed monogalactosyldiacylglycerol containing a palmitoyl (MGDG-palmitoyl), being reported for the first time, as the active fraction, and its bactericidal property against ESBL producers was determined. The active fraction appears to damage the bacterial membrane leading to lysis of the cell, as revealed in confocal laser scanning microscopy (CLSM) analysis, that was confirmed in scanning electron microscopic analysis. Cytotoxicity assay revealed the O. acuminata compound to be safe to a normal cell line HEK293 (human embryonic kidney cell). The in silico analysis of MGDG-palmitoyl revealed two successive H-bonding interactions with Leu198 of TEM1 β-lactamase. Taken together, the MGDG-palmitoyl from O. acuminata NTAPC05 offers potential to develop analogs as a therapeutic for bacteremia caused by ESBL producers.

Emergence of blaCTX-M-15, blaTEM-169 and blaPER-1 extended-spectrum β-lactamase genes among different Salmonella enterica serovars from human faecal samples

BACKGROUND

Broad-spectrum β-lactams are used for empirical therapy of severe infections with non-typhoid Salmonella serotypes; however, activities of these drugs against the strains producing different β-lactamase is not so clear. This study investigated the prevalence of β-lactamase genes among isolates of S. enterica serovars from human faecal samples and determined their diversity in activity against different β-lactams.

METHODS

Antimicrobial resistance of faecal isolates of S. enterica to extended-spectrum cephalosporins was analysed and MIC values were determined for the strains presenting extended-spectrum β-lactamases (ESBLs) phenotypes. The β-lactamase genes were identified by PCR and sequencing. β-lactamase activity of the Salmonella strains exhibiting ESBL phenotype was detected by biological, iodometric, spectrophotometry and nitrocefin assays.

RESULTS

Out of 202 S. enterica isolates, ESBLs phenotype was detected among 3.4% (7/202) of the strains. blaTEM-1 and blaCTX-M-15 were among the frequent β-lactamase genes. Detection of blaTEM-169 in S. enterica serovar Typhimurium and S. enterica serovar Bredeney and blaPER-1 in S. enterica serovar Infantis was a new finding in this experiment. Location of blaCTX-M-15/blaTEM-169/blaPER-1 genes on plasmid was confirmed in a transformation experiment. While crude extracts of the enzymes from each strain showed higher activity against cephalothin and cefotaxime, the lowest activity was detected against ceftazidime. The greatest synergistic activity was seen in a strain of S. enterica that carried blaCTX-M-15 and blaPER-1 genes compared with those presenting blaCTX-M-15/blaTEM-169 or blaCTX-M-15/blaTEM-1 genotypes.

CONCLUSIONS

The results show dissemination of ESBLs encoding genes and their combined activity among different serovars of S. enterica that are a threat for future treatment options.