scholarly journals Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Mo Jia ◽  
Ifigenia Geornaras ◽  
Jennifer N. Martin ◽  
Keith E. Belk ◽  
Hua Yang
Keyword(s):  
Escherichia Coli ◽  
Metabolic Pathway ◽  
Genome Analysis ◽  
Feedlot Cattle ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Foodborne Outbreak ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Red Recombination

A comparative whole genome analysis was performed on three newly sequenced Escherichia coli O157:H7 strains with different stx profiles, previously isolated from feedlot cattle [C1-010 (stx1−, stx2c+), C1-057 (stx−), and C1-067 (stx1+, stx2a+)], as well as five foodborne outbreak strains and six stx-negative strains from NCBI. Phylogenomic analysis demonstrated that the stx2c-carrying C1-010 and stx-negative C1-057 strains were grouped with the six NCBI stx-negative E. coli O157:H7 strains in Cluster 1, whereas the stx2a-carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one stx2a-carrying strain, and the six NCBI stx-negative strains and identify their prophages at the stx insertion sites. All stx-carrying prophages contained both the three Red recombination genes (exo, bet, gam) and their repressor cI. On the other hand, the majority of the stx-negative prophages carried only the three Red recombination genes, but their repressor cI was absent. In the absence of the repressor cI, the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of stx genes. We further investigated each of the 10 selected E. coli O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two stx2a-carrying strains and one in the single stx2c-carrying and seven stx-negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in stx2a-carrying E. coli O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the stx2c-carrying and stx-negative E. coli O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic E. coli O157:H7 in livestock and downstream food production environments.

scholarly journals First Report of the Globally Disseminated IncX4 Plasmid Carrying themcr-1Gene in a Colistin-Resistant Escherichia coli Sequence Type 101 Isolate from a Human Infection in Brazil

2016 ◽  
Vol 60 (10) ◽  
pp. 6415-6417 ◽  
Author(s):  
Miriam R. Fernandes ◽  
John A. McCulloch ◽  
Marco A. Vianello ◽  
Quézia Moura ◽  
Paula J. Pérez-Chaparro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Analysis ◽  
Human Infection ◽  
Sequence Type ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Diabetic Foot Infection ◽  
E Coli ◽  
Food Animal

ABSTRACTA colistin-resistantEscherichia colistrain was recovered from a patient with a diabetic foot infection in Brazil. Whole-genome analysis revealed that theE. coliisolate belonged to the widespread sequence type (ST) 101 and harbored themcr-1gene on an IncX4 plasmid that was highly similar tomcr-1-bearing IncX4 plasmids that were recently identified inEnterobacteriaceaefrom food, animal, and human samples recovered on different continents. These results suggest that self-transmissible IncX4-type plasmids may represent promiscuous plasmids contributing to the intercontinental spread of themcr-1gene.

scholarly journals A Spontaneous rapZ Mutant Impairs Infectivity of Lytic Bacteriophage vB_EcoM_JS09 against Enterotoxigenic Escherichia coli

mSphere ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Yan Zhou ◽  
Hongduo Bao ◽  
Hui Zhang ◽  
Maoda Pang ◽  
Shujiao Zhu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Analysis ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Lytic Bacteriophage ◽  
Whole Genome Analysis ◽  
Content Type ◽  
E Coli ◽  
Stop Mutation ◽  
Phage Receptor

ABSTRACT Our understanding of the mechanisms underlying phage-bacterium interactions remains limited. In Escherichia coli, RapZ regulates glucosamine-6-phosphate (GlcN6P) metabolism, the formation of which initiates synthesis of the bacterial cell envelope, including lipopolysaccharides (LPS). However, the role of RapZ, if any, on phage infectivity remains to be investigated. Here, we isolated strains of enterotoxigenic E. coli (ETEC) resistant to its specific lytic bacteriophage vB_EcoM_JS09 (JS09) in a phage aerosol spray experiment. Whole-genome analysis of phage-resistant bacteria revealed the rapZ gene acquired a premature stop mutation at amino acid 227. Here, we report that the mutation in the rapZ gene confers resistance by inhibiting 93.5% phage adsorption. Furthermore, this mutation changes the morphology of phage plaques, reduces efficiency of plating and phage propagation efficiency, and impairs the infectivity of phage JS09 against ETEC. Using scanning electron microscopy assays, we attribute the inability of the phage to adsorb to the loss of receptors in strains with defective RapZ. Analysis of the LPS profile shows that strains with defective RapZ inhibit phage infection by changing the LPS profile in E. coli. Preincubation of phage JS09 with LPS extracted from a wild-type (WT) strain blocked infection, suggesting LPS is the host receptor for phage JS09 adsorption. Our data uncover the mechanism by which ETEC resists infection of phage JS09 by mutating the rapZ gene and then increasing the expression of glmS and changing the phage receptor-LPS profile. These findings provide insight into the function of the rapZ gene for efficient infection of phage JS09. IMPORTANCE The development of phage-resistant bacteria is a challenging problem for phage therapy. However, our knowledge of phage resistance mechanisms is still limited. RapZ is an RNase adaptor protein encoded by the rapZ gene and plays an important function in Gram-positive and Gram-negative bacteria. Here, we report the whole-genome analysis of a phage-resistant enterotoxigenic Escherichia coli (ETEC) strain, which revealed that the rapZ gene acquired a premature stop mutation (E227Stop). We show that the premature stop mutation of rapZ impairs the infectivity of phage JS09 in ETEC. Furthermore, our findings indicate that ETEC becomes resistant against the adsorption and infection of phage JS09 by mutating the rapZ gene, increasing the expression of glmS, and changing the phage receptor-LPS profile. It is also first reported here that RapZ is essential for efficient infection of phage JS09.

scholarly journals Phylogenomic analysis of Pseudomonas nitroreducens strains FY43 and FY47

2022 ◽  
pp. 1-11
Author(s):  
Xue Li Tan ◽  
Wei Yee Wee ◽  
Boon Chin Tan ◽  
Chee How Teo
Keyword(s):  
Genome Analysis ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Novel ◽  
Species Classification ◽  
Whole Genome Analysis ◽  
Pseudomonas Nitroreducens ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Diversity Studies

Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.

scholarly journals Association of Genetically Related Escherichia coli Strains with Ulcerative Colitis - A Preliminary Study

2011 ◽  
Vol 2 (2) ◽  
pp. 93-96
Author(s):  
Ritu Agarwal ◽  
Chaman Deep ◽  
Saurabh K Patel ◽  
Ashok K Jain ◽  
Gopal Nath
Keyword(s):  
Escherichia Coli ◽  
Ulcerative Colitis ◽  
Genetic Relatedness ◽  
Bacterial Species ◽  
Rectal Mucosa ◽  
Whole Genome ◽  
Medical Sciences ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Major Cluster

Objective: To explore the genetic relatedness among the Escherichia coli isolates recovered from rectal mucosa of patients with Ulcerative Colitis(UC) as well as from non specific diarrhoea patients by using ERIC PCR (whole genome analysis). Material & Methods: A total of 44 strains of E coli, each from patients suffering from UC with exacerbation while on maintenance therapy, were isolated to see if there is any association with specific genotype of E coli with the clini-cal condition. For comparison, 20 strains of E coli were also isolated from patients suffering from non specific diarrhoea. These isolates were subjected to ERIC PCR for analysing similarity/ dissimilarity with each other based on the distribution of ERIC sequences in the whole genome of the bacterial species. Results: The dendrogram prepared on the basis of banding pattern showed that majority of UC patients (39/44, 88.6%) grouped in to one major cluster while second major cluster comprised mostly strains isolated from patients with non specific diarrhoea i.e. controls (17/18, 94.4%). Moreover, in the cluster representing UC patients, a total of 11 strains were observed to be genotypically similar followed by 8 strains by ERIC PCR. Conclusion: Our results strongly indicate that specific Escherichia coli strains may be involved/ associated with UC and its relapse. Key Words: Ulcerative colitis; Escherichia coli; ERIC; PCR DOI: http://dx.doi.org/10.3126/ajms.v2i2.4769Asian Journal of Medical Sciences 2 (2011) 93-96

Whole-genome analysis of EC129, an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli ST167 strain isolated from Japan

2019 ◽  
Vol 18 ◽  
pp. 148-150 ◽  
Author(s):  
Yoko Nukui ◽  
Alafate Ayibieke ◽  
Makoto Taniguchi ◽  
Yoshibumi Aiso ◽  
Yuka Shibuya ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
M 14

Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli

2004 ◽  
Vol 322 (3) ◽  
pp. 1038-1044 ◽  
Author(s):  
Peter M. Power ◽  
Robert A. Jones ◽  
Ifor R. Beacham ◽  
Carolyn Bucholtz ◽  
Michael P. Jennings
Keyword(s):  
Escherichia Coli ◽  
Genome Analysis ◽  
Whole Genome ◽  
Signal Sequences ◽  
Whole Genome Analysis ◽  
Optimal Codons ◽  
High Incidence
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