scholarly journals Horsing Around: Escherichia coli ST1250 of Equine Origin Harboring Epidemic IncHI1/ST9 Plasmid with blaCTX-M-1 and an Operon for Short-Chain Fructooligosaccharide Metabolism

2021 ◽  
Vol 65 (5) ◽  
Author(s):  
Adam Valcek ◽  
Petra Sismova ◽  
Kristina Nesporova ◽  
Søren Overballe-Petersen ◽  
Ibrahim Bitar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Integration Site ◽  
Draft Genome ◽  
Short Chain ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Plasmid Content ◽  
E Coli ◽  
Long Read

ABSTRACT The relatedness of the equine-associated Escherichia coli strain ST1250 and its single- and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total of 54 isolates of E. coli ST1250 and ST1250-SLV/DLV from healthy and hospitalized horses across Europe (Czech Republic [n = 23], The Netherlands [n = 18], Germany [n = 9], Denmark [n = 3], and France [n = 1]) from 2008 to 2017 were subjected to whole-genome sequencing. An additional 25 draft genome assemblies of E. coli ST1250 and ST1250-SLV/DLV were obtained from the public databases. The isolates were compared for genomic features, virulence genes, clade structure, and plasmid content. The complete nucleotide sequences of eight IncHI1/ST9 plasmids and one IncHI1/ST2 plasmid were obtained using long-read sequencing by PacBio or MinION. In the collection of 79 isolates, only 10 were phylogenetically close (<8 single nucleotide polymorphisms [SNP]). The majority of isolates belonged to phylogroup B1 (73/79 [92.4%]) and carried blaCTX-M-1 (58/79 [73.4%]). The plasmid content of the isolates was dominated by IncHI1 of ST9 (56/62 [90.3%]) and ST2 (6/62 [9.7%]), while 84.5% (49/58) of the blaCTX-M-1 genes were associated with the presence of the IncHI1 replicon of ST9 and 6.9% (4/58) with the IncHI1 replicon of ST2 within the corresponding isolates. The operon for the utilization of short-chain fructooligosaccharides (the fos operon) was present in 55 of 79 (69.6%) isolates, and all of these carried IncHI1/ST9 plasmids. The eight complete IncHI1/ST9 plasmid sequences showed the presence of blaCTX-M-1 and the fos operon within the same molecule. Sequences of IncHI1/ST9 plasmids were highly conserved (>98% similarity) regardless of country of origin and differed only in the structure and integration site of the multidrug resistance (MDR) region. E. coli ST1250 and ST1250-SLV/DLV are phylogenetically diverse strains associated with horses. A strong linkage of E. coli ST1250 with the epidemic multidrug resistance plasmid lineage IncHI1/ST9 carrying blaCTX-M-1 and the fos operon was identified.

scholarly journals Draft Genome Sequences of the Multiresistant Escherichia coli C20 Strain, Isolated from Domestic Chicken Gut Microbiota

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Rong-Chuan Tian ◽  
Wei Huang
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Gut Microbiota ◽  
Draft Genome ◽  
Domestic Chicken ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
Final Assembly ◽  
Chicken Gut Microbiota

ABSTRACT Escherichia coli C20, isolated from domestic chicken gut microbiota, demonstrated multidrug resistance to the tested antibiotics. Here, we present the draft genomic sequences of E. coli C20, along with that of its plasmid. The final assembly yielded a chromosome of 4,640,940 bp and plasmid of 277,380 bp, with average coverages of 146.95-fold and 35.63-fold, respectively.

scholarly journals Genotypic and Phenotypic Traits That Distinguish Neonatal Meningitis-Associated Escherichia coli from Fecal E. coli Isolates of Healthy Human Hosts

2012 ◽  
Vol 78 (16) ◽  
pp. 5824-5830 ◽  
Author(s):  
Catherine M. Logue ◽  
Curt Doetkott ◽  
Paul Mangiamele ◽  
Yvonne M. Wannemuehler ◽  
Timothy J. Johnson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Group ◽  
Neonatal Meningitis ◽  
Phenotypic Traits ◽  
Healthy Human ◽  
Content Type ◽  
Plasmid Content ◽  
E Coli ◽  
Healthy Humans ◽  
Definition Of

ABSTRACTNeonatal meningitisEscherichia coli(NMEC) is one of the top causes of neonatal meningitis worldwide. Here, 85 NMEC and 204 fecalE. coliisolates from healthy humans (HFEC) were compared for possession of traits related to virulence, antimicrobial resistance, and plasmid content. This comparison was done to identify traits that typify NMEC and distinguish it from commensal strains to refine the definition of the NMEC subpathotype, identify traits that might contribute to NMEC pathogenesis, and facilitate choices of NMEC strains for future study. A large number ofE. colistrains from both groups were untypeable, with the most common serogroups occurring among NMEC being O18, followed by O83, O7, O12, and O1. NMEC strains were more likely than HFEC strains to be assigned to the B2 phylogenetic group. Few NMEC or HFEC strains were resistant to antimicrobials. Genes that best discriminated between NMEC and HFEC strains and that were present in more than 50% of NMEC isolates were mainly from extraintestinal pathogenicE. coligenomic and plasmid pathogenicity islands. Several of these defining traits had not previously been associated with NMEC pathogenesis, are of unknown function, and are plasmid located. Several genes that had been previously associated with NMEC virulence did not dominate among the NMEC isolates. These data suggest that there is much about NMEC virulence that is unknown and that there are pitfalls to studying single NMEC isolates to represent the entire subpathotype.

scholarly journals Draft Genome Sequence of Escherichia Phage PGN829.1, Active against Highly Drug-Resistant Uropathogenic Escherichia coli

2018 ◽  
Vol 7 (20) ◽  
Author(s):  
Naveen Chaudhary ◽  
Balvinder Mohan ◽  
Neelam Taneja
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Tertiary Care ◽  
Draft Genome ◽  
Uropathogenic Escherichia Coli ◽  
North India ◽  
Drug Resistant ◽  
Content Type ◽  
E Coli ◽  
Multiple Strains

The Escherichia phage PGN829.1 was isolated from sewage of a tertiary care referral hospital in North India. It lyses multiple strains of highly drug-resistant uropathogenic E. coli.

scholarly journals Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Jee Loon Foo ◽  
Heather M. Jensen ◽  
Robert H. Dahl ◽  
Kevin George ◽  
Jay D. Keasling ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Production Capacity ◽  
Short Chain ◽  
Methionine Biosynthesis ◽  
Content Type ◽  
E Coli ◽  
Improve Production ◽  
Starting Point ◽  
Microbial Tolerance

ABSTRACT Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerance phenotypes belonged to diverse functional groups, such as oxidative stress response (soxS, fpr, and nrdH), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production. IMPORTANCE The use of microbial host platforms for the production of bulk commodities, such as chemicals and fuels, is now a focus of many biotechnology efforts. Many of these compounds are inherently toxic to the host microbe, which in turn places a limit on production despite efforts to optimize the bioconversion pathways. In order to achieve economically viable production levels, it is also necessary to engineer production strains with improved tolerance to these compounds. We demonstrate that microbial tolerance engineering using transcriptomics data can also identify targets that improve production. Our results include an exporter and a methionine biosynthesis regulator that improve isopentenol production, providing a starting point to further engineer the host for biogasoline production.

scholarly journals Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces

2012 ◽  
Vol 194 (18) ◽  
pp. 5149-5150 ◽  
Author(s):  
Mincheol Kim ◽  
Hana Yi ◽  
Yong-Joon Cho ◽  
Jeonghwan Jang ◽  
Hor-Gil Hur ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
South Korea ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Enteric Bacterium ◽  
Content Type ◽  
E Coli

ABSTRACTAn enteric bacterium,Escherichia coliW26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging toE. coliphylogroup B1.

scholarly journals Temporal Trends in Antimicrobial Resistance and Virulence-Associated Traits within the Escherichia coli Sequence Type 131 Clonal Group and ItsH30 andH30-Rx Subclones, 1968 to 2012

2014 ◽  
Vol 58 (11) ◽  
pp. 6886-6895 ◽  
Author(s):  
Bente Olesen ◽  
Jakob Frimodt-Møller ◽  
Rikke Fleron Leihof ◽  
Carsten Struve ◽  
Brian Johnston ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Temporal Trends ◽  
Sequence Type ◽  
Esbl Production ◽  
Content Type ◽  
E Coli ◽  
Biofilm Production

ABSTRACTTo identify possible explanations for the recent global emergence ofEscherichia colisequence type (ST) 131 (ST131), we analyzed temporal trends within ST131 O25 for antimicrobial resistance, virulence genes, biofilm formation, and theH30 andH30-Rx subclones. For this, we surveyed the WHOE. coliandKlebsiellaCentre'sE. colicollection (1957 to 2011) for ST131 isolates, characterized them extensively, and assessed them for temporal trends. Overall, antimicrobial resistance increased temporally in prevalence and extent, due mainly to the recent appearance of theH30 (1997) andH30-Rx (2005) ST131 subclones. In contrast, neither the total virulence gene content nor the prevalence of biofilm production increased temporally, although non-H30 isolates increasingly qualified as extraintestinal pathogenicE. coli(ExPEC). Whereas virotype D occurred from 1968 forward, virotypes A and C occurred only after 2000 and 2002, respectively, in association with theH30andH30-Rx subclones, which were characterized by multidrug resistance (including extended-spectrum-beta-lactamase [ESBL] production:H30-Rx) and absence of biofilm production. Capsular antigen K100 occurred exclusively amongH30-Rx isolates (55% prevalence). Pulsotypes corresponded broadly with subclones and virotypes. Thus, ST131 should be regarded not as a unitary entity but as a group of distinctive subclones, with its increasing antimicrobial resistance having a strong clonal basis, i.e., the emergence of theH30 andH30-Rx ST131 subclones, rather than representing acquisition of resistance by diverse ST131 strains. Distinctive characteristics of theH30-Rx subclone—including specific virulence genes (iutA,afaanddra,kpsII), the K100 capsule, multidrug resistance, and ESBL production—possibly contributed to epidemiologic success, and some (e.g., K100) might serve as vaccine targets.

scholarly journals Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Meat

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Aixia Xu ◽  
James R. Johnson ◽  
Shiowshuh Sheen ◽  
David S. Needleman ◽  
Christopher Sommers
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Meat Products ◽  
Chicken Meat ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
Safety Research ◽  
Pathogenic Escherichia Coli ◽  
Retail Chicken Meat

ABSTRACT Potential extraintestinal pathogenic Escherichia coli strains DP254, WH333, WH398, F356, FEX675, and FEX725 were isolated from retail chicken meat products. Here, we report the draft genome sequences for these six E. coli isolates, which are currently being used in food safety research.

scholarly journals Draft Genome Sequences of Escherichia coli Strains Isolated at Calving from the Uterus, Vagina, Vulva, and Rectoanal Junction of a Dairy Cow That Later Developed Metritis

2017 ◽  
Vol 5 (11) ◽  
Author(s):  
Soo Jin Jeon ◽  
Federico Cunha ◽  
Amber Ginn ◽  
KwangCheol Casey Jeong ◽  
Klibs N. Galvão
Keyword(s):  
Escherichia Coli ◽  
Dairy Cow ◽  
Phylogenetic Relationships ◽  
Draft Genome ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
Insight Into

ABSTRACT Escherichia coli is involved in the pathogenicity of metritis in cows. We report here the genome sequences of E. coli strains isolated at calving from the uterus, vagina, vulva, and rectoanal junction of a dairy cow that later developed metritis. The genomic similarities will give an insight into phylogenetic relationships among strains.

scholarly journals Draft Genome Sequences of Two Enteroinvasive Escherichia coli Strains Representative of Major Enteroinvasive E. coli Clades

2021 ◽  
Vol 10 (23) ◽  
Author(s):  
Michael J. Sikorski ◽  
Tracy H. Hazen ◽  
Gopi Vyas ◽  
Jane M. Michalski ◽  
David A. Rasko
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Genomic Data ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
E Coli ◽  
Clinical Illness

There are six described pathotypes of Escherichia coli that cause significant clinical illness in humans. Enteroinvasive E. coli (EIEC) strains have been shown to be separated into three phylogenomic clades. To add to a limited body of EIEC genomic data, we report two high-quality draft genomes representing different EIEC phylogenomic clades.

scholarly journals Draft Genome Sequences of 113 Escherichia coli Strains Isolated from Intramammary Infections in Dairy Cattle

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Dongyun Jung ◽  
Soyoun Park ◽  
Janina Ruffini ◽  
Simon Dufour ◽  
Jennifer Ronholm
Keyword(s):  
Escherichia Coli ◽  
Dairy Cattle ◽  
Draft Genome ◽  
Bovine Mastitis ◽  
Holstein Cows ◽  
Genome Sequences ◽  
Content Type ◽  
Intramammary Infections ◽  
E Coli ◽  
Etiological Agents

ABSTRACT Escherichia coli is one of the most common etiological agents responsible for clinical bovine mastitis. Here, we report the draft genome sequences and annotations of 113 E. coli strains that were isolated from Holstein cows with intramammary infections in Canada.

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