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Sule IO, Mendelsohn A, Panas RM. The Causes and Control Measures of Extended Spectrum Beta-Lactamase Producing Enterobacteriaceae in Long-Term Care Facilities: A Systematic Review and Meta-Analysis. Health Serv Res Manag Epidemiol 2022; 9:23333928221131709. [PMID: 36277608 PMCID: PMC9580105 DOI: 10.1177/23333928221131709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Background Due to extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE), infections among residents are increasing in long-term care facilities (LTCFs), resulting in a high rate of morbidity and healthcare costs. A designated infection control team is unavailable to control the disease. Methods A systematic review and meta-analysis were conducted to characterize the causes of ESBL-PE and evaluate the infection control strategies within LTCFs. Multiple regression analysis (MRA) was included as supplementary statistical analysis to identify relationships between LTCFs, geographical locations, infection control measures (ICMs), and ESBL-PE. A systematic search was conducted for studies from January 2008 to December 2018. Twenty-two of the 3106 studies met the inclusion criteria. Results The pooled prevalence for ESBL-PE among LTCFs residents was a mean difference (MD) of 15.78 (95% CI: 0.04, 31.53). Risk factors included the influence of regional areas was a standardized mean difference (SMD) of 0.61(95% CI: 0.32, 0.91) in Europe, SMD was 14.92 (95% CI: 9.17, 20.68) in Asia, and SMD was 0.51(95% CI: 0.35, 0.67) in other regions (North America and Australia). Nine of 22 studies reported ICMs were MD of 13.59 (95% CI: 5.32, 21.86). Conclusions Meta-analysis and MRA revealed a statistically significant association between LTCF and ESBL-PE among residents (p = .05). Strict adherence to infection control measures in LTCFs is needed to address this ESBL-PE prevalence among residents. The potential positive social change is promoting knowledge about vulnerable residents in LTCFs and the community factors responsible for ESBL infection.
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Affiliation(s)
- Ismaila Olatunji Sule
- Microbiology Department, NHS Western Isles, Stornoway, Isle of Lewis, Scotland,Microbiology Department, Biomedical Science Consulting Service, IG4M, Belfast, United Kingdom,Ismaila Olatunji Sule, Biomedical Science Consulting Service, IG4M, 7 Moatview Crescent. Bt16 2bg Belfast, UK.
| | - Aaron Mendelsohn
- Senior Contributing Faculty, Public Health Department, College of Health Professions, Walden University, Minneapolis, USA
| | - Raymond M Panas
- Senior Contributing Faculty, Public Health Department, College of Health Professions, Walden University, Minneapolis, USA
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Ludden C, Decano AG, Jamrozy D, Pickard D, Morris D, Parkhill J, Peacock SJ, Cormican M, Downing T. Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones. Microb Genom 2020; 6:e000352. [PMID: 32213258 PMCID: PMC7276707 DOI: 10.1099/mgen.0.000352] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/23/2020] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (n=69) with other Irish (n=35) and global (n=690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short- and long-read genome sequencing, de novo assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that Clade C was the most prevalent (686 out of 794 isolates, 86 %) of the three major ST131 clades circulating worldwide (A with fimH41, B with fimH22, C with fimH30), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in c. 1985 and subsequently acquired different ESBL gene variants (blaCTX-M-14 vs blaCTX-M-15). An ISEcp1-mediated transposition of the blaCTX-M-15 gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of blaCTX-M-15 at the mppA gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10), highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.
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Affiliation(s)
- Catherine Ludden
- London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Dorota Jamrozy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Derek Pickard
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Dearbhaile Morris
- Discipline of Bacteriology, School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute Centre for One Health, National University of Ireland Galway, Ireland
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Martin Cormican
- Discipline of Bacteriology, School of Medicine, National University of Ireland, Galway, Ireland
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
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O'Kelly F, Kavanagh S, Manecksha R, Thornhill J, Fennell JP. Characteristics of gram-negative urinary tract infections caused by extended spectrum beta lactamases: pivmecillinam as a treatment option within South Dublin, Ireland. BMC Infect Dis 2016; 16:620. [PMID: 27806687 PMCID: PMC5093942 DOI: 10.1186/s12879-016-1797-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 08/23/2016] [Indexed: 11/17/2022] Open
Abstract
Background The prevalence of urinary tract infections (UTIs) caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing and the therapeutic options are limited, especially in primary care. Recent indications have suggested pivmecillinam to be a suitable option. This pilot study aimed to assess the viability of pivmecillinam as a therapeutic option in a Dublin cohort of mixed community and healthcare origin. Methods A prospective measurement of mean and fractional inhibitory concentrations of antibiotic use in 95 patients diagnosed with UTI caused by ESBL-producing Enterobacteriaceae was carried out. 36 % patients were from general practice, 40 % were admitted to hospital within south Dublin, and 25 % samples arose from nursing homes. EUCAST breakpoints were used to determine if an isolate was sensitive or resistant to antibiotic agents. Results Sixty-nine percent of patients (N = 66) with urinary ESBL isolates were female. The mean age of females was 66 years compared with a mean age of 74 years for males. Thirty-six percent of isolates originated from primary care, hospital inpatients (26 %), and nursing homes (24 %). The vast majority of ESBL isolates were E. coli (80 %). The E tests for mecillinam and co-amoxiclav had concentration ranges from 0.16 mg/L up to 256 mg/L. The mean inhibitory concentration (MIC) of mecillinam ranged from 0.25 to 256 mg/L, while co-amoxiclav MICs ranged from 6 to 256 mg/L. The percentage of isolates resistant to mecillinam and co-amoxiclav was found to be 5.26 and 94.74 % respectively. Conclusions This is the first study exploring the use of pivmecillinam in an Irish cohort and has demonstrated that its use in conjunction with or without co-amoxiclav is an appropriate and useful treatment for urinary tract infections caused by ESBL-producing organisms.
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Affiliation(s)
- Fardod O'Kelly
- Department of Urological Surgery, AMNCH, Tallaght Hospital, Dublin 24, Ireland
| | - Siobhan Kavanagh
- Department of Clinical Microbiology, AMNCH, Tallaght Hospital, Dublin 24, Ireland
| | - Rustom Manecksha
- Department of Urological Surgery, AMNCH, Tallaght Hospital, Dublin 24, Ireland
| | - John Thornhill
- Department of Urological Surgery, AMNCH, Tallaght Hospital, Dublin 24, Ireland
| | - Jérôme P Fennell
- Department of Clinical Microbiology, AMNCH, Tallaght Hospital, Dublin 24, Ireland.
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Downing T. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics. Microorganisms 2015; 3:236-67. [PMID: 27682088 PMCID: PMC5023239 DOI: 10.3390/microorganisms3020236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 11/16/2022] Open
Abstract
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)-a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.
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Affiliation(s)
- Tim Downing
- School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin 9, Ireland.
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Ludden C, Cormican M, Vellinga A, Johnson JR, Austin B, Morris D. Colonisation with ESBL-producing and carbapenemase-producing Enterobacteriaceae, vancomycin-resistant enterococci, and meticillin-resistant Staphylococcus aureus in a long-term care facility over one year. BMC Infect Dis 2015; 15:168. [PMID: 25887288 PMCID: PMC4399485 DOI: 10.1186/s12879-015-0880-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background This study examined colonisation with and characteristics of antimicrobial-resistant organisms among residents of a long-term care facility (LTCF) over one year, including strain persistence and molecular diversity among isolates of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. Methods Sixty-four residents of a LTCF were recruited (51 at baseline, 13 during the year). Data on dependency levels, hospitalisations, and antimicrobial prescribing were collected. Nasal and rectal swabs and catheter urine specimens were examined quarterly, using chromogenic agars, for ESBL-producing Enterobacteriaceae, carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE), and meticillin-resistant S. aureus (MRSA). All ESBL-producing E. coli (ESBL-EC) were characterised by pulsed-field gel electrophoresis (PFGE) and PCR to assess for sequence type (ST) ST131, its resistance-associated H30 and H30-Rx subclones, and blaCTX-M,blaTEM,blaSHV, and blaOXA-1. Results The overall number of residents colonised, by organism, was as follows: ESBL-EC, 35 (55%); MRSA, 17 (27%); ESBL-producing K. pneumoniae (ESBL-KP), 5 (8%); VRE, 2 (3%) and CPE, 0 (0%). All 98 ESBL-EC isolates were H30-Rx ST131, with blaCTX-M-group 1. By PFGE, a group of 91 ESBL-EC (from 33 participants) had ≥ 85% similar profiles and resembled UK epidemic strain A/ international pulsotype PFGE812. Sequential ESBL-EC from individual residents were closely related. Six ESBL-KP isolates, from five participants, had blaCTX-M-group 1 and by PFGE were closely related. Colonisation with ESBL and MRSA was associated with location within the LTCF and previous exposure to antimicrobials. Conclusions Among LTCF residents, colonisation with ESBL-EC and MRSA was common. All ESBL-EC were H30-Rx ST131, consistent with clonal dissemination.
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Affiliation(s)
- Catherine Ludden
- Discipline of Bacteriology, School of Medicine, National University of Ireland Galway, Galway, Ireland.
| | - Martin Cormican
- Discipline of Bacteriology, School of Medicine, National University of Ireland Galway, Galway, Ireland. .,Centre for Health from Environment, Ryan Institute, National University of Ireland Galway, Galway, Ireland.
| | - Akke Vellinga
- Discipline of Bacteriology, School of Medicine, National University of Ireland Galway, Galway, Ireland.
| | | | - Bernie Austin
- St. Brendan's Home, Community Nursing Unit, Galway, Ireland.
| | - Dearbháile Morris
- Discipline of Bacteriology, School of Medicine, National University of Ireland Galway, Galway, Ireland.
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Fennell J, Vellinga A, Hanahoe B, Morris D, Boyle F, Higgins F, Lyons M, O'Connell K, Keady D, Cormican M. Increasing prevalence of ESBL production among Irish clinical Enterobacteriaceae from 2004 to 2008: an observational study. BMC Infect Dis 2012; 12:116. [PMID: 22587773 PMCID: PMC3462136 DOI: 10.1186/1471-2334-12-116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 04/10/2012] [Indexed: 11/10/2022] Open
Abstract
Background Extended spectrum β-lactamase (ESBL) producing Enterobacteriaceae infections are associated with delayed initiation of appropriate treatment, poor outcomes and increased hospital stay and expense. Although initially associated with healthcare settings, more recent international reports have shown increasing isolation of ESBLs in the community. Both hospital and community ESBL epidemiology in Ireland are poorly defined. Methods This report describes clinical and laboratory data from three hospitals over 4.5 years. All significant isolates of Enterobacteriaceae were subjected to standardized antimicrobial susceptibility testing and screening for ESBL production. Available patient data from hospital databases were reviewed. Results The database included 974 ESBL producing organisms from 464 patients. Urine and blood isolates represented 84% and 3% of isolates respectively. E. coli predominated (90.9%) followed by K. pneumoniae (5.6%). The majority of patients (n = 246, 53.0%) had been admitted to at least one of the study hospitals in the year prior to first isolation of ESBL. The overall 30-day all-cause mortality from the date of culture positivity was 9.7% and the 1 year mortality was 61.4%. A Cox regression analysis showed age over 60, male gender and previous hospital admissions were significant risk factors for death within 30 days of ESBL isolation. Numbers of ESBL-producing E. coli isolated from urine and blood cultures increased during the study. Urine isolates were more susceptible than blood isolates. Co-resistance to other classes of antimicrobial agents was more common in ESBL producers from residents of long stay facilities (LSF) compared with hospital inpatients who lived at home. Conclusions This work demonstrates a progressively increasing prevalence of ESBL Enterobacteriaceae in hospital, LSF and community specimens in a defined catchment area over a long time period . These results will improve clinician awareness of this problem and guide the development of empiric antimicrobial regimens for community acquired bloodstream and urinary tract infections.
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Affiliation(s)
- Jérôme Fennell
- Department of Medical Microbiology, Galway University Hospitals, Galway, Ireland
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Enumeration and characterization of antimicrobial-resistant Escherichia coli bacteria in effluent from municipal, hospital, and secondary treatment facility sources. Appl Environ Microbiol 2010; 76:4772-9. [PMID: 20525867 DOI: 10.1128/aem.02898-09] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a modification of the most probable number (MPN) method for rapid enumeration of antimicrobial-resistant Escherichia coli bacteria in aqueous environmental samples. E. coli (total and antimicrobial-resistant) bacteria were enumerated in effluent samples from a hospital (n = 17) and municipal sewers upstream (n = 5) and downstream (n = 5) from the hospital, effluent samples from throughout the treatment process (n = 4), and treated effluent samples (n = 13). Effluent downstream from the hospital contained a higher proportion of antimicrobial-resistant E. coli than that upstream from the hospital. Wastewater treatment reduced the numbers of E. coli bacteria (total and antimicrobial resistant); however, antimicrobial-resistant E. coli was not eliminated, and E. coli resistant to cefotaxime (including extended-spectrum beta-lactamase [ESBL] producers), ciprofloxacin, and cefoxitin was present in treated effluent samples.
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