8 results on '"Blane, Beth"'
Search Results
2. Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients
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Moradigaravand, Danesh, Gouliouris, Theodore, Blane, Beth, Naydenova, Plamena, Ludden, Catherine, Crawley, Charles, Brown, Nicholas M, Török, M Estée, Parkhill, Julian, Peacock, Sharon J, Ludden, Catherine [0000-0001-9503-0744], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
Within-host evolution ,lcsh:QH426-470 ,Research ,lcsh:R ,Enterococcus faecium ,lcsh:Medicine ,Bacteremia ,Genome sequencing ,Polymorphism, Single Nucleotide ,Evolution, Molecular ,lcsh:Genetics ,Immunocompromised Host ,Drug Resistance, Bacterial ,Humans ,Genome, Bacterial ,Gram-Positive Bacterial Infections - Abstract
Background Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. Methods We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment. Results A phylogenetic tree based on single nucleotide polymorphisms (SNPs) in the core genome of the 180 isolates demonstrated several distinct clones. This was highly concordant with the population structure inferred by Bayesian methods, which contained four main BAPS (Bayesian Analysis of Population Structure) groups. The majority of isolates from each patient resided in a single group, but all four patients also carried minority populations in stool from multiple phylogenetic groups. Bloodstream isolates from each case belonged to a single BAPS group, which differed in all four patients. Analysis of 87 isolates (56 from blood) belonging to a single BAPS group that were cultured from the same patient over 54 days identified 30 SNPs in the core genome (nine intergenic, 13 non-synonymous, eight synonymous), and 250 accessory genes that were variably present. Comparison of these genetic variants in blood isolates versus those from stool or environment did not identify any variants associated with bloodstream infection. The substitution rate for these isolates was estimated to be 128 (95% confidence interval 79.82 181.77) mutations per genome per year, more than ten times higher than previous estimates for E. faecium. Within-patient variation in vancomycin resistance associated with vanA was common and could be explained by plasmid loss, or less often by transposon loss. Conclusions These findings demonstrate the diversity of E. faecium carriage by individual patients and significant within-host diversity of E. faecium, but do not provide evidence for adaptive genetic variation associated with invasion. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0507-0) contains supplementary material, which is available to authorized users.
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- 2017
3. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.
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Peacock, Sharon, Runcharoen, Chakkaphan, Paksanont, Suporn, Chantratita, Narisara, Raven, Kathy, Reuter, Sandra, Blane, Beth, Kallonen, Teemu, Parkhill, Julian, Thammachote, Jeeranan, and Anun, Suthatip
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NUCLEOTIDE sequencing ,BACTERIAL genetics ,ESCHERICHIA coli ,BETA lactamases ,REPRODUCTIVE isolation ,PATIENTS ,AGRICULTURAL wastes ,CANALS - Abstract
Background: Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. Methods: We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. Results: The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples ( n = 2) or a hospital sewer ( n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical ( n = 1) and canal water ( n = 2)) were resistant to colistin (encoded by mcr- 1); no isolates were resistant to both carbapenems and colistin. Conclusions: Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous. [ABSTRACT FROM AUTHOR]
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- 2017
- Full Text
- View/download PDF
4. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.
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Brodrick, Hayley J., Raven, Kathy E., Kallonen, Teemu, Jamrozy, Dorota, Blane, Beth, Brown, Nicholas M., Martin, Veronique, Török, M. Estée, Parkhill, Julian, and Peacock, Sharon J.
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LONG-term care facilities ,MULTIDRUG resistance in bacteria ,ESCHERICHIA coli ,BACTERIAL genetics ,BETA lactamase genetics ,NUCLEOTIDE sequencing ,PREVENTION - Abstract
Background: Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcareassociated infections. Here, we describe the value derived from a longitudinal epidemiological and genomic surveillance study of drug-resistant Escherichia coli in a LTCF in the United Kingdom (UK). Methods: Forty-five of 90 (50%) residents were recruited and followed for six months in 2014. Participants were screened weekly for carriage of extended-spectrum beta-lactamase (ESBL) producing E. coli. Participants positive for ESBL E. coli were also screened for ESBL-negative E. coli. Phenotypic antibiotic susceptibility of E. coli was determined using the Vitek2 instrument and isolates were sequenced on an Illumina HiSeq2000 instrument. Information was collected on episodes of clinical infection and antibiotic consumption. Results: Seventeen of 45 participants (38%) carried ESBL E. coli. Twenty-three of the 45 participants (51%) had 63 documented episodes of clinical infection treated with antibiotics. Treatment with antibiotics was associated with higher risk of carrying ESBL E. coli. ESBL E. coli was mainly sequence type (ST)131 (16/17, 94%). Non-ESBL E. coli from these 17 cases was more genetically diverse, but ST131 was found in eight (47%) cases. Whole-genome analysis of 297 ST131 E. coli from the 17 cases demonstrated highly related strains from six participants, indicating acquisition from a common source or person-to-person transmission. Five participants carried highly related strains of both ESBL-positive and ESBL-negative ST131. Genome-based comparison of ST131 isolates from the LTCF study participants with ST131 associated with bloodstream infection at a nearby acute hospital and in hospitals across England revealed sharing of highly related lineages between the LTCF and a local hospital. Conclusions: This study demonstrates the power of genomic surveillance to detect multidrug-resistant pathogens and confirm their connectivity within a healthcare network. [ABSTRACT FROM AUTHOR]
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- 2017
- Full Text
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5. Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae.
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Runcharoen, Chakkaphan, Moradigaravand, Danesh, Blane, Beth, Paksanont, Suporn, Thammachote, Jeeranan, Anun, Suthatip, Parkhill, Julian, Chantratita, Narisara, and Peacock, Sharon J.
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KLEBSIELLA pneumoniae ,GRAM-negative bacteria ,NUCLEOTIDE sequencing ,ENTEROBACTERIACEAE ,MICROBIAL virulence ,VIRULENCE of bacteria - Abstract
Background: Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly diverse population of K. pneumoniae, the evolution and clinical significance of environmental K. pneumoniae, as well as the relationship between clinical and environmental K. pneumoniae, are poorly defined. Methods: We isolated and sequenced K. pneumoniae from in-patients in a single hospital in Thailand, as well as hospital sewage, and surrounding canals and farms within a 20-km radius. Results: Phylogenetic analysis of 77 K. pneumoniae (48 clinical and 29 non-clinical isolates) demonstrated that the two groups were intermixed throughout the tree and in some cases resided in the same clade, suggesting recent divergence from a common ancestor. Phylogenetic comparison of the 77 Thai genomes with 286 K. pneumoniae from a global collection showed that Thai isolates were closely related to the clinical sub-population of the global collection, indicating that Thai clinical isolates belonged to globally circulating lineages. Dating of four Thai K. pneumoniae clades indicated that they emerged between 50 and 150 years ago. Despite their phylogenetic relatedness, virulence factors and β-lactamase resistance genes were more numerous in clinical than in environmental isolates. Our results indicate that clinical and environmental K. pneumoniae are closely related, but that hospitals may select for isolates with a more resistant and virulent genotype. Conclusions: These findings highlight the clinical relevance of environmental K. pneumoniae isolates. [ABSTRACT FROM AUTHOR]
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- 2017
- Full Text
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6. Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks.
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Harrison, Ewan M., Ludden, Catherine, Brodrick, Hayley J., Blane, Beth, Brennan, Gráinne, Morris, Dearbháile, Coll, Francesc, Reuter, Sandra, Brown, Nicholas M., Holmes, Mark A., O'Connell, Brian, Parkhill, Julian, Török, M. Estee, Cormican, Martin, and Peacock, Sharon J.
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METHICILLIN-resistant staphylococcus aureus ,STAPHYLOCOCCUS aureus ,DRUG resistance in bacteria ,STAPHYLOCOCCUS aureus infections ,LONG-term care facilities - Abstract
Background: Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF. Methods: Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners). Results: We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission. Conclusions: These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum. [ABSTRACT FROM AUTHOR]
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- 2016
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- View/download PDF
7. Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network.
- Author
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Brodrick, Hayley J., Raven, Kathy E., Harrison, Ewan M., Blane, Beth, Reuter, Sandra, Török, M. Estée, Parkhill, Julian, and Peacock, Sharon J.
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NUCLEOTIDE sequencing ,VANCOMYCIN resistance ,ENTEROCOCCUS faecium ,MEDICAL care research ,PATHOGENIC microorganisms - Abstract
Background: Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrug-resistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmission of vancomycin-resistant enterococci (VRE) within a long-term care facility (LTCF), and between this and an acute hospital in the United Kingdom (UK). Methods: A longitudinal prospective observational study of faecal VRE carriage was conducted in a LTCF in Cambridge, UK. Stool samples were collected at recruitment, and then repeatedly until the end of the study period, discharge or death. Selective culture media were used to isolate VRE, which were subsequently sequenced and analysed. We also analysed the genomes of 45 bloodstream isolates collected at Cambridge Enterococcus faecium University Hospitals NHS Foundation Trust (CUH). Results: Forty-five residents were recruited during a 6-month period in 2014, and 693 stools were collected at a frequency of at least 1 week apart. Fifty-one stool samples from 3/45 participants (7 %) were positive for vancomycin-resistant. Two residents carried multiple VRE lineages, and one carried a single VRE lineage. E. faecium Genome analyses based on single nucleotide polymorphisms (SNPs) in the core genome indicated that VRE carried by each of the three residents were unrelated. Participants had extensive contact with the local healthcare network. We found that VRE genomes from LTCF residents and hospital-associated bloodstream infection were interspersed throughout the phylogenetic tree, with several instances of closely related VRE strains from the two settings. Conclusions: A proportion of LTCF residents are long-term carriers of VRE. Evidence for genetic relatedness between these and VRE associated with bloodstream infection in a nearby acute NHS Trust indicate a shared bacterial population. [ABSTRACT FROM AUTHOR]
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- 2016
- Full Text
- View/download PDF
8. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.
- Author
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Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, Anun S, Blane B, Parkhill J, Peacock SJ, and Chantratita N
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- Escherichia coli enzymology, Escherichia coli genetics, Escherichia coli physiology, Escherichia coli Infections physiopathology, Farms, Hospitals, Humans, Sequence Analysis, DNA, Thailand, beta-Lactamases, Drug Resistance, Multiple, Escherichia coli isolation & purification, Escherichia coli Infections microbiology, Wastewater microbiology, beta-Lactam Resistance
- Abstract
Background: Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas., Methods: We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing., Results: The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin., Conclusions: Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.
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- 2017
- Full Text
- View/download PDF
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