Possible Dissemination of Escherichia coli Sequence Type 410 Closely Related to B4/H24RxC in Ghana

Extra-intestinal pathogenic Escherichia coli (ExPEC) is one of the world’s leading causes of bloodstream infections with high mortality. Sequence type 410 (ST410) is an emerging ExPEC clone resistant to a wide range of antibiotics. In this study, we investigated the epidemiology of 21 ST410 E. coli isolates from two Ghanaian hospitals. We also investigated the isolates within a global context to provide further insight into the dissemination of this highly pathogenic clone. A phylogenetic tree of the 21 isolate genomes, along with 102 others from global collection, was constructed representing the ensuing clades and sub-clades of the ST: A/H53, B2/H24R, B3/H24Rx, and B4/H24RxC. The carbapenem-resistant sub-clade B4/H24RxC is reported to have emerged in the early 2000s when ST410 acquired an IncX3 plasmid carrying a blaOXA–181 carbapenemase gene, and a second carbapenemase gene, blaNDM–5, on a conserved IncFII plasmid in 2014. We identified, in this study, one blaOXA–181–carrying isolate belonging to B4/H24RxC sub-lineage and one carrying blaNDM–1 belonging to sub-lineage B3/H24Rx. The blaOXA–181 gene was found on a 51kb IncX3 plasmid; pEc1079_3. The majority (12/21) of our Ghanaian isolates were clustered with international strains described by previous authors as closely related strains to B4/H24RxC. Six others were clustered among the ESBL-associated sub-lineage B3/H24Rx and three with the globally disseminated sub-lineage B4/H24RxC. The results show that this highly pathogenic clone is disseminated in Ghana and, given its ability to transmit between hosts, it poses a serious threat and should be monitored closely.

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Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study

10.1101/2021.06.18.21258557 ◽

2021 ◽

Author(s):

Elita Jauneikaite ◽

Kate Honeyford ◽

Oliver Blandy ◽

Mia Mosavie ◽

Max Pearson ◽

...

Keyword(s):

Escherichia Coli ◽

Length Of Stay ◽

Single Agent ◽

Bloodstream Infections ◽

Outcome Data ◽

Sequence Type ◽

Adverse Outcomes ◽

Beta Lactam ◽

E Coli ◽

Sequence Types

Background Escherichia coli bloodstream infections have increased rapidly in the UK, for reasons that are unclear. The relevance of highly fit, or multi-drug resistant lineages such as ST131 to overall E. coli disease burden remains to be fully determined. We set out to characterise the prevalence of E. coli multi-locus sequence types (MLST) and determine if these were associated with adverse outcomes in an urban population of E. coli bacteraemia patients. Methods We undertook whole genome sequencing of E. coli blood isolates from all patients with diagnosed E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned multi-locus sequence types to all isolates. Isolate sequence types were linked to routinely collected antimicrobial susceptibility, patient demographic, and clinical outcome data to explore relationships between the E. coli sequence types, patient factors, and outcomes. Findings A total of 551 E. coli genomes were available for analysis. More than half of these cases were caused by four E. coli sequence types: ST131 (21%), ST73 (15%), ST69 (9%) and ST95 (8%). E. coli genotype ST131-C2 was associated with non-susceptibility to quinolones and third-generation cephalosporins, and also to amoxicillin, augmentin, gentamicin and trimethoprim. An association between the ST131-C2 lineage and longer length-of-stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli sequence type and mortality. However, a number of unexpected associations were identified, including gentamicin non-susceptibility, ethnicity, and sex that might influence mortality and length-of-stay, requiring further research. Interpretation Although E. coli sequence type was associated with antimicrobial non-susceptibility patterns and length-of-stay, we did not find that E. coli sequence type was associated with increased mortality. Where ST131 is prevalent, caution is required when pairing beta-lactam agents with gentamicin or using single agent aminoglycosides.

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Outbreak Caused by NDM-1- and RmtB-Producing Escherichia coli in Bulgaria

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02571-13 ◽

2014 ◽

Vol 58 (4) ◽

pp. 2472-2474 ◽

Cited By ~ 34

Author(s):

Laurent Poirel ◽

Encho Savov ◽

Arzu Nazli ◽

Angelina Trifonova ◽

Iva Todorova ◽

...

Keyword(s):

Escherichia Coli ◽

16S Rrna ◽

Sequence Type ◽

Content Type ◽

E Coli ◽

Carbapenem Resistant ◽

The World ◽

High Level ◽

16S Rrna Methylase ◽

Level Resistance

ABSTRACTTwelve consecutive carbapenem-resistantEscherichia coliisolates were recovered from patients (infection or colonization) hospitalized between March and September 2012 in different units at a hospital in Bulgaria. They all produced the carbapenemase NDM-1 and the extended-spectrum-β-lactamase CTX-M-15, together with the 16S rRNA methylase RmtB, conferring high-level resistance to all aminoglycosides. All those isolates were clonally related and belonged to the same sequence type, ST101. In addition to being the first to identify NDM-producing isolates in Bulgaria, this is the very first study reporting an outbreak of NDM-1-producingE. coliin the world.

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

mSphere ◽

10.1128/msphere.00337-18 ◽

2018 ◽

Vol 3 (4) ◽

pp. e00337-18 ◽

Cited By ~ 51

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.

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Draft Genomic Sequences of Three Escherichia coli Sequence Type 131 Isolates (H45, H43ii, and H43iii) from Patients in Lagos, Nigeria

Microbiology Resource Announcements ◽

10.1128/mra.00076-20 ◽

2020 ◽

Vol 9 (17) ◽

Author(s):

Yishan Yang ◽

Christopher H. Sommers ◽

Eyitayo O. Adenipekun ◽

Marina Ceruso ◽

Charlene R. Jackson ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Sequence Type ◽

Urine Samples ◽

Genomic Sequences ◽

Content Type ◽

E Coli

Escherichia coli sequence type 131 (ST131) has recently emerged as a leading multidrug-resistant pathogen that causes urinary tract and bloodstream infections in humans. Here, we report the draft genomic sequences of three E. coli ST131 isolates, H45, H43ii, and H43iii, from urine samples of patients in Lagos, Nigeria.

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Molecular Characterization ofblaNDM-5Carried on an IncFII Plasmid in an Escherichia coli Isolate from a Nontraveler Patient in Spain

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04040-14 ◽

2014 ◽

Vol 59 (1) ◽

pp. 659-662 ◽

Cited By ~ 41

Author(s):

Cristina Pitart ◽

Mar Solé ◽

Ignasi Roca ◽

Angely Román ◽

Asunción Moreno ◽

...

Keyword(s):

Escherichia Coli ◽

Female Patient ◽

Urine Culture ◽

Sequence Type ◽

Content Type ◽

Pcr Screening ◽

Coli Isolate ◽

E Coli ◽

Carbapenem Resistant ◽

Indian Origin

ABSTRACTA carbapenem-resistantEscherichia coliisolate (sequence type 448 [ST448]) was recovered from a urine culture of a female patient with no recent record of traveling. PCR screening identified the presence ofblaNDM-5,blaTEM-1,blaOXA-1,blaCMY-42, andrmtB. blaNDM-5was carried in a conjugative IncFII-type plasmid (90 kb) together withblaTEM-1andrmtB. The genetic environment ofblaNDM-5showed a structure similar to those of pMC-NDM and pGUE-NDM, identified in Poland and France inE. coliof African and Indian origin, respectively.

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Shedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: an outbreak in 2018

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.39.1900071 ◽

2019 ◽

Vol 24 (39) ◽

Cited By ~ 6

Author(s):

Aurélien Nigg ◽

Michael Brilhante ◽

Valentina Dazio ◽

Mathieu Clément ◽

Alexandra Collaud ◽

...

Keyword(s):

Escherichia Coli ◽

Prospective Observational Study ◽

Core Genome ◽

Ad Hoc ◽

Companion Animals ◽

E Coli ◽

Carbapenem Resistant ◽

Carbapenemase Gene ◽

Carbapenem Resistant Enterobacteriaceae

Background Carbapenem-resistant Enterobacteriaceae pose a serious threat to public health worldwide, and the role of companion animals as a reservoir is still unclear. Aims This 4-month prospective observational study evaluated carriage of carbapenem-resistant Enterobacteriaceae at admission and after hospitalisation in a large referral hospital for companion animals in Switzerland. Methods Rectal swabs of dogs and cats expected to be hospitalised for at least 48 h were taken from May to August 2018 and analysed for the presence of carbapenem-resistant Enterobacteriaceae using selective agar plates. Resistant isolates were further characterised analysing whole genome sequences for resistance gene and plasmid identification, and ad hoc core genome multilocus sequence typing. Results This study revealed nosocomial acquisition of Escherichia coli harbouring the carbapenemase gene bla OXA-181, the pAmpC cephalosporinase gene bla CMY-42 as well as quinolone resistance associated with qnrS1 and mutations in the topoisomerases II (GyrA) and IV (ParC). The bla OXA-181 and qnrS1 genes were identified on a 51 kb IncX3 plasmid and bla CMY-42 on a 47 kb IncI1 plasmid. All isolates belonged to sequence type ST410 and were genetically highly related. This E. coli clone was detected in 17 of 100 dogs and four of 34 cats after hospitalisation (21.6%), only one of the tested animals having tested positive at admission (0.75%). Two positive animals were still carriers 4 months after hospital discharge, but were negative after 6 months. Conclusions Companion animals may acquire carbapenemase-producing E. coli during hospitalisation, posing the risk of further dissemination to the animal and human population and to the environment.

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Virulence of Escherichia coli Clinical Isolates in a Murine Sepsis Model in Relation to Sequence Type ST131 Status, Fluoroquinolone Resistance, and Virulence Genotype

Infection and Immunity ◽

10.1128/iai.06388-11 ◽

2012 ◽

Vol 80 (4) ◽

pp. 1554-1562 ◽

Cited By ~ 77

Author(s):

James R. Johnson ◽

Stephen B. Porter ◽

George Zhanel ◽

Michael A. Kuskowski ◽

Erick Denamur

Keyword(s):

Escherichia Coli ◽

Study Groups ◽

Sequence Type ◽

Clinical Isolates ◽

Fluoroquinolone Resistance ◽

Content Type ◽

E Coli ◽

Sepsis Model ◽

Virulence Potential ◽

Wide Range

ABSTRACTEscherichia colisequence type ST131 (O25b:H4) has emerged over the past decade as a globally disseminated, multidrug-resistant pathogen. Unlike traditional antimicrobial-resistantE. coli, ST131 derives from virulence-associated phylogenetic group B2 and exhibits extraintestinal virulence factors. This, plus preliminary evidence of virulence in experimental animals, has suggested that ST131's epidemic emergence may be due to high virulence potential, compared with otherE. colitypes. To test this hypothesis, we compared a large number of matched ST131 and non-ST131E. coliclinical isolates, both fluoroquinolone resistant and susceptible, plus isolates from classic extraintestinal pathogenicE. coli(ExPEC) sequence types (STs) and case report ST131 household transmission isolates, for virulence in a mouse subcutaneous sepsis model. Overall, in mice, the study isolates produced a wide range of lethality and clinical illness. However, neither ST131 status nor fluoroquinolone phenotype correlated with this diversity of illness severity, which occurred within each of the 6 study groups. In contrast, multiple known or suspected ExPEC virulence genes, includingpap(P fimbriae),vat(vacuolating toxin),kpsMII (group 2 capsule),ibeA(invasion of brain endothelium), andclbB/N(colibactin synthesis), plus molecularly defined ExPEC status, were significantly associated with virulence. These findings point away from ST131 isolates as having higher virulence potential compared with otherE. colitypes in causing invasive extraintestinal infections and suggest instead that ST131's epidemiological success may reflect enhanced fitness for upstream steps in pathogenesis or in colonization and transmission. Additionally, the extensive within-ST virulence diversity suggests an opportunity to compare closely related strains to identify the responsible genetic determinants.

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1054. Biofilm Formation Among Escherichia coli Bloodstream Infection Isolates Is Associated With Source of Bacteremia and Bacterial Sequence Type

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.891 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S315-S315

Author(s):

Carolyn Chang ◽

Felicia Ruffin ◽

Vance G Fowler ◽

Joshua T Thaden

Keyword(s):

Escherichia Coli ◽

Biofilm Formation ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Clinical Impact ◽

Sequence Type ◽

Apache Ii Score ◽

E Coli ◽

Biofilm Production ◽

Bacterial Sequence

Abstract Background The clinical impact of Escherichia coli biofilm formation is unknown. Methods Adults with E. coli bloodstream infections (BSI) were prospectively enrolled from 2002 to 2015. All E. coli isolates were genotyped using Multilocus sequence typing (MLST) and underwent crystal violet biofilm formation assay quantified by absorbance at 540 nm (OD540) in triplicate. Associations between biofilm formation and patient/bacterial characteristics were characterized by t-tests and ANOVA tests. Results Ninety-eight percent (186) of the 189 isolates formed detectable biofilms. Bacterial sequence type (ST) was associated with biofilm formation (P < 0.001), as ST73 (average OD540 = 0.017) and ST393 (average OD540 = 0.016) had higher average biofilm formation while ST69 (average OD540 = 0.007) and ST405 (average OD540 = 0.002) had lower biofilm formation. E. coli isolates with non-multidrug-resistant (non-MDR) phenotype were associated with increased biofilm formation (MDR: average OD540 = 0.006; average non-MDR: OD540 = 0.01; P = 0.003). BSI isolates arising from pneumonia or urine/pyelonephritis were associated with the highest biofilm production (P = 0.04). No associations were identified between biofilm formation and route of infection, APACHE-II score, mortality, or complications of BSI. Conclusion In this prospective study of E. coli BSI isolates, biofilm formation was associated with ST, non-MDR phenotype, and BSI source. Disclosures All authors: No reported disclosures.

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Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections.

10.1101/2021.04.17.440283 ◽

2021 ◽

Author(s):

Oliver Mounsey ◽

Kezia Wareham ◽

Ashley Hammond ◽

Jacqueline Findlay ◽

Virginia C Gould ◽

...

Keyword(s):

Escherichia Coli ◽

United Kingdom ◽

Urinary Tract ◽

Opportunistic Infections ◽

Bloodstream Infections ◽

E Coli ◽

The United Kingdom ◽

Wide Range ◽

Faecal Carriage ◽

Tract Infections

We report a survey (August 2017 to March 2018) and risk factor analysis of faecal carriage of antibacterial-resistant (ABR) Escherichia coli in 223 sixteen-week-old dogs in the United Kingdom. Raw feeding was associated with the presence of E. coli resistant to fluoroquinolones, tetracycline, amoxicillin, and streptomycin, but not to cefalexin or cefotaxime. Whole genome sequencing of 30 fluoroquinolone-resistant (FQ-R), 22 cefotaxime-resistant (CTX-R) and seven dual FQ-R/CTX-R E. coli isolates showed a wide range of sequence types (STs), an approximately 50:50 split of CTX-M:AmpC-mediated CTX-R, and almost exclusively mutational FQ-R dominated by ST744 and ST162. Comparisons between E. coli isolates from puppies known to be located within a 50 x 50 km region with those isolated from human urinary tract and bloodstream infections (isolated in parallel in the same region) identified a clone of ST963 E. coli carrying chromosomal blaCMY-2 in two puppies and causing two urinary tract infections and one bloodstream infection. Furthermore, an ST744 FQ-R clone was carried by one puppy and caused one urinary tract infection. Accordingly, we conclude that raw feeding is associated with carriage of ABR E. coli in dogs even at sixteen weeks of age and that bacteria carried by these dogs are shared with humans and cause serious opportunistic infections. We therefore suggest that those who feed their dogs raw meat seriously consider the potential ABR-transmission threat their pet may become as a result and deploy appropriate hygiene practices in mitigation.

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Complete genomic characterisation of two Escherichia coli lineages responsible for a cluster of carbapenem resistant infections in a Chinese hospital

10.1101/100941 ◽

2017 ◽

Cited By ~ 1

Author(s):

Zhiyong Zong ◽

Samuel Fenn ◽

Christopher Connor ◽

Yu Feng ◽

Alan McNally

Keyword(s):

Escherichia Coli ◽

Carbapenem Resistance ◽

Health Crisis ◽

West China Hospital ◽

E Coli ◽

Carbapenem Resistant ◽

Carbapenemase Gene ◽

Intergenic Regions ◽

Resistant Strains ◽

Drug Resistant Strains

AbstractThe increase in infections as a result of multi-drug resistant strains of Escherichia coli is a global health crisis. The emergence of globally disseminated lineages of E. coli carrying ESBL genes has been well characterised. An increase in strains producing carbapenemase enzymes and mobile colistin resistance is now being reported, but to date there is little genomic characterisation of such strains. Routine screening of patients within an ICU of West China Hospital identified a number of E. coli carrying the blaNDM-5 carbapenemase gene, found to be two distinct clones, E. coli ST167 and ST617. Interrogation of publically available data shows isolation of ESBL and carbapenem resistant strains of both lineages from clinical cases across the world. Further analysis of a large collection of publically available genomes shows that ST167 and ST617 have emerged in distinct patterns from the ST10 clonal complex of E. coli, but share evolutionary events involving switches in LPS genetics, intergenic regions and anaerobic metabolism loci. These may be evolutionary events which underpin the emergence of carbapenem resistance plasmid carriage in E. coli.

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