scholarly journals Genomic characterization of bacteriophage BI-EHEC infecting strains of Enterohemorrhagic Escherichia coli

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Marta Nisita Dewanggana ◽  
Diana Elizabeth Waturangi ◽  
Yogiara
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Enterohemorrhagic Escherichia Coli ◽  
Lytic Cycle ◽  
Tail Fiber ◽  
Lytic Bacteriophage ◽  
Food Preservatives ◽  
Genome Database ◽  
Related Proteins

Abstract Objective The aims of this research were to determine the genomic properties of BI-EHEC to control Enterohemorrhagic Escherichia coli (EHEC), which was isolated from previous study. Genomic analysis of this phage is essential for the assessment of this bacteriophage for further application as food preservatives. Results Genome of BI-EHEC was successfully annotated using multiPhATE2. Structural and lytic cycle-related proteins such as head, tail, capsid, and lysozyme (lysin) were annotated. The phylogenetic tree of tail fiber protein and BRIG results showed that BI-EHEC was similar to phages of the same host in the bacteriophage genome database. There were no indications of virulence properties, antibiotic resistance genes and lysogenic protein among annotated genes which implied BI-EHEC followed a lytic life cycle. PHACTS analysis was done to confirm this notion further and yielded a lytic cycle result. Further analysis using CARD found that BI-EHEC does not contain residual ARGs per recommended parameter. Furthermore, BI-EHEC confirmed as lytic bacteriophage, making it a good candidate for biocontrol agent.

Antibiotic susceptibility profiles and frequency of resistance genes in clinical Shiga toxin-producing Escherichia coli isolates from Michigan over a 14-year period

2021 ◽  
Author(s):  
Sanjana Mukherjee ◽  
Heather M. Blankenship ◽  
Jose A. Rodrigues ◽  
Rebekah E. Mosci ◽  
James T. Rudrik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Shiga Toxin ◽  
Antibiotic Susceptibility ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Mechanisms Of Resistance ◽  
Susceptibility Profiles

Background: Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that contributes to over 250,000 infections in the US each year. Because antibiotics are not recommended for STEC infections, resistance in STEC has not been widely researched despite an increased likelihood for the transfer of resistance gene from STEC to opportunistic pathogens residing within the same microbial community. Methods: Between 2001 and 2014, 969 STEC isolates were collected from Michigan patients. Serotyping and antibiotic susceptibility profiles to clinically relevant antibiotics were determined using disc diffusion, while epidemiological data was used to identify factors associated with resistance. Whole genome sequencing was used to examine genetic relatedness and identify genetic determinants and mechanisms of resistance in the non-O157 isolates. Results: Increasing frequencies of resistance to at least one antibiotic was observed over the 14 years (p=0.01). While the non-O157 serogroups were more commonly resistant than O157 (Odds Ratio: 2.4; 95% Confidence Interval:1.43-4.05), the frequency of ampicillin resistance among O157 isolates was significantly higher in Michigan compared to the national average (p=0.03). Genomic analysis of 321 non-O157 isolates uncovered 32 distinct antibiotic resistance genes (ARGs). Although mutations in genes encoding resistance to ciprofloxacin and ampicillin were detected in four isolates, most of the horizontally acquired ARGs conferred resistance to aminoglycosides, β-lactams, sulfonamides and/or tetracycline. Conclusions: This study provides insight into the mechanisms of resistance in a large collection of clinical non-O157 STEC isolates and demonstrates that antibiotic resistance among all STEC serogroups has increased over time, prompting the need for enhanced surveillance.

scholarly journals Virulent Drexlervirial Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Muhammad Saleem Iqbal Khan ◽  
Xiangzheng Gao ◽  
Keying Liang ◽  
Shengsheng Mei ◽  
Jinbiao Zhan
Keyword(s):  
Multidrug Resistant ◽  
The Other ◽  
Structural Proteins ◽  
Resistant Bacteria ◽  
Tail Fiber ◽  
Lytic Bacteriophage ◽  
Tail Fiber Protein ◽  
Multidrug Resistant Bacteria ◽  
Genome Database ◽  
Fiber Protein

Phage-host interactions are likely to have the most critical aspect of phage biology. Phages are the most abundant and ubiquitous infectious acellular entities in the biosphere, where their presence remains elusive. Here, the novel Escherichia coli lytic bacteriophage, named MSK, was isolated from the lysed culture of E. coli C (phix174 host). The genome of phage MSK was sequenced, comprising 45,053 bp with 44.8% G + C composition. In total, 73 open reading frames (ORFs) were predicted, out of which 24 showed a close homology with known functional proteins, including one tRNA-arg; however, the other 49 proteins with no proven function in the genome database were called hypothetical. Electron Microscopy and genome characterization have revealed that MSK phage has a rosette-like tail tip. There were, in total, 46 ORFs which were homologous to the Rtp genome. Among these ORFs, the tail fiber protein with a locus tag of MSK_000019 was homologous to Rtp 43 protein, which determines the host specificity. The other protein, MSK_000046, encodes lipoprotein (cor gene); that protein resembles Rtp 45, responsible for preventing adsorption during cell lysis. Thirteen MSK structural proteins were identified by SDS-PAGE analysis. Out of these, 12 were vital structural proteins, and one was a hypothetical protein. Among these, the protein terminase large (MSK_000072) subunit, which may be involved in DNA packaging and proposed packaging strategy of MSK bacteriophage genome, takes place through headful packaging using the pac-sites. Biosafety assessment of highly stable phage MSK genome analysis has revealed that the phage did not possess virulence genes, which indicates proper phage therapy. MSK phage potentially could be used to inhibit the multidrug-resistant bacteria, including AMP, TCN, and Colistin. Further, a comparative genome and lifestyle study of MSK phage confirmed the highest similarity level (87.18% ANI). These findings suggest it to be a new lytic isolated phage species. Finally, Blast and phylogenetic analysis of the large terminase subunit and tail fiber protein put it in Rtp viruses’ genus of family Drexlerviridae.

scholarly journals Vitamin K Analogs Influence the Growth and Virulence Potential of Enterohemorrhagic Escherichia coli

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Anne Kijewski ◽  
Ingun Lund Witsø ◽  
Hildegunn Iversen ◽  
Helene Thorsen Rønning ◽  
Trine L'Abée-Lund ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Vitamin K ◽  
Bacterial Growth ◽  
Shiga Toxin ◽  
Treatment Options ◽  
Inhibitory Effect ◽  
Enterohemorrhagic Escherichia Coli ◽  
Lytic Cycle ◽  
Content Type ◽  
Negative Effect

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) causes serious foodborne disease worldwide. It produces the very potent Shiga toxin 2 (Stx2). The Stx2-encoding genes are located on a prophage, and production of the toxin is linked to the synthesis of Stx phages. There is, currently, no good treatment for EHEC infections, as antibiotics may trigger lytic cycle activation of the phages and increased Stx production. This study addresses how four analogs of vitamin K, phylloquinone (K1), menaquinone (K2), menadione (K3), and menadione sodium bisulfite (MSB), influence growth, Stx2-converting phage synthesis, and Stx2 production by the EHEC O157:H7 strain EDL933. Menadione and MSB conferred a concentration-dependent negative effect on bacterial growth, while phylloquinone or menaquinone had little and no effect on bacterial growth, respectively. All four vitamin K analogs affected Stx2 phage production negatively in uninduced cultures and in cultures induced with either hydrogen peroxide (H2O2), ciprofloxacin, or mitomycin C. Menadione and MSB reduced Stx2 production in cultures induced with either H2O2 or ciprofloxacin. MSB also had a negative effect on Stx2 production in two other EHEC isolates tested. Phylloquinone and menaquinone had, on the other hand, variable and concentration-dependent effects on Stx2 production. MSB, which conferred the strongest inhibitory effect on both Stx2 phage and Stx2 production, improved the growth of EHEC in the presence of H2O2 and ciprofloxacin, which could be explained by the reduced uptake of ciprofloxacin into the bacterial cell. Together, the data suggest that vitamin K analogs have a growth- and potential virulence-reducing effect on EHEC, which could be of therapeutic interest. IMPORTANCE Enterohemorrhagic E. coli (EHEC) can cause serious illness and deaths in humans by producing toxins that can severely damage our intestines and kidneys. There is currently no optimal treatment for EHEC infections, as antibiotics can worsen disease development. Consequently, the need for new treatment options is urgent. Environmental factors in our intestines can affect the virulence of EHEC and help our bodies fight EHEC infections. The ruminant intestine, the main reservoir for EHEC, contains high levels of vitamin K, but the levels are variable in humans. This study shows that vitamin K analogs can inhibit the growth of EHEC and/or production of its main virulence factor, the Shiga toxin. They may also inhibit the spreading of the Shiga toxin encoding bacteriophage. Our findings indicate that vitamin K analogs have the potential to suppress the development of serious disease caused by EHEC.

scholarly journals Intracellular d-Serine Accumulation Promotes Genetic Diversity via Modulated Induction of RecA in Enterohemorrhagic Escherichia coli

2016 ◽  
Vol 198 (24) ◽  
pp. 3318-3328 ◽  
Author(s):  
James P. R. Connolly ◽  
Andrew J. Roe
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Dna Damage ◽  
Mutation Frequency ◽  
Sos Response ◽  
Enterohemorrhagic Escherichia Coli ◽  
Lytic Bacteriophage ◽  
Content Type ◽  
Lexa Repressor ◽  
Physiological Relevance

ABSTRACTWe recently discovered that exposure of enterohemorrhagicEscherichia coli(EHEC) tod-serine resulted in accumulation of this unusual amino acid, induction of the SOS regulon, and downregulation of the type III secretion system that is essential for efficient colonization of the host. Here, we have investigated the physiological relevance of this elevated SOS response, which is of particular interest given the presence of Stx toxin-carrying lysogenic prophages on the EHEC chromosome that are activated during the SOS response. We found that RecA elevation in response tod-serine, while being significant, was heterogeneous and not capable of activatingstxexpression orstxphage transduction to a nonlysogenic recipient. This “SOS-like response” was, however, capable of increasing the mutation frequency associated with low-level RecA activity, thus promoting genetic diversity. Furthermore, this response was entirely dependent on RecA and enhanced in the presence of a DNA-damaging agent, indicating a functional SOS response, but did not result in observable cleavage of the LexA repressor alone, indicating a controlled mechanism of induction. This work demonstrates that environmental factors not usually associated with DNA damage are capable of promoting an SOS-like response. We propose that this modulated induction of RecA allows EHEC to adapt to environmental insults such asd-serine while avoiding unwanted phage-induced lysis.IMPORTANCEThe SOS response is a global stress network that is triggered by the presence of DNA damage due to breakage or stalled replication forks. Activation of the SOS response can trigger the replication of lytic bacteriophages and promote genetic diversification through error-prone polymerases. We have demonstrated that the host-associated metabolited-serine contributes toEscherichia coliniche specification and accumulates inside cells that cannot catabolize it. This results in a modulated activation of the SOS antirepressor RecA that is insufficient to trigger lytic bacteriophage but capable of increasing the SOS-associated mutation frequency. These findings describe how relevant signals not normally associated with DNA damage can hijack the SOS response, promoting diversity asE. colistrains adapt while avoiding unwanted phage lysis.

scholarly journals Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7

2011 ◽  
Vol 78 (1) ◽  
pp. 58-69 ◽  
Author(s):  
Minjung Park ◽  
Ju-Hoon Lee ◽  
Hakdong Shin ◽  
Minsik Kim ◽  
Jeongjoon Choi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Salmonella Enterica ◽  
Burst Size ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Tail Fiber ◽  
Content Type ◽  
E Coli ◽  
Development Of Resistance

ABSTRACTSalmonella entericaandEscherichia coliO157:H7 are major food-borne pathogens causing serious illness. Phage SFP10, which revealed effective infection of bothS. entericaandE. coliO157:H7, was isolated and characterized. SFP10 contains a 158-kb double-stranded DNA genome belonging to the Vi01 phage-like familyMyoviridae.In vitroadsorption assays showed that the adsorption constant rates to bothSalmonella entericaserovar Typhimurium andE. coliO157:H7 were 2.50 × 10−8ml/min and 1.91 × 10−8ml/min, respectively. One-step growth analysis revealed that SFP10 has a shorter latent period (25 min) and a larger burst size (>200 PFU) than ordinaryMyoviridaephages, suggesting effective host infection and lytic activity. However, differential development of resistance to SFP10 inS.Typhimurium andE. coliO157:H7 was observed; bacteriophage-insensitive mutant (BIM) frequencies of 1.19 × 10−2CFU/ml forS.Typhimurium and 4.58 × 10−5CFU/ml forE. coliO157:H7 were found, indicating that SFP10 should be active and stable for control ofE. coliO157:H7 with minimal emergence of SFP10-resistant pathogens but may not be forS.Typhimurium. Specific mutation ofrfaLinS.Typhimurium andE. coliO157:H7 revealed the O antigen as an SFP10 receptor for both bacteria. Genome sequence analysis of SFP10 and its comparative analysis with homologousSalmonellaVi01 andShigellaphiSboM-AG3 phages revealed that their tail fiber and tail spike genes share low sequence identity, implying that the genes are major host specificity determinants. This is the first report identifying specific infection and inhibition ofSalmonellaTyphimurium andE. coliO157:H7 by a single bacteriophage.

scholarly journals Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sabrina I. Green ◽  
Carmen Gu Liu ◽  
Xue Yu ◽  
Shelley Gibson ◽  
Wilhem Salmen ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Multidrug Resistant ◽  
Protein Product ◽  
Lytic Cycle ◽  
Mammalian Host ◽  
Tail Fiber ◽  
Lytic Bacteriophage ◽  
Epithelial Surface ◽  
Content Type ◽  
Mucosal Surfaces

ABSTRACT The human gastrointestinal mucosal surface consists of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. In the gastrointestinal tract, the interaction of bacteriophages (phages) and their prokaryotic hosts influences the health of the mammalian host, especially colonization with invasive pathobionts. Antibiotics may be used, but they also kill protective commensals. Here, we report a novel phage whose lytic cycle is enhanced in intestinal environments. The tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, positions it near its bacterial host, a type of locational targeting mechanism. This finding offers the prospect of developing mucosal targeting phage to selectively remove invasive pathobiont species from mucosal surfaces. IMPORTANCE Invasive pathobionts or microbes capable of causing disease can reside deep within the mucosal epithelium of our gastrointestinal tract. Targeted effective antibacterial therapies are needed to combat these disease-causing organisms, many of which may be multidrug resistant. Here, we isolated a lytic bacteriophage (phage) that can localize to the epithelial surface by binding heparan sulfated glycans, positioning it near its host, Escherichia coli. This targeted therapy can be used to selectively remove invasive pathobionts from the gastrointestinal tract, preventing the development of disease.

scholarly journals Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy

2020 ◽  
Vol 8 (8) ◽  
pp. 1232
Author(s):  
Vittoria Mattioni Marchetti ◽  
Ibrahim Bitar ◽  
Aurora Piazza ◽  
Alessandra Mercato ◽  
Elena Fogato ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Care Facility ◽  
Genomic Analysis ◽  
Coli Strain ◽  
Beta Lactam ◽  
Aminoglycoside Resistance ◽  
Term Care ◽  
Antimicrobial Resistance Genes

Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using “Microbial Assembly”. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6′)-Ib4, ant(3″)-Ia, aph(3″)-Ib, aph(3′)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.

scholarly journals Human Microbiota-Secreted Factors Inhibit Shiga Toxin Synthesis by Enterohemorrhagic Escherichia coli O157:H7

2008 ◽  
Vol 77 (2) ◽  
pp. 783-790 ◽  
Author(s):  
Thibaut de Sablet ◽  
Christophe Chassard ◽  
Annick Bernalier-Donadille ◽  
Marjolaine Vareille ◽  
Alain P. Gobert ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Factor ◽  
Shiga Toxin ◽  
Enterohemorrhagic Escherichia Coli ◽  
Lytic Cycle ◽  
E Coli ◽  
Human Microbiota ◽  
Shiga Toxin 2 ◽  
Uremic Syndrome ◽  
Serious Disease

ABSTRACT Escherichia coli O157:H7 is a food-borne pathogen causing hemorrhagic colitis and hemolytic-uremic syndrome, especially in children. The main virulence factor responsible for the more serious disease is the Shiga toxin 2 (Stx2), which is released in the gut after oral ingestion of the organism. Although it is accepted that the amount of Stx2 produced by E. coli O157:H7 in the gut is critical for the development of disease, the eukaryotic or prokaryotic gut factors that modulate Stx2 synthesis are largely unknown. In this study, we examined the influence of prokaryotic molecules released by a complex human microbiota on Stx2 synthesis by E. coli O157:H7. Stx2 synthesis was assessed after growth of E. coli O157:H7 in cecal contents of gnotobiotic rats colonized with human microbiota or in conditioned medium having supported the growth of complex human microbiota. Extracellular prokaryotic molecules produced by the commensal microbiota repress stx 2 mRNA expression and Stx2 production by inhibiting the spontaneous and induced lytic cycle mediated by RecA. These molecules, with a molecular mass of below 3 kDa, are produced in part by Bacteroides thetaiotaomicron, a predominant species of the normal human intestinal microbiota. The microbiota-induced stx 2 repression is independent of the known quorum-sensing pathways described in E. coli O157:H7 involving SdiA, QseA, QseC, or autoinducer 3. Our findings demonstrate for the first time the regulatory activity of a soluble factor produced by the complex human digestive microbiota on a bacterial virulence factor in a physiologically relevant context.

scholarly journals Draft Genome Sequences of Enterohemorrhagic Escherichia coli O103:H2 Strains Isolated from Feces of Feedlot Cattle

2017 ◽  
Vol 5 (19) ◽  
Author(s):  
Lance W. Noll ◽  
Jay N. Worley ◽  
Xun Yang ◽  
Pragathi B. Shridhar ◽  
Jianfa Bai ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Feedlot Cattle ◽  
Enterohemorrhagic Escherichia Coli ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
Virulence Potential ◽  
A Minor

ABSTRACT The enterohemorrhagic pathotype represents a minor proportion of the Escherichia coli O103 strains shed in the feces of cattle. We report here the genome sequences of 43 strains of enterohemorrhagic E. coli (EHEC) O103:H2 isolated from feedlot cattle feces. The genomic analysis will provide information on the genetic diversity and virulence potential of bovine EHEC O103.

scholarly journals Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Marta Nisita Dewanggana ◽  
Clare Evangeline ◽  
Maurita Delia Ketty ◽  
Diana Elizabeth Waturangi ◽  
Yogiara ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bioinformatic Analysis ◽  
Food Samples ◽  
Food Preservation ◽  
Lytic Cycle ◽  
Enterotoxigenic Escherichia Coli ◽  
Tail Fiber ◽  
Bacterial Cells ◽  
Fiber Assembly ◽  
Traditional Approaches

AbstractAmong food preservation methods, bacteriophage treatment can be a viable alternative method to overcome the drawbacks of traditional approaches. Bacteriophages are naturally occurring viruses that are highly specific to their hosts and have the capability to lyse bacterial cells, making them useful as biopreservation agents. This study aims to characterize and determine the application of bacteriophage isolated from Indonesian traditional Ready-to-Eat (RTE) food to control Enterotoxigenic Escherichia coli (ETEC) population in various foods. Phage DW-EC isolated from Indonesian traditional RTE food called dawet with ETEC as its host showed a positive result by the formation of plaques (clear zone) in the bacterial host lawn. Transmission electron microscopy (TEM) results also showed that DW-EC can be suspected to belong to the Myoviridae family. Molecular characterization and bioinformatic analysis showed that DW-EC exhibited characteristics as promising biocontrol agents in food samples. Genes related to the lytic cycle, such as lysozyme and tail fiber assembly protein, were annotated. There were also no signs of lysogenic genes among the annotation results. The resulting PHACTS data also indicated that DW-EC was leaning toward being exclusively lytic. DW-EC significantly reduced the ETEC population (P ≤ 0.05) in various food samples after two different incubation times (1 day and 6 days) in chicken meat (80.93%; 87.29%), fish meat (63.78%; 87.89%), cucumber (61.42%; 71.88%), tomato (56.24%; 74.51%), and lettuce (46.88%; 43.38%).

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