Assessment of the surface water quality and primary health risk in urban wastewater and its receiving river Kathajodi, Cuttack of eastern India.

Kathajodi, the principal southern distributary of the Mahanadi River, is the vital source of irrigation and domestic water use for densely populated Cuttack city which receives anthropogenic wastes abundantly. This study assesses the contamination level and primary health status of urban wastewater, and its receiving river Kathajodi based on the physicochemical quality indices employing inductively coupled plasma mass spectroscopy and aligning with guidelines from the United States Environmental Protection Agency (USEPA) and WHO. The high WQI, HPI, and HEI in the catchment area (KJ2, KJ3, and KJ4) indicate poor water quality due to the influx of domestic waste through the primary drainage system and effluents of healthcare units. A high BOD (4.33-19.66 mg L-1) in the catchment indicates high organic matter, animal waste, bacteriological contamination, and low DO, resulting in deterioration of water quality. CR values beyond limits (1.00E - 06 to 1.00E - 04) in three locations of catchment due to higher Cd, Pb, and As indicate significant carcinogenic risk, while high Mn, Cu, and Al content is responsible for several non-carcinogenic ailments and arsenic-induced physiological disorders. The elevated heavy metals Cd, Cu, Fe, Mn, Ni, and Zn, in Kathajodi, could be due to heavy coal combustion, vehicle exhaust, and industrial waste. On the other hand, Cu, Fe, K, and Al could be from agricultural practices, weathered rocks, and crustal materials. Positive significant (p ≤ 0.05) Pearson correlations between physicochemical parameters indicate their common anthropogenic origin and similar chemical characteristics. A strong correlation of PCA between elements and physiological parameters indicates their role in water quality deterioration. Assessing the surface water quality and heavy metal contents from this study will offer critical data to policymakers for monitoring and managing public health concerns.

Urban wastewater contributes to the emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) in an urban receiving river in eastern India.

The present study revealed the emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) and the associated driving factors in an urban river system surrounding Cuttack city, Odisha. The high contamination factor and contamination degree indicate poor water quality. The CRKP isolates showed 100% resistance against piperacillin, amoxicillin-clavulanic acid, piperacillin-tazobactam, ceftriaxone, ceftazidime, meropenem, and imipenem but less resistance to colistin (12.85%). Among the CRKP isolates, carbapenemase genes blaNDM, blaOXA-48-like, and blaKPC were detected in 94.28%, 35%, and 10% of isolates, respectively. The resistance genes (blaNDM, blaTEM, and blaCTX-M) were found to be significantly correlated with toxic metals (As, Cd, Co, Cu, Fe, Mn, Pb) (P < 0.05). Detection of virulence factors (yersiniabactin and aerobactin) and capsular serotypes (K1, K2, and K54 types) explain the pathogenicity of CRKP isolates. Enterobacterial repetitive intergenic consensus-PCR based molecular typing separated the CRKP strains into 13 clusters, of which VI and XI clusters showed similar resistance and virulence determinants, indicating the dissemination of clones from wastewater to the river system. Our results provide first-hand information on assessing risks to public health posed by the CRKP isolates and toxic metals in the Kathajodi River. Molecular surveillance of nearby hospitals for the prevalence of CRKP will help trace their transmission route.

Characterization of novel metagenomic-derived lipase from Indian hot spring.

Extreme environments are the main source of industrially suitable biocatalysts. The non-cultivable approach of searching enzymes is known to provide ample scope to accomplish novelty for their industrial applications. Lip479 clone out of seven lipase-producing clones obtained from Taptapani hot spring was found to be optimally active at pH 8.0 and temperature 65 °C. The recombinant Lip479 was highly stable in organic solvents, methanol, DMF, DMSO, acetone, and dichloromethane. Lip479 lipase activity was enhanced in the presence of K+, Mn2+, Na+, Zn2+, and Ca2+ except for Fe3+. The ability of Lip479 lipase to act on long carbon chain of 4-nitrophenyl myristate suggests it might be a true lipase. Lip479 clone was found to have ORF of 1251 bp encoding 416 amino acid residues of 42.57 KDa size (theoretically calculated). The presence of conserved motif Ala-His-Ser-Gln-Gly and Zn2+-binding consensus sequence (GAAHAAKH) of the clone assigns the protein to lipase family 1.5. Phylogenetic lineage of the protein sequence of Lip479 was traced to family 1.5 as it was clubbed up with those of reported lipases of the same family. The above biochemical features indicated that Lip479 lipase can be a potential biocatalyst for its use in various industries.

Parameter optimization for thermostable lipase production and performance evaluation as prospective detergent additive.

Lipase based formulations has been a rising interest to laundry detergent industry for their eco-friendly property over phosphate-based counterparts and compatibility with chemical detergents ingredients. A thermo-stable Anoxybacillus sp. ARS-1 isolated from Taptapani Hotspring, India was characterized for optimum lipase production employing statistical model central composite design (CCD) under four independent variables (temperature, pH, % moisture and bio-surfactant) by solid substrate fermentation (SSF) using mustard cake. The output was utilized to find the effect of parameters and their interaction employing response surface methodology (RSM). A quadratic regression with R2 = 0.955 established the model to be statically best fitting and a predicted highest lipase production of 29.4 IU/g at an optimum temperature of 57.5 °C, pH 8.31, moisture 50% and 1.2 mg of bio-surfactant. Experimental production of 30.3 IU/g lipase at above conditions validated the fitness of model. Anoxybacillus sp. ARS-1 produced lipase was found to resist almost all chemical detergents as well as common laundry detergent, proving it to be a prospective additive for incorporation.

Molecular characterization of extended spectrum ß-lactamase-producing Enterobacteriaceae strains isolated from a tertiary care hospital.

Infectious diseases caused by ESBL producing Enterobacteriaceae are an emerging problem worldwide which increases the empirical treatment failure, hospital cost, rate of morbidity and mortality. This also leads to the Hospital infection outbreak. Present study was undertaken to determine the frequency of blaTEM, blaCTX-M and blaSHV genes among Enterobacteriaceae. A total of 751 non-repeated clinical isolates of Enterobacteriaceae family were included in this study. Antibiotic susceptibility test was done and minimal inhibitory concentration (MIC) against four antibiotics was carried out. Five hundred fifteen multi drug resistant isolates were tested for ESBL by CLSI confirmatory method. Isolates showing ESBL positive by phenotypic method were screened for blaTEM, blaCTX-M and blaSHV genes by monoplex PCR. Two blaTEM and two blaCTX-M amplified products were selected randomly for sequencing. Sequencing data was submitted to NCBI data base. Of the 515 MDR isolates, 140 showed ESBL production by phenotypic method. All the ESBL producing isolates showed resistant to ceftazidime (100%). IMP, TGC and CL drugs could be preferred for the treatment of ESBL producers as these drugs showed a lower rate of resistance. blaTEM gene was the predominant (96.42%) followed by blaCTX-M (75%) and blaSHV (17.85%). All the three bla genes were occurred in 22 (17.14%) isolates. All the phenotypically confirmed ESBL producers were found contain any one of the three bla genes. It is concluded from the study that the blaTEM was predominantly found in Enterobacteriaceae and blaCTX-M gene also seemed to emerging.

Statistical optimization for lipase production from solid waste of vegetable oil industry.

The production of biofuel using thermostable bacterial lipase from hot spring bacteria out of low-cost agricultural residue olive oil cake is reported in the present paper. Using a lipase enzyme from Bacillus licheniformis, a 66.5% yield of methyl esters was obtained. Optimum parameters were determined, with maximum production of lipase at a pH of 8.2, temperature 50.8°C, moisture content of 55.7%, and biosurfactant content of 1.693 mg. The contour plots and 3D surface responses depict the significant interaction of pH and moisture content with biosurfactant during lipase production. Chromatographic analysis of the lipase transesterification product was methyl esters, from kitchen waste oil under optimized conditions, generated methyl palmitate, methyl stearate, methyl oleate, and methyl linoleate.

Genetic diversity study of various ß-lactamase-producing multidrug-resistant Escherichia coli isolates from a tertiary care hospital using ERIC-PCR.

BACKGROUND & OBJECTIVES: The prevalence of multidrug-resistant (MDR) Escherichia coli isolates producing ß-lactamase enzyme is a growing problem across the globe. Strain typing is an epidemiologically important tool not only for detecting the cross transmission of nosocomial pathogens but also for determining the source of infection. The present study was conducted to understand the clonal relationship among various ß-lactamase-producing MDR E. coli isolates using enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR). METHODS: A total of 41 MDR E. coli isolates were randomly collected from various clinical samples and processed. Isolated organisms were tested for antibiotics resistance pattern. Phenotypic detection of metallo ß-lactamases (MBL) was carried out by the imipenem-ethylenediaminetetraacetic acid disc diffusion/double-disc synergy test. AmpC enzyme production was tested by a modified three-dimensional extract test. RESULTS: Almost all isolates were found sensitive to colistin. A high percentage of drug resistance was observed in these isolates against ceftazidime (100%), cefotaxime (100%), cefepime (100%), ofloxacin (97.56%), amoxicillin/clavulanic acid (97.56%) and norfloxacin (85.36%). Of the 41 isolates, ESBL producers were found to be predominant, i.e., 22 (53.65%), followed by AmpC (6, 14.63%) and MBL (5, 12.19%). INTERPRETATION & CONCLUSIONS: At 60 per cent similarity cut-off value, the dendrogram analysis showed that there were a total of 14 unique clusters of ERIC (CL-1 - CL-14) within the 41 E. coli isolates, which revealed the genetic diversity existing between them.

A novel thermoalkaliphilic xylanase from Gordonia sp. is salt, solvent and surfactant tolerant.

Two aerobic bacterial consortia namely Con T and Con R were developed by enrichment technique from termite gut and cow dung respectively, using xylan as a sole carbon source. Molecular characterization of Con R based on 16S rRNA sequence analysis showed the presence of Pannonibacter sp. R-3 and Pseudoxanthomas sp. R-5. On the other hand, Con T showed the presence of Pseudoxanthomas sp. T-5, Cellulosimicrobium sp. T-21, and Gordonia sp. T-30. Being the maximum xylanase producer among the five isolates and being a novel xylanase producing bacterial genus, Gordonia sp. T-30 was selected. Xylanase produced by Gordonia sp. T-30 showed optimum activity at 60 °C and pH 9. Xylanase was 95% stable for 120 min at pH 9.0 and 98% stable at 60 °C for 90 min. Xylanase activity was stimulated in the presence of organic solvents such as petroleum ether, acetone, diethyl ether, n-hexane, and benzene. Detergent like cetyltrimethylammonium bromide and presence of NaCl also accelerated the xylanase function. Comparative evaluation was studied between sterilized and non-sterilized solid fermentation to produce xylanase by Gordonia sp. T-30 using various agricultural residues as growth substrate in cost effective manner. Industrially important features endowed by this xylanase make it a very promising candidate for food, feed, and fuel industry.

Molecular docking, molecular dynamics simulation, and MM/PBSA analysis of ginger phytocompounds as a potential inhibitor of AcrB for treating multidrug-resistant Klebsiella pneumoniae infections.

The emergence of Multidrug resistance (MDR) in human pathogens has defected the existing antibiotics and compelled us to understand more about the basic science behind alternate anti-infective drug discovery. Soon, proteome analysis identified AcrB efflux pump protein as a promising drug target using plant-driven phytocompounds used in traditional medicine systems with lesser side effects. Thus, the present study aims to explore the novel, less toxic, and natural inhibitors of Klebsiella pneumoniae AcrB pump protein from 69 Zingiber officinale phyto-molecules available in the SpiceRx database through computational-biology approaches. AcrB protein's homology-modelling was carried out to get a 3D structure. The multistep-docking (HTVS, SP, and XP) were employed to eliminate less-suitable compounds in each step based on the docking score. The chosen hit-compounds underwent induced-fit docking (IFD). Based on the XP GScore, the top three compounds, epicatechin (-10.78), 6-gingerol (-9.71), and quercetin (-9.09) kcal/mol, were selected for further calculation of binding free energy (MM/GBSA). Furthermore, the short-listed compounds were assessed for their drug-like properties based on in silico ADMET properties and Pa, Pi values. In addition, the molecular dynamics simulation (MDS) studies for 250 ns elucidated the binding mechanism of epicatechin, 6-gingerol, and quercetin to AcrB. From the dynamic binding free energy calculations using MM/PBSA, 6-gingerol exhibited a strong binding affinity towards AcrB. Further, the 6-gingerol complex's energy fluctuation was observed from the free energy landscape. In conclusion, 6-gingerol has a promising inhibiting potential against the AcrB efflux pump and thus necessitates further validation through in vitro and in vivo experiments.Communicated by Ramaswamy H. Sarma.

Development of pharmacophore models for AcrB protein and the identification of potential adjuvant candidates for overcoming efflux-mediated colistin resistance.

Growing multi-drug resistance (MDR) among ESKAPE pathogens is a huge challenge. Increased resistance to last-resort antibiotics, like colistin, has further aggravated this. Efflux is identified as a major route of colistin resistance. So, finding an FDA-approved efflux inhibitor for potential application as an adjuvant to colistin was the primary objective of this study. E. coli-AcrB pump inhibitors and substrates were used to develop and validate the pharmacophoric model. Drugs confirming this pharmacophore were subjected to molecular docking to identify hits for the AcrB binding pocket. The efflux inhibition potential of the top hit was validated through the in vitro evaluation of the minimum inhibitory concentration (MIC) in combination with colistin. The checkerboard assay was done to demonstrate synergism, which was further corroborated by the Time-kill assay. Ten common pharmacophore hypotheses were successfully generated using substrate/inhibitors. Following enrichment analysis, AHHNR.100 was identified as the top-ranked hypothesis, and 207 unique compounds were found to conform to this hypothesis. The multi-step docking of these compounds against the AcrB protein revealed argatroban as the top non-antibiotic hit. This significantly inhibited the efflux activity of colistin-resistant clinical isolates K. pneumoniae (n = 1) and M. morganii (n = 2). Further, their combination with colistin enhanced the susceptibility of these isolates, and the effect was found to be synergistic. Accordingly, the time-kill assay of this combination showed 8-log and 2-log reductions against K. pneumoniae and M. morganii, respectively. In conclusion, this study found argatroban as a bacterial efflux inhibitor that can be potentially used to overcome efflux-mediated resistance.

Ag-loaded BiFeO3/CuS heterostructured based composite: an efficient photocatalyst for removal of antibiotics and antibacterial activities.

The performance of advanced materials in environmental applications using green energy is the tremendous interest among researchers. The visible light responsive BiFeO3 (BFO), BiFeO3/CuS (BFOC), and Ag-loaded BiFeO3/CuS (Ag-BFOC) heterostructures have been synthesized by reflux method followed by hydrothermal and wetness impregnation method. These synthesized composites are well characterized through X-ray diffraction, UV diffuse reflectance spectroscopy, scanning electron microscope, and Fourier transfer infrared spectroscopy techniques. Compared with BFO and BFOC, Ag-BFOC exhibits the highest photocatalytic performance towards the degradation of antibiotics ciprofloxacin (76%) within 120-min time and also showed better antibacterial performance towards gram-negative (Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii) bacteria. Moreover, the novelty of the present work is the addition of CuS on the surface of BiFeO3 from heterojunction type II and facilitates the electron-hole channelization at the interfaces between BiFeO3 and CuS. Again, the loading of Ag on BiFeO3/CuS helps in shifting the absorption band towards the red end, is eligible to absorb more sunlight due to surface plasmon resonance effect, improves the separation efficiency of photo-generated charge carriers, and enhances the photocatalytic degradation of ciprofloxacin. The antibacterial property of Ag gives a best result towards antimicrobial activity. The prepared composites have proved their durability and stability by four successive cycles and prove the versatility of the composite.

All-atoms molecular dynamics study to screen potent efflux pump inhibitors against KpnE protein of Klebsiella pneumoniae.

The Small Multidrug Resistance efflux pump protein KpnE, plays a pivotal role in multi-drug resistance in Klebsiella pneumoniae. Despite well-documented study of its close homolog, EmrE, from Escherichia coli, the mechanism of drug binding to KpnE remains obscure due to the absence of a high-resolution experimental structure. Herein, we exclusively elucidate its structure-function mechanism and report some of the potent inhibitors through drug repurposing. We used molecular dynamics simulation to develop a dimeric structure of KpnE and explore its dynamics in lipid-mimetic bilayers. Our study identified both semi-open and open conformations of KpnE, highlighting its importance in transport process. Electrostatic surface potential map suggests a considerable degree of similarity between KpnE and EmrE at the binding cleft, mostly occupied by negatively charged residues. We identify key amino acids Glu14, Trp63 and Tyr44, indispensable for ligand recognition. Molecular docking and binding free energy calculations recognizes potential inhibitors like acarbose, rutin and labetalol. Further validations are needed to confirm the therapeutic role of these compounds. Altogether, our membrane dynamics study uncovers the crucial charged patches, lipid-binding sites and flexible loop that could potentiate substrate recognition, transport mechanism and pave the way for development of novel inhibitors against K. pneumoniae.Communicated by Ramaswamy H. Sarma.

Synergistic action of 6-gingerol as an adjuvant to colistin for susceptibility enhancement in multidrug-resistant Klebsiella pneumoniae isolates.

The growing threat to human health posed by multidrug-resistant Klebsiella pneumoniae (MDR-KP) indicates an urgent need to develop alternative therapeutic options. The emergence of colistin resistance further adds to the complexity. The study aims to explore in silico-screened phytomolecule 6-gingerol, the most potent active constituent of ginger, as an adjuvant to restore sensitivity in MDR-KP isolates to colistin. The screening of phytocompounds of Zingiber officinale were obtained from the spiceRx database, and molecular docking with efflux pump protein AcrB was performed using Schrödinger's Glide program. The synergistic and bactericidal effects of 6-gingerol in combination with colistin against MDR-KP isolates were determined following broth micro-dilution (MIC), checkerboard assay, and time-kill study. 6-Gingerol showed a good binding affinity with AcrB protein (-9.32 kcal mol-1) and followed the Lipinski rule of (RO5), demonstrating favourable drug-like properties. Further, the synergistic interaction of 6-gingerol with colistin observed from checkerboard assays against efflux-mediated colistin resistance MDR-KP isolates reveals it to be a prospectus adjuvant. The time-killing assays showed the effect of 6-gingerol in combination with colistin to be bactericidal against MSK9 and bacteriostatic against MSK4 and MSK7. Overall, the study provides insights into the potential use of 6-gingerol as a safe and easily available natural product to treat multidrug-resistant K. pneumoniae infections combined with colistin but needs in vivo toxicity evaluation before further recommendations can be made.

Investigating microbiome and transcriptome data to uncover the key microbial community involved in lignocellulose degradation within the Deulajhari hot spring consortium.

Geothermally heated spring water contaminated with decomposed leaf biomass creates unique hot spring ecosystems that support the recycling of diverse nutrients and harbor microbial consortia capable of degrading lignocellulose. We present microbiome and transcriptome data from the bacterial consortium of Deulajhari hot springs, characterized by a temperature of approximately 58 °C and surrounded by a dense population of pandanus plants in Angul, Odisha, India. Metagenomics and metatranscriptomics datasets were generated by extracting total DNA and RNA from the consortium sample of hotspring sediment, followed by shotgun sequencing using the Illumina HiSeq 2500 platform. The metagenomics dataset produced approximately 38,694 contigs, while the metatranscriptomics dataset yielded 9226 contigs, resulting in a total nucleotide size of 89,857,616 and 15,541,403 bps, respectively. Analysis using MEGAN6 against the NCBI "taxonomy" database revealed the presence of 18 and 12 phyla, including candidate phyla, in respective datasets. Proteobacteria exhibited the highest relative abundance in the metagenomics dataset, while Firmicutes was highly abundant in the metatranscriptomics dataset. At the genus level, a total of 92 and 25 genera were predicted in both datasets, with lignocellulose degrading Meiothermus being highly abundant in both metagenomics and metatranscriptomics datasets. We also observed that the unknown bacteria and unidentified sequences were found in significant proportion in the metatranscriptomics dataset. We assembled and functionally annotated approximately 23,960 contigs using the Prokka pipeline. Among the SEED category, the most expressed and annotated microbial genes fall under the unknown category as well as Biotin synthesis and their utilization. Furthermore, some of these genes were implicated in the degradation of aromatic amino acids, D-mannitol, and D-mannose. These findings contribute to our understanding of how the composition and abundance of bacterial communities facilitate lignocellulose degradation in extreme environments and biofuel generation.

NDM-5-carrying Klebsiella pneumoniae ST437 belonging to high-risk clonal complex (CC11) from an urban river in eastern India.

In this study, we described the carbapenem bla NDM-5-carrying extensive drug-resistant (XDR) K. pneumoniae ST437 from an urban river water Kathajodi in Odisha, India. The presence of carbapenem and co-occurrence of other resistance determinants (bla NDM-5, bla CTX-M, bla SHV, and bla TEM), virulence factors (fimH, mrkD, entB, irp-1, and ybtS), and capsular serotype (K54) represent its pathogenic potential. The insertion sequence ISAba125 and the bleomycin resistance gene ble MBL at upstream and downstream, respectively, could play a significant role in the horizontal transmission of the bla NDM-5. Its biofilm formation ability contributes toward environmental protection and its survivability. MLST analysis assigned the isolate to ST437 and clonal lineage to ST11 (CC11) with a single locus variant. The ST437 K. pneumoniae, a global epidemic clone, has been reported in North America, Europe, and Asia. This work contributes in understanding of the mechanisms behind the spread of bla NDM-5 K. pneumoniae ST437 and demands extensive molecular surveillance of river and nearby hospitals for better community health. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03556-5.

Identification of core therapeutic targets for Monkeypox virus and repurposing potential of drugs against them: An in silico approach.

Monkeypox virus (mpox virus) outbreak has rapidly spread to 82 non-endemic countries. Although it primarily causes skin lesions, secondary complications and high mortality (1-10%) in vulnerable populations have made it an emerging threat. Since there is no specific vaccine/antiviral, it is desirable to repurpose existing drugs against mpox virus. With little knowledge about the lifecycle of mpox virus, identifying potential inhibitors is a challenge. Nevertheless, the available genomes of mpox virus in public databases represent a goldmine of untapped possibilities to identify druggable targets for the structure-based identification of inhibitors. Leveraging this resource, we combined genomics and subtractive proteomics to identify highly druggable core proteins of mpox virus. This was followed by virtual screening to identify inhibitors with affinities for multiple targets. 125 publicly available genomes of mpox virus were mined to identify 69 highly conserved proteins. These proteins were then curated manually. These curated proteins were funnelled through a subtractive proteomics pipeline to identify 4 highly druggable, non-host homologous targets namely; A20R, I7L, Top1B and VETFS. High-throughput virtual screening of 5893 highly curated approved/investigational drugs led to the identification of common as well as unique potential inhibitors with high binding affinities. The common inhibitors, i.e., batefenterol, burixafor and eluxadoline were further validated by molecular dynamics simulation to identify their best potential binding modes. The affinity of these inhibitors suggests their repurposing potential. This work can encourage further experimental validation for possible therapeutic management of mpox.

Genomic insight of extremely drug-resistant Klebsiella pneumoniae ST5378 from a paediatric bloodstream infection.

OBJECTIVES: This study investigated the draft genome and phylogeny of an extremely drug-resistant and novel sequence type Klebsiella pneumoniae isolated from a paediatric bloodstream infection. METHODS: An isolate from a 7-year-old child with severe respiratory infection was identified, and the whole genome was sequenced using the Illumina MiSeq platform. High-quality reads were de novo assembled via Unicycler and annotated via PROKKA. Antimicrobial resistance genes, virulence factors, and plasmid and phage sequences were identified using the resistance gene identifier, VFanalyzer, Plasmidfinder, and PHASTER, respectively. Phylogenetics of closely related strains were inferred using core-genome multi-locus sequence typing and single nucleotide polymorphism. RESULTS: The draft genome of carbapenem-resistant K. pneumoniae RKS87 was 5 580 330 bp in size, with a GC content of 57.73%. The final assembly resulted in 38 contigs comprising 5075 CDS, 124 pseudo genes, 83 tRNA, 25 rRNA, and 10 ncRNA. The strain was assigned to a novel sequence type, ST5378, and harboured blaSHV-11, blaCTX-M-15, blaTEM-1, blaNDM-1, APH(3')-VI, OqxA, QnrS1, and fosA. We also identified the mutations in outer membrane porin (OmpK36 and OmpK37) and two-component system genes (PmrB and EptB). Three biomarkers (iroE, iroN, and iutA) associated with hypervirulent phenotype were also present in the genome. Phylogenetics of closely related strains revealed the clonal lineage of ST2938. CONCLUSIONS: The genome sequence and phylogenetics of the strain offer valuable insight into the clonal lineage, resistance genes, and pathogenicity of the novel sequence type ST5378.

Taxonomic Assignment-Based Genome Reconstruction from Apical Periodontal Metagenomes to Identify Antibiotic Resistance and Virulence Factors.

Primary apical periodontitis occurs due to various insults to the dental pulp including microbial infections, physical and iatrogenic trauma, whereas inadequate elimination of intraradicular infection during root canal treatment may lead to secondary apical periodontitis. We explored the complex intra-radicular microbial communities and their functional potential through genome reconstruction. We applied shotgun metagenomic sequencing, binning and functional profiling to identify the significant contributors to infection at the acute and chronic apical periodontal lesions. Our analysis revealed the five classified clusters representing Enterobacter, Enterococcus, Lacticaseibacillus, Pseudomonas, Streptococcus and one unclassified cluster of contigs at the genus level. Of them, the major contributors were Pseudomonas, with 90.61% abundance in acute conditions, whereas Enterobacter followed by Enterococcus with 69.88% and 15.42% abundance, respectively, in chronic conditions. Enterobacter actively participated in antibiotic target alteration following multidrug efflux-mediated resistance mechanisms, predominant in the chronic stage. The prediction of pathways involved in the destruction of the supportive tissues of the tooth in Enterobacter and Pseudomonas support their crucial role in the manifestation of respective disease conditions. This study provides information about the differential composition of the microbiome in chronic and acute apical periodontitis. It takes a step to interpret the role of a single pathogen, solely or predominantly, in establishing endodontic infection types through genome reconstruction following high throughput metagenomic DNA analysis. The resistome prediction sheds a new light on the therapeutic treatment guidelines for endodontists. However, it needs further conclusive research to support this outcome using a larger number of samples with similar etiological conditions, but different demographic origin.

In vitro synergistic interaction of colistin and other antimicrobials against intrinsic colistin-resistant Morganella morganii isolates.

Morganella morganii, a non-negligent opportunistic pathogen of the family Enterobacteriaceae, enlisted recently in the global priority pathogens by WHO for its swift propensity to acquire drug-resistant genes, engendering enhanced death rates. A combination of diverse antimicrobials could be recycled to overcome the ongoing acquisition of resistance mechanisms by M. morganii. Herein, we investigated the in vitro synergistic effect of colistin with meropenem, rifampicin, minocycline and linezolid against three intrinsic colistin-resistant M. morganii strains collected from critical departments of tertiary care hospitals. The strains were identified and tested for antimicrobial susceptibility by VITEK 2 automated system. The 16S rRNA sequencing was used to reconfirm the species identification. Minimum inhibitory concentrations (MICs) of colistin, meropenem, rifampicin, minocycline and linezolid were determined by the broth microdilution method. Synergistic interactions were studied by checkerboard and time-kill assay. The VITEK 2 identification and 16S rRNA sequencing confirmed that the strains were M. morganii. The automated antimicrobial susceptibility test revealed that all three isolates were multi-drug resistant. The checkerboard analysis demonstrated the synergy of all four combinations with FICI values ranging from 0.06 to 0.31 in all three isolates. These results suggest a potential role of meropenem as an adjuvant for treating M. morganii infections. The current work presented the first evidence of synergy between colistin and other antibiotics against M. morganii infection, which needs validation through in vitro and in vivo studies using a larger number of isolates. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03551-w.

Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.

BACKGROUND: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. METHODS: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. RESULTS: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. CONCLUSIONS: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.