15 results on '"Blane, Beth"'
Search Results
2. Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya.
- Author
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Obanda, Benear Apollo, Gibbons, Cheryl L., Fèvre, Eric M., Bebora, Lilly, Gitao, George, Ogara, William, Wang, Shu-Hua, Gebreyes, Wondwossen, Ngetich, Ronald, Blane, Beth, Coll, Francesc, Harrison, Ewan M., Kariuki, Samuel, Peacock, Sharon J., and Cook, Elizabeth A. J.
- Subjects
STAPHYLOCOCCUS aureus ,SLAUGHTERING ,WHOLE genome sequencing ,MICROBIAL sensitivity tests ,BACTERIAL cultures ,MICROCOCCACEAE - Abstract
Abattoir workers have been identified as high-risk for livestock-associated Staphylococcus aureus carriage. This study investigated S. aureus carriage in abattoir workers in Western Kenya. Nasal swabs were collected once from participants between February-November 2012. S. aureus was isolated using bacterial culture and antibiotic susceptibility testing performed using the VITEK 2 instrument and disc diffusion methods. Isolates underwent whole genome sequencing and Multi Locus Sequence Types were derived from these data. S. aureus (n = 126) was isolated from 118/737 (16.0%) participants. Carriage was higher in HIV-positive (24/89, 27.0%) than HIV–negative participants (94/648, 14.5%; p = 0.003). There were 23 sequence types (STs) identified, and half of the isolates were ST152 (34.1%) or ST8 (15.1%). Many isolates carried the Panton-Valentine leucocidin toxin gene (42.9%). Only three isolates were methicillin resistant S. aureus (MRSA) (3/126, 2.4%) and the prevalence of MRSA carriage was 0.4% (3/737). All MRSA were ST88. Isolates from HIV-positive participants (37.0%) were more frequently resistant to sulfamethoxazole/trimethoprim compared to isolates from HIV-negative participants (6.1%; p < 0.001). Similarly, trimethoprim resistance genes were more frequently detected in isolates from HIV-positive (81.5%) compared to HIV-negative participants (60.6%; p = 0.044). S. aureus in abattoir workers were representative of major sequence types in Africa, with a high proportion being toxigenic isolates. HIV-positive individuals were more frequently colonized by antimicrobial resistant S. aureus which may be explained by prophylactic antimicrobial use. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
3. Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya.
- Author
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Obanda, Benear Apollo, Cook, Elizabeth A. J., Fèvre, Eric M., Bebora, Lilly, Ogara, William, Wang, Shu-Hua, Gebreyes, Wondwossen, Ngetich, Ronald, Wandede, Dolphine, Muyodi, Johnstone, Blane, Beth, Coll, Francesc, Harrison, Ewan M., Peacock, Sharon J., and Gitao, George C.
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METHICILLIN ,MUPIROCIN ,STAPHYLOCOCCUS aureus ,TOXIC shock syndrome ,OPPORTUNISTIC infections ,DRUG resistance in bacteria ,HOSPITALS - Abstract
Staphylococcus aureus is an important pathogen associated with hospital, community, and livestock-acquired infections, with the ability to develop resistance to antibiotics. Nasal carriage by hospital inpatients is a risk for opportunistic infections. Antibiotic susceptibility patterns, virulence genes and genetic population structure of S. aureus nasal isolates, from inpatients at Busia County Referral Hospital (BCRH) were analyzed. A total of 263 inpatients were randomly sampled, from May to July 2015. The majority of inpatients (85.9%) were treated empirically with antimicrobials, including ceftriaxone (65.8%) and metronidazole (49.8%). Thirty S. aureus isolates were cultured from 29 inpatients with a prevalence of 11% (10.3% methicillin-susceptible S. aureus (MSSA), 0.8% methicillin resistant S. aureus (MRSA)). Phenotypic and genotypic resistance was highest to penicillin-G (96.8%), trimethoprim (73.3%), and tetracycline (13.3%) with 20% of isolates classified as multidrug resistant. Virulence genes, Panton-Valentine leukocidin (pvl), toxic shock syndrome toxin-1 (tsst-1), and sasX gene were detected in 16.7%, 23.3% and 3.3% of isolates. Phylogenetic analysis showed 4 predominant clonal complexes CC152, CC8, CC80, and CC508. This study has identified that inpatients of BCRH were carriers of S. aureus harbouring virulence genes and resistance to a range of antibiotics. This may indicate a public health risk to other patients and the community. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
4. Defining metrics for whole-genome sequence analysis of MRSA in clinical practice
- Author
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Raven, Kathy E, Blane, Beth, Kumar, Narender, Leek, Danielle, Bragin, Eugene, Coll, Francesc, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
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Methicillin-Resistant Staphylococcus aureus ,Whole Genome Sequencing ,translational ,Computational Biology ,High-Throughput Nucleotide Sequencing ,MRSA ,Staphylococcal Infections ,Polymorphism, Single Nucleotide ,United Kingdom ,Workflow ,quality metrics ,Bacterial Proteins ,whole-genome sequencing ,Humans ,Penicillin-Binding Proteins - Abstract
Bacterial sequencing will become increasingly adopted in routine microbiology laboratories. Here, we report the findings of a technical evaluation of almost 800 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, in which we sought to define key quality metrics to support MRSA sequencing in clinical practice. We evaluated the accuracy of mapping to a generic reference versus clonal complex (CC)-specific mapping, which is more computationally challenging. Focusing on isolates that were genetically related (50 bp apart to identify same-species contamination for MRSA. These metrics were combined into a quality-control (QC) flowchart to determine whether sequence runs and individual clinical isolates passed QC, which could be adapted by future automated analysis systems to enable rapid hands-off sequence analysis by clinical laboratories.
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- 2020
- Full Text
- View/download PDF
5. Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory
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Raven, Kathy E, Blane, Beth, Leek, Danielle, Churcher, Carol, Kokko-Gonzales, Paula, Pugazhendhi, Dhamayanthi, Fraser, Louise, Betley, Jason, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], and Apollo - University of Cambridge Repository
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Methicillin-Resistant Staphylococcus aureus ,Microbiological Techniques ,clinical application ,Whole Genome Sequencing ,whole-genome sequencing ,Diagnostic Tests, Routine ,Humans ,MRSA ,Staphylococcal Infections ,Laboratories, Hospital ,Genome, Bacterial ,Multilocus Sequence Typing - Abstract
There is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of methicillin-resistant Staphylococcus aureus (MRSA) isolates. Using a test panel of 25 MRSA isolates previously associated with outbreak investigations, we devised modifications to library preparation that reduced the processing time by 1 hour. We determined the maximum number of isolates that could be sequenced per run using an Illumina MiniSeq platform and a 13-hour (overnight) run time, which equated to 21 MRSA isolates and 3 controls (no template, positive, and negative). Repeatability and reproducibility assays based on this sequencing methodology demonstrated 100% accuracy in assigning species and sequence type (ST) and in detecting mecA Established genetic relatedness between isolates was recapitulated. Quality control (QC) metrics were evaluated over nine sequencing runs. Of the test panel MRSA genomes, 168/173 (97%) passed QC metrics based on the correct species assigned, detection of mecA and ST, and depth/coverage metrics. An evaluation of contamination in these 9 runs showed that positive and negative controls and test MRSA sequence files contained
- Published
- 2019
6. Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013
- Author
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Toleman, Michelle S, Reuter, Sandra, Jamrozy, Dorota, Wilson, Hayley J, Blane, Beth, Harrison, Ewan M, Coll, Francesc, Hope, Russell J, Kearns, Angela, Parkhill, Julian, Peacock, Sharon J, Török, M Estée, Harrison, Ewan [0000-0003-2720-0507], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
Adult ,Male ,Methicillin-Resistant Staphylococcus aureus ,bacteraemia ,Adolescent ,Bacteremia ,MRSA ,Disease Outbreaks ,Cohort Studies ,Humans ,Public Health Surveillance ,Prospective Studies ,Child ,Phylogeny ,Aged ,Aged, 80 and over ,Cross Infection ,Molecular Epidemiology ,Whole Genome Sequencing ,public health ,Infant, Newborn ,Infant ,Sequence Analysis, DNA ,biochemical phenomena, metabolism, and nutrition ,Middle Aged ,Staphylococcal Infections ,bacterial infections and mycoses ,England ,whole-genome sequencing ,Child, Preschool ,Epidemiological Monitoring ,surveillance ,Feasibility Studies ,epidemiology ,Female ,WGS ,Genome, Bacterial - Abstract
BackgroundMandatory reporting of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) has occurred in England for over 15years. Epidemiological information is recorded, but routine collection of isolates for characterisation has not been routinely undertaken. Ongoing developments in whole-genome sequencing (WGS) have demonstrated its value in outbreak investigations and for determining the spread of antimicrobial resistance and bacterial population structure. Benefits of adding genomics to routine epidemiological MRSA surveillance are unknown.AimTo determine feasibility and potential utility of adding genomics to epidemiological surveillance of MRSA.MethodsWe conducted an epidemiological and genomic survey of MRSA BSI in England over a 1-year period (1 October 2012--30 September 2013).ResultsDuring the study period, 903 cases of MRSA BSI were reported; 425 isolates were available for sequencing of which, 276 (65%) were clonal complex (CC) 22. Addition of 64 MRSA genomes from published outbreak investigations showed that the study genomes could provide context for outbreak isolates and supported cluster identification. Comparison to other MRSA genome collections demonstrated variation in clonal diversity achieved through different sampling strategies and identified potentially high-risk clones e.g. USA300 and local expansion of CC5 MRSA in South West England.ConclusionsWe demonstrate the potential utility of combined epidemiological and genomic MRSA BSI surveillance to determine the national population structure of MRSA, contextualise previous MRSA outbreaks, and detect potentially high-risk lineages. These findings support the integration of epidemiological and genomic surveillance for MRSA BSI as a step towards a comprehensive surveillance programme in England.
- Published
- 2019
- Full Text
- View/download PDF
7. Are commercial providers a viable option for clinical bacterial sequencing?
- Author
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Raven, Kathy, Blane, Beth, Churcher, Carol, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
DNA, Bacterial ,Methicillin-Resistant Staphylococcus aureus ,Whole Genome Sequencing ,MRSA ,Sequence Analysis, DNA ,Contract Services ,Staphylococcal Infections ,Polymorphism, Single Nucleotide ,United Kingdom ,Disease Outbreaks ,clinical application ,whole-genome sequencing ,Humans ,Genome, Bacterial ,Multilocus Sequence Typing - Abstract
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.
- Published
- 2018
8. Transmission of methicillin-resistant $\textit{Staphylococcus aureus}$ in long-term care facilities and their related healthcare networks
- Author
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Harrison, Ewan, Ludden, Catherine, Brodrick, Hayley J, Blane, Beth, Brennan, Gráinne, Morris, Dearbháile, Coll, Francesc, Reuter, Sandra, Brown, Nicholas M, Holmes, Mark, O’Connell, Brian, Parkhill, Julian, Török, M Estee, Cormican, Martin, Peacock, Sharon, Harrison, Ewan [0000-0003-2720-0507], Ludden, Catherine [0000-0001-9503-0744], Holmes, Mark [0000-0002-5454-1625], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
nursing home ,$\textit{Staphylococcus aureus}$ ,whole-genome sequencing ,transmission ,MRSA ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses ,molecular epidemiology ,long-term care facilities - Abstract
$\textbf{Background:}$ Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant $\textit{Staphylococcus aureus}$ (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. $\textbf{Methods:}$ 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). $\textbf{Results:}$ 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. $\textbf{Conclusions:}$ 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., UKCRC Translational Infection Research (TIR) Initiative, Medical Research Council (Grant ID: G1000803), Biotechnology and Biological Sciences Research Council, National Institute for Health Research, Chief Scientist Office of the Scottish Government Health Directorate, Hospital Infection Society (Major Research Grant), Wellcome Trust (Grant ID: 098051), Academy of Medical Sciences, Health Foundation, National Institute for Health Research Cambridge Biomedical Research Centre, This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13073-016-0353-5
- Published
- 2016
- Full Text
- View/download PDF
9. Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks
- Author
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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, Peacock, Sharon J, Harrison, Ewan [0000-0003-2720-0507], Ludden, Catherine [0000-0001-9503-0744], Holmes, Mark [0000-0002-5454-1625], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
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Adult ,DNA, Bacterial ,Male ,Methicillin-Resistant Staphylococcus aureus ,Staphylococcus aureus ,MRSA ,Genetics ,Transmission ,Humans ,Genetics(clinical) ,Prospective Studies ,Molecular Biology ,Aged ,Aged, 80 and over ,Whole-genome sequencing ,Cross Infection ,Infection Control ,Long-term care facilities ,Nursing home ,Research ,High-Throughput Nucleotide Sequencing ,Middle Aged ,Staphylococcal Infections ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses ,Long-Term Care ,United Kingdom ,Molecular epidemiology ,Health Facility Environment ,Molecular Medicine ,Female ,Multilocus Sequence Typing - 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. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0353-5) contains supplementary material, which is available to authorized users.
- Published
- 2016
10. Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England
- Author
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Toleman, Michelle S, Reuter, Sandra, Coll, Francesc, Harrison, Ewan M, Blane, Beth, Brown, Nicholas M, Török, M Estée, Parkhill, Julian, Peacock, Sharon J, Harrison, Ewan [0000-0003-2720-0507], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
Adult ,Male ,Methicillin-Resistant Staphylococcus aureus ,Staphylococcus aureus ,Adolescent ,Genotype ,MRSA ,molecular epidemiology ,Young Adult ,Disease Transmission, Infectious ,Humans ,Prospective Studies ,Child ,skin and connective tissue diseases ,health care economics and organizations ,Aged ,Aged, 80 and over ,Family Health ,Family Characteristics ,USA300 ,Sequence Analysis, DNA ,Middle Aged ,Staphylococcal Infections ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses ,England ,whole-genome sequencing ,Child, Preschool ,Epidemiological Monitoring ,Female - Abstract
BACKGROUND: The spread of USA300 methicillin-resistant Staphylococcus aureus (MRSA) across the United States resulted in an epidemic of infections. In Europe, only sporadic cases or small clusters of USA300 infections are described, and its prevalence in England is unknown. We conducted prospective surveillance for USA300 in the east of England. METHODS: We undertook a 12-month prospective observational cohort study of all individuals with MRSA isolated from community and hospital samples submitted to a microbiology laboratory. At least 1 MRSA isolate from each individual underwent whole-genome sequencing. USA300 was identified on the basis of sequence analysis, and phylogenetic comparisons were made between these and USA300 genomes from the United States. RESULTS: Between April 2012 and April 2013, we sequenced 2283 MRSA isolates (detected during carriage screening and in clinical samples) from 1465 individuals. USA300 was isolated from 24 cases (1.6%). Ten cases (42%) had skin and soft tissue infection, and 2 cases had invasive disease. Phylogenetic analyses identified multiple introductions and household transmission of USA300. CONCLUSIONS: Use of a diagnostic laboratory as a sentinel for surveillance has identified repeated introductions of USA300 in eastern England in 2012-2013, with evidence for limited transmission. Our results show how systematic surveillance could provide an early warning of strain emergence and dissemination.
- Published
- 2016
11. Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Author
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Reuter, Sandra, Török, M Estée, Holden, Matthew TG, Reynolds, Rosy, Raven, Kathy E, Blane, Beth, Donker, Tjibbe, Bentley, Stephen D, Aanensen, David M, Grundmann, Hajo, Feil, Edward J, Spratt, Brian G, Parkhill, Julian, Peacock, Sharon J, National Institute for Health Research, Wellcome Trust, Medical Research Council (MRC), Microbes in Health and Disease (MHD), University of St Andrews. Biomedical Sciences Research Complex, University of St Andrews. Infection Group, University of St Andrews. School of Medicine, Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
Methicillin-Resistant Staphylococcus aureus ,Resource ,Biochemistry & Molecular Biology ,METHICILLIN-RESISTANT ,BACTEREMIA ,TRANSMISSION ,Bioinformatics ,OUTBREAK ,MRSA ,Disease Outbreaks ,EMERGENCE ,PHYLOGENETIC TREES ,Humans ,Phylogeny ,Genetics & Heredity ,Surveillance ,Science & Technology ,RESISTANT STAPHYLOCOCCUS-AUREUS ,DAS ,Genomics ,QR Microbiology ,11 Medical And Health Sciences ,Sequence Analysis, DNA ,06 Biological Sciences ,Staphylococcal Infections ,Corrigenda ,EVOLUTION ,United Kingdom ,QR ,Biotechnology & Applied Microbiology ,Molecular Diagnostic Techniques ,Epidemiological Monitoring ,RA Public aspects of medicine ,Methicillin Resistance ,SPREAD ,BDC ,RA ,Life Sciences & Biomedicine ,Ireland ,Genome, Bacterial ,CLONES - Abstract
The study was supported by grants from the UKCRC Translational Infection Research Initiative, and the Medical Research Council Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate (to Prof. Peacock); and by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute. MET is Clinician Scientist Fellow supported by the Academy of Medical Sciences and the Health Foundation. The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a UK MRSA database containing over 1,000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland and the Republic of Ireland over a decade. We sequenced 1,013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England, and otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualise MRSA outbreak investigations, and to detect the spread of resistance. The majority of isolates (n=783, 77%) belonged to CC22, which contains the dominant UK epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the UK and Ireland, and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance. Publisher PDF
- Published
- 2016
12. Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting
- Author
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Toleman, Michelle S, Watkins, Emmeline R, Williams, Tom, Blane, Beth, Sadler, Belinda, Harrison, Ewan M, Coll, Francesc, Parkhill, Julian, Nazareth, Bernadette, Brown, Nicholas M, and Peacock, Sharon J
- Subjects
Adult ,DNA, Bacterial ,Male ,Methicillin-Resistant Staphylococcus aureus ,Adolescent ,General Practice ,Bacteremia ,MRSA ,Disease Outbreaks ,Young Adult ,Humans ,Prospective Studies ,Child ,Phylogeny ,Aged ,Aged, 80 and over ,Cross Infection ,Whole Genome Sequencing ,Sequence Analysis, DNA ,Middle Aged ,Staphylococcal Infections ,United Kingdom ,3. Good health ,genome sequencing ,community ,epidemiology ,Female ,Public Health ,Genome, Bacterial - Abstract
BACKGROUND: Whole-genome sequencing (WGS) has typically been used to confirm or refute hospital/ward outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) identified through routine practice. However, appropriately targeted WGS strategies that identify routinely "undetectable" transmission remain the ultimate aim. METHODS: WGS of MRSA isolates sent to a regional microbiological laboratory was performed as part of a 12-month prospective observational study. Phylogenetic analyses identified a genetically related cluster of E-MRSA15 isolated from patients registered to the same general practice (GP) surgery. This led to an investigation to identify epidemiological links, find additional cases, and determine potential for ongoing transmission. RESULTS: We identified 15 MRSA-positive individuals with 27 highly related MRSA isolates who were linked to the GP surgery, 2 of whom died with MRSA bacteremia. Of the 13 cases that were further investigated, 11 had attended a leg ulcer/podiatry clinic. Cases lacked epidemiological links to hospitals, suggesting that transmission occurred elsewhere. Environmental and staff screening at the GP surgery did not identify an ongoing source of infection. CONCLUSIONS: Surveillance in the United Kingdom shows that the proportion of MRSA bacteremias apportioned to hospitals is decreasing, suggesting the need for greater focus on the detection of MRSA outbreaks and transmission in the community. This case study confirms that the typically nosocomial lineage (E-MRSA15) can transmit within community settings. Our study exemplifies the continued importance of WGS in detecting outbreaks, including those which may be missed by routine practice, and suggests that universal WGS of bacteremia isolates may help detect outbreaks in low-surveillance settings.
13. Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks
- Author
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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
- Subjects
Adult ,DNA, Bacterial ,Male ,Methicillin-Resistant Staphylococcus aureus ,Staphylococcus aureus ,MRSA ,Transmission ,Humans ,Prospective Studies ,Aged ,Aged, 80 and over ,Whole-genome sequencing ,Cross Infection ,Infection Control ,Long-term care facilities ,Nursing home ,High-Throughput Nucleotide Sequencing ,biochemical phenomena, metabolism, and nutrition ,Middle Aged ,Staphylococcal Infections ,bacterial infections and mycoses ,Long-Term Care ,United Kingdom ,3. Good health ,Molecular epidemiology ,Health Facility Environment ,Female ,Multilocus Sequence Typing - 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.
14. Are commercial providers a viable option for clinical bacterial sequencing?
- Author
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Raven, Kathy, Blane, Beth, Churcher, Carol, Parkhill, Julian, and Peacock, Sharon J
- Subjects
DNA, Bacterial ,Methicillin-Resistant Staphylococcus aureus ,Whole Genome Sequencing ,MRSA ,Sequence Analysis, DNA ,Contract Services ,Staphylococcal Infections ,Polymorphism, Single Nucleotide ,United Kingdom ,3. Good health ,Disease Outbreaks ,clinical application ,whole-genome sequencing ,Humans ,Genome, Bacterial ,Multilocus Sequence Typing - Abstract
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.
15. Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory
- Author
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Raven, Kathy E, Blane, Beth, Leek, Danielle, Churcher, Carol, Kokko-Gonzales, Paula, Pugazhendhi, Dhamayanthi, Fraser, Louise, Betley, Jason, Parkhill, Julian, and Peacock, Sharon J
- Subjects
Methicillin-Resistant Staphylococcus aureus ,Microbiological Techniques ,clinical application ,Whole Genome Sequencing ,whole-genome sequencing ,Diagnostic Tests, Routine ,Humans ,MRSA ,Staphylococcal Infections ,Laboratories, Hospital ,Genome, Bacterial ,3. Good health ,Multilocus Sequence Typing - Abstract
There is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of methicillin-resistant Staphylococcus aureus (MRSA) isolates. Using a test panel of 25 MRSA isolates previously associated with outbreak investigations, we devised modifications to library preparation that reduced the processing time by 1 hour. We determined the maximum number of isolates that could be sequenced per run using an Illumina MiniSeq platform and a 13-hour (overnight) run time, which equated to 21 MRSA isolates and 3 controls (no template, positive, and negative). Repeatability and reproducibility assays based on this sequencing methodology demonstrated 100% accuracy in assigning species and sequence type (ST) and in detecting mecA Established genetic relatedness between isolates was recapitulated. Quality control (QC) metrics were evaluated over nine sequencing runs. Of the test panel MRSA genomes, 168/173 (97%) passed QC metrics based on the correct species assigned, detection of mecA and ST, and depth/coverage metrics. An evaluation of contamination in these 9 runs showed that positive and negative controls and test MRSA sequence files contained
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