scholarly journals Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

mSphere ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
David M. Gordon ◽  
Sarah Geyik ◽  
Olivier Clermont ◽  
Claire L. O’Brien ◽  
Shiwei Huang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Structure Analysis ◽  
Relative Frequency ◽  
Clonal Complex ◽  
Scale Structure ◽  
Relative Fitness ◽  
Fine Scale ◽  
Content Type ◽  
The Past ◽  
Extraintestinal Infection

ABSTRACT Escherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages. The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCE Escherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.

scholarly journals Prominence of an O75 Clonal Group (Clonal Complex 14) among Non-ST131 Fluoroquinolone-Resistant Escherichia coli Causing Extraintestinal Infections in Humans and Dogs in Australia

2012 ◽  
Vol 56 (7) ◽  
pp. 3898-3904 ◽  
Author(s):  
Joanne L. Platell ◽  
Darren J. Trott ◽  
James R. Johnson ◽  
Peter Heisig ◽  
Anke Heisig ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Clonal Complex ◽  
Resistance Mechanism ◽  
Multidrug Resistant ◽  
Phylogenetic Group ◽  
Mechanism Analysis ◽  
Content Type ◽  
Clonal Group ◽  
E Coli ◽  
Animal Medicine

ABSTRACTFluoroquinolone (FQ)-resistant extraintestinal pathogenicEscherichia coli(FQrExPEC) strains from phylogenetic group B2 are undergoing epidemic spread. Isolates belonging to phylogenetic group B2 are generally more virulent than otherE. coliisolates; therefore, resistance to FQs among group B2 isolates is concerning. Although clonal expansion of sequence type 131 (ST131) is a major factor, the contribution of additional clonal groups has not been quantified. Group B2 FQrExPEC isolates from humans (n= 250) and dogs (n= 12) in Australia were screened for ST131, a recently recognized and rapidly emerging multidrug-resistant and virulent clonal group that is important in both human and companion animal medicine. Non-ST131 isolates underwent virulence genotyping, PCR-based O typing, partial multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and FQ resistance mechanism analysis. Of 49 non-ST131 isolates (45 human, 4 canine), 49% (24 human, 2 canine) represented O-type O75 and exhibited conserved virulence genotypes (F10papAallele,iha,fimH,sat,vat,fyuA,iutA,kpsMII,usp,ompT,malX, K1/K5 capsule) and MLST allele profiles corresponding with clonal complex CC14. Two clusters, each containing canine and human isolates, were identified by PFGE (differentiated by K1 and K5 capsules). Australian FQrO75 isolates exhibited commonality with an historical FQ-susceptible O75 urosepsis isolate (also CC14). The isolation from humans and dogs of highly similar FQrderivatives of the classic O75:K1/K5 (CC14) ExPEC lineage suggests recent acquisition of FQ resistance and potential cross-host-species transfer. This lineage should be targeted with ST131 in future epidemiological investigations of FQrExPEC.

scholarly journals Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

2016 ◽  
Vol 55 (2) ◽  
pp. 616-623 ◽  
Author(s):  
Marie A. Chattaway ◽  
Ulf Schaefer ◽  
Rediat Tewolde ◽  
Timothy J. Dallman ◽  
Claire Jenkins
Keyword(s):  
Escherichia Coli ◽  
Clonal Complex ◽  
Shigella Flexneri ◽  
Bacterial Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Shigella Species ◽  
Close Phylogenetic Relationship ◽  
Initial Identification

ABSTRACTEscherichia coliandShigellaspecies are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species ofShigellaare therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982Escherichia coliandShigellasp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasiveE. coliisolates that were misidentified asShigella flexneriorS. boydiiby the kmer ID, and 8 wereS. flexneriisolates misidentified by TB&S asS. boydiidue to nonfunctionalS. flexneriO antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising bothS. boydiiandS. dysenteriaestrains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data.Shigellacan be differentiated fromE. coliand accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species ofShigella, and identified emerging pathoadapted lineages.

scholarly journals Escherichia coliSequence Type 410 Is Causing New International High-Risk Clones

mSphere ◽  
2018 ◽  
Vol 3 (4) ◽  
pp. e00337-18 ◽  
Author(s):  
Louise Roer ◽  
Søren Overballe-Petersen ◽  
Frank Hansen ◽  
Kristian Schønning ◽  
Mikala Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Risk ◽  
Antimicrobial Resistance ◽  
Sequence Type ◽  
Recurrent Infections ◽  
Content Type ◽  
E Coli ◽  
The Past ◽  
Carbapenemase Gene ◽  
Globally Distributed

ABSTRACTEscherichia colisequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410E. coliisolates from Danish patients. Furthermore,E. coliST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genesblaOXA-181andblaNDM-5of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework ofE. coliST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades inE. coliST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum β-lactamase (ESBL)-encoding geneblaCTX-M-15and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying ablaOXA-181carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene,blaNDM-5, on a conserved IncFII plasmid. From an epidemiological investigation of 49E. coliST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients withblaOXA-181- andblaNDM-5-carrying B4/H24RxC isolates. The accumulated multidrug resistance inE. coliST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus,E. coliST410 should be considered a lineage with emerging “high-risk” clones, which should be monitored closely in the future.IMPORTANCEExtraintestinal pathogenicEscherichia coli(ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of theE. coliST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively.

scholarly journals Complete Genome Sequence of a Shiga Toxin-Producing Escherichia coli O26:H11 Strain (Sequence Type 21) and Two Draft Genome Sequences of Listeria monocytogenes Strains (Clonal Complex 1 [CC1] and CC59) Isolated from Fresh Produce in Germany

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Gregor Fiedler ◽  
Jan Kabisch ◽  
Erik Brinks ◽  
Sabrina Sprotte ◽  
Christina Boehnlein ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
Shiga Toxin ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Clonal Complex ◽  
Draft Genome ◽  
Sequence Type ◽  
Genome Sequences ◽  
Content Type

ABSTRACT The complete genome sequence of a Shiga toxin-producing Escherichia coli (STEC) O26:H11 strain, MBT-5 (sequence type 21 [ST21], stx1a, stx2a, eae, ehxA), and two draft genome sequences of Listeria monocytogenes strains MBT-6 and MBT-7 belonging to the virulent sequence types 1 (ST1, clonal complex 1 [CC1]) and 59 (ST59, CC59), respectively, were determined. The strains were isolated in 2015 from ready-to-eat mixed greens in Germany.

scholarly journals De NovoCharacterization of Genes That Contribute to High-Level Ciprofloxacin Resistance in Escherichia coli

2016 ◽  
Vol 60 (10) ◽  
pp. 6353-6355 ◽  
Author(s):  
Thu Tran ◽  
Qinghong Ran ◽  
Lev Ostrer ◽  
Arkady Khodursky
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Susceptibility ◽  
Relative Fitness ◽  
Resistant Bacteria ◽  
Wild Type ◽  
Content Type ◽  
Wild Type Level ◽  
Transposon Insertion ◽  
Ciprofloxacin Resistance ◽  
High Level

ABSTRACTSensitization of resistant bacteria to existing antibiotics depends on the identification of candidate targets whose activities contribute to resistance. Using a transposon insertion library in anEscherichia colimutant that was 2,000 times less susceptible to ciprofloxacin than its parent and the relative fitness scores, we identified 19 genes that contributed to the acquired ciprofloxacin resistance and mapped the shortest genetic path that increased the antibiotic susceptibility of the resistant bacteria back to a near wild-type level.

scholarly journals Multifactorial Effects of Ambient Temperature, Precipitation, Farm Management, and Environmental Factors Determine the Level of Generic Escherichia coli Contamination on Preharvested Spinach

2015 ◽  
Vol 81 (7) ◽  
pp. 2635-2650 ◽  
Author(s):  
Sangshin Park ◽  
Sarah Navratil ◽  
Ashley Gregory ◽  
Arin Bauer ◽  
Indumathi Srinath ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Negative Binomial ◽  
Precipitation Amount ◽  
Farm Management ◽  
Content Type ◽  
E Coli ◽  
The Past ◽  
Average Maximum ◽  
Average Precipitation ◽  
Contamination Event

ABSTRACTA repeated cross-sectional study was conducted to identify farm management, environment, weather, and landscape factors that predict the count of genericEscherichia colion spinach at the preharvest level.E. coliwas enumerated for 955 spinach samples collected on 12 farms in Texas and Colorado between 2010 and 2012. Farm management and environmental characteristics were surveyed using a questionnaire. Weather and landscape data were obtained from National Resources Information databases. A two-part mixed-effect negative binomial hurdle model, consisting of a logistic and zero-truncated negative binomial part with farm and date as random effects, was used to identify factors affectingE. colicounts on spinach. Results indicated that the odds of a contamination event (non-zero versus zero counts) vary by state (odds ratio [OR] = 108.1). Odds of contamination decreased with implementation of hygiene practices (OR = 0.06) and increased with an increasing average precipitation amount (mm) in the past 29 days (OR = 3.5) and the application of manure (OR = 52.2). On contaminated spinach,E. colicounts increased with the average precipitation amount over the past 29 days. The relationship betweenE. colicount and the average maximum daily temperature over the 9 days prior to sampling followed a quadratic function with the highest bacterial count at around 24°C. These findings indicate that the odds of a contamination event in spinach are determined by farm management, environment, and weather factors. However, once the contamination event has occurred, the count ofE. colion spinach is determined by weather only.

scholarly journals Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Dong-Dong Yang ◽  
Ashley Alexander ◽  
Margie Kinnersley ◽  
Emily Cook ◽  
Amy Caudy ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Fluorescent Protein ◽  
Rank Order ◽  
Relative Fitness ◽  
Positive Density ◽  
Microbial World ◽  
Content Type ◽  
Secondary Resources ◽  
Density Dependent ◽  
Constant Environment

ABSTRACT The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new “species.” We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation. IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.

scholarly journals Fungal β-1,3-Glucan Increases Ofloxacin Tolerance of Escherichia coli in a Polymicrobial E. coli/Candida albicans Biofilm

2015 ◽  
Vol 59 (6) ◽  
pp. 3052-3058 ◽  
Author(s):  
Katrijn De Brucker ◽  
Yulong Tan ◽  
Katlijn Vints ◽  
Kaat De Cremer ◽  
Annabel Braem ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Candida Albicans ◽  
Content Type ◽  
Related Research ◽  
E Coli ◽  
The Past ◽  
Exogenous Addition ◽  
Multiple Species ◽  
Matrix Degrading Enzymes

ABSTRACTIn the past, biofilm-related research has focused mainly on axenic biofilms. However, in nature, biofilms are often composed of multiple species, and the resulting polymicrobial interactions influence industrially and clinically relevant outcomes such as performance and drug resistance. In this study, we show thatEscherichia colidoes not affectCandida albicanstolerance to amphotericin or caspofungin in anE. coli/C. albicansbiofilm. In contrast, ofloxacin tolerance ofE. coliis significantly increased in a polymicrobialE. coli/C. albicansbiofilm compared to its tolerance in an axenicE. colibiofilm. The increased ofloxacin tolerance ofE. coliis mainly biofilm specific, as ofloxacin tolerance ofE. coliis less pronounced in polymicrobialE. coli/C. albicansplanktonic cultures. Moreover, we found that ofloxacin tolerance ofE. colidecreased significantly whenE. coli/C. albicansbiofilms were treated with matrix-degrading enzymes such as the β-1,3-glucan-degrading enzyme lyticase. In line with a role for β-1,3-glucan in mediating ofloxacin tolerance ofE. coliin a biofilm, we found that ofloxacin tolerance ofE. coliincreased even more inE. coli/C. albicansbiofilms consisting of a high-β-1,3-glucan-producingC. albicansmutant. In addition, exogenous addition of laminarin, a polysaccharide composed mainly of poly-β-1,3-glucan, to anE. colibiofilm also resulted in increased ofloxacin tolerance. All these data indicate that β-1,3-glucan fromC. albicansincreases ofloxacin tolerance ofE. coliin anE. coli/C. albicansbiofilm.

scholarly journals Recent Emergence of Escherichia coli with Cephalosporin Resistance Conferred byblaCTX-Mon Washington State Dairy Farms

2015 ◽  
Vol 81 (13) ◽  
pp. 4403-4410 ◽  
Author(s):  
Margaret A. Davis ◽  
William M. Sischo ◽  
Lisa P. Jones ◽  
Dale A. Moore ◽  
Sara Ahmed ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dairy Farms ◽  
Washington State ◽  
Human Populations ◽  
Human Pathogens ◽  
Content Type ◽  
E Coli ◽  
The Past ◽  
Recent Emergence ◽  
Cephalosporin Resistance

ABSTRACTEnterobacteriaceae-associatedblaCTX-Mgenes have become globally widespread within the past 30 years. Among isolates from Washington State cattle,Escherichia colistrains carryingblaCTX-M(CTX-ME. colistrains) were absent from a set of 2008 isolates but present in a set of isolates from 2011. On 30 Washington State dairy farms sampled in 2012, CTX-ME. coliprevalence was significantly higher on eastern than on northwestern Washington farms, on farms with more than 3,000 adult cows, and on farms that recently received new animals. The addition of fresh bedding to calf hutches at least weekly and use of residual fly sprays were associated with lower prevalence of CTX-ME. coli. In Washington State, the occurrence of human pathogens carryingblaCTX-Mgenes preceded the emergence ofblaCTX-M-associatedE. coliin cattle, indicating that these resistance determinants and/or their bacterial hosts may have emerged in human populations prior to their dissemination to cattle populations.

Sign in / Sign up

Export Citation Format

Share Document