Whole genome sequencing and in vitro activity data of Escherichia phage NTEC3 against multidrug-resistant Uropathogenic and extensively drug-resistant Uropathogenic E. coli isolates

Chaudhary, Naveen; Singh, Dharminder; Maurya, Ravi Kumar; Mohan, Balvinder; Mavuduru, Ravimohan; Taneja, Neelam

doi:10.1016/j.dib.2022.108479

Cited by 3 publications

(4 citation statements)

References 14 publications

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“…The genomic DNA was extracted using a phage DNA isolation kit (Norgen Bioteck, Thorold, ON, Canada) [16]. Whole-genome sequencing was executed on the Illumina HiSeq X Ten platform using a paired-end library with a 2 × 150 bp read length.…”

Section: Genomic Dna Extraction and Sequence Analysismentioning

confidence: 99%

Genome Analysis and Antibiofilm Activity of Phage 590B against Multidrug-Resistant and Extensively Drug-Resistant Uropathogenic Escherichia coli Isolates, India

et al. 2022

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Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Uropathogenic Escherichia coli (UPEC), which are the most frequent agents causing community as well as hospital-acquired UTIs, have become highly drug-resistant, thus making the treatment of these infections challenging. Recently, the use of bacteriophages (or ‘phages’) against multidrug-resistant (MDR) and extensively drug-resistant (XDR) microorganisms has garnered significant global attention. Bacterial biofilms play a vital role in the pathogenesis of UTIs caused by UPEC. Phages have the potential to disrupt bacterial biofilms using lytic enzymes such as EPS depolymerases and endolysins. We isolated a lytic phage (590B) from community sewage in Chandigarh, which was active against multiple MDR and XDR biofilm-forming UPEC strains. During whole-genome sequencing, the 44.3 kb long genome of phage 590B encoded 75 ORFs, of which 40 were functionally annotated based on homology with similar phage proteins in the database. Comparative analysis of associated phage genomes indicated that phage 590B evolved independently and had a distinct taxonomic position within the genus Kagunavirus in the subfamily Guernseyvirinae of Siphoviridae. The phage disrupted biofilm mass effectively when applied to 24 h old biofilms formed on the Foley silicon catheter and coverslip biofilm models. To study the effect of intact biofilm architecture on phage predation, the biofilms were disrupted. The phage reduced the viable cells by 0.6–1.0 order of magnitude after 24 h of incubation. Regrowth and intact bacterial cells were observed in the phage-treated planktonic culture and biofilms, respectively, which indicated the emergence of phage-resistant bacterial variants. The phage genome encoded an endolysin which might have a role in the disruption and inhibition of bacterial biofilms. Moreover, the genome lacked genes encoding toxins, virulence factors, antibiotic resistance, or lysogeny. Therefore, lytic phage 590B may be a good alternative to antibiotics and can be included in phage cocktails for the treatment of UTIs caused by biofilm-forming MDR and XDR UPEC strains.

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Section: Genomic Dna Extraction and Sequence Analysismentioning

confidence: 99%

Genome Analysis and Antibiofilm Activity of Phage 590B against Multidrug-Resistant and Extensively Drug-Resistant Uropathogenic Escherichia coli Isolates, India

et al. 2022

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“…The whole-genome analysis of two E. coli phages revealed that they lack virulence, antibiotic resistance, and bacterial toxin-related genes, making them suitable for treating bacterial infections (40). The identification of genes encoding for endolysin and depolymerases in these phages opens up exciting possibilities for biocontrol applications (41).…”

Section: Discussionmentioning

confidence: 99%

Role of Phage–Antibiotic Combinations in Reducing ESBL-Producing and Carbapenem-ResistantEscherichia coli

Shamsuzzaman,

Kim,

Kim

2024

Preprint

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The emergence of extended-spectrumβ-lactamase (ESBL)-producingE. coliand carbapenem-resistantE. coli(CREC) poses a significant global health concern. Here, we isolated and characterized two novel phages and studied their effectiveness with antibiotics against ESBL-producingE. coliand CREC. The isolated phages, EC.W1-9 and EC.W15-4, belonged to thePodoviridaeandMyoviridaefamilies, respectively. They are safe for bacterial control as they do not contain integrase or toxin-coding genes. The phage combination considerably enhanced lytic ability, effectively lysing 61.7% of the 60E. coliisolates, compared to lysis in the 41.6% –55% range by individual phages. Phages EC.W1-9 and EC.W15-4 combined demonstrated 100% susceptibility against differentE. colisequence types, including ST73, ST648, ST2311, ST405, ST7962, ST131, ST13003, and ST167. Additionally, studies showed synergy between antibiotics and phage combinations against ESBL-producingE.coli, with susceptibility of 73.3% and 54% for CREC. The combined treatment of isolated phages and antibiotics significantly increased survival rates in BALB/c mice exposed to various ST types of ESBL-producingE. coliand CREC, including ST131, ST648, and ST410. Survival rates against KBN7288 (ST131) increased by approximately 75% and 50% compared to individual phages EC.W1-9 and EC.W15-4, respectively. When phages and antibiotics were combined, survival rates againstE. coliisolates KBN5617 (ST410), KBN6241 (ST410), and KBN4004 (ST648) ranged from 75% – 100%. Finally, this study highlights the importance of phage and phage-antibiotic combinations to prepare phages for killing different ST types of ESBL-producingE. coliand CREC isolates.IMPORTANCEWhen combined with antibiotics, phage therapy shows promise in fighting multidrug-resistant bacteria. However, antagonism between phages and antibiotics has been reported. This research isolates and characterizes two novel phages, EC.W1-9 and EC.W15-4, from thePodoviridaeandMyoviridaefamilies, respectively, and evaluates their effectiveness against ESBL-producingE. coliand CREC. These phages, lacking integrase or toxin-coding genes, showed significant promise in bacterial control. Combined phage treatment lysed 61.7% ofE.coliisolates, outperforming individual phages. The phage combination showed 100% susceptibility against differentE. colisequence types. Additionally, the synergy between phages and antibiotics increased susceptibility rates to 73.3% for ESBL-producingE. coliand 54% for CREC. In BALB/c mice, combined treatments significantly improved survival rates against variousE. coliisolates. Finally. this study emphasizes the potential of phage and phage-antibiotic combinations in targeting various ST types of ESBL-producingE. coliand CREC.

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“…The resuspended mixture was filtered by a 0.45 µm syringe filter. Final purification was carried out using the dialysis method with the help of the dialysis membrane (MWCO 14,000, Himedia Laboratories, Mumbai, India) [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

“…Plaque morphology was determined using the plaque assay [ 14 ]. The plaque diameter was calculated in millimeters (mm).…”

Section: Methodsmentioning

confidence: 99%

Vibrio Phage VMJ710 Can Prevent and Treat Disease Caused by Pathogenic MDR V. cholerae O1 in an Infant Mouse Model

et al. 2023

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Cholera, a disease of antiquity, is still festering in developing countries that lack safe drinking water and sewage disposal. Vibrio cholerae, the causative agent of cholera, has developed multi-drug resistance to many antimicrobial agents. In aquatic habitats, phages are known to influence the occurrence and dispersion of pathogenic V. cholerae. We isolated Vibrio phage VMJ710 from a community sewage water sample of Manimajra, Chandigarh, in 2015 during an outbreak of cholera. It lysed 46% of multidrug-resistant V. cholerae O1 strains. It had significantly reduced the bacterial density within the first 4–6 h of treatment at the three multiplicity of infection (MOI 0.01, 0.1, and 1.0) values used. No bacterial resistance was observed against phage VMJ710 for 20 h in the time–kill assay. It is nearest to an ICP1 phage, i.e., Vibrio phage ICP1_2012 (MH310936.1), belonging to the class Caudoviricetes. ICP1 phages have been the dominant bacteriophages found in cholera patients’ stools since 2001. Comparative genome analysis of phage VMJ710 and related phages indicated a high level of genetic conservation. The phage was stable over a wide range of temperatures and pH, which will be an advantage for applications in different environmental settings. The phage VMJ710 showed a reduction in biofilm mass growth, bacterial dispersal, and a clear disruption of bacterial biofilm structure. We further tested the phage VMJ710 for its potential therapeutic and prophylactic properties using infant BALB/c mice. Bacterial counts were reduced significantly when phages were administered before and after the challenge of orogastric inoculation with V. cholerae serotype O1. A comprehensive whole genome study revealed no indication of lysogenic genes, genes associated with possible virulence factors, or antibiotic resistance. Based on all these properties, phage VMJ710 can be a suitable candidate for oral phage administration and could be a viable method of combatting cholera infection caused by MDR V. cholerae pathogenic strains.

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Whole genome sequencing and in vitro activity data of Escherichia phage NTEC3 against multidrug-resistant Uropathogenic and extensively drug-resistant Uropathogenic E. coli isolates

Cited by 3 publications

References 14 publications

Genome Analysis and Antibiofilm Activity of Phage 590B against Multidrug-Resistant and Extensively Drug-Resistant Uropathogenic Escherichia coli Isolates, India

Genome Analysis and Antibiofilm Activity of Phage 590B against Multidrug-Resistant and Extensively Drug-Resistant Uropathogenic Escherichia coli Isolates, India

Role of Phage–Antibiotic Combinations in Reducing ESBL-Producing and Carbapenem-ResistantEscherichia coli

Vibrio Phage VMJ710 Can Prevent and Treat Disease Caused by Pathogenic MDR V. cholerae O1 in an Infant Mouse Model

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