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Price V, Dunn SJ, Moran RA, Swindells J, McNally A. Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit. Microb Genom 2022; 8. [PMID: 35696727 PMCID: PMC9455706 DOI: 10.1099/mgen.0.000841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In some neonatal units, the screening of isolates for antimicrobial-resistant organisms is a matter of routine, with theoretical benefits including the prevention or early detection of outbreaks. This study sought to use whole-genome sequencing (WGS) retrospectively to characterize the genomic epidemiology of Gram-negative organisms obtained from a screening programme in a 32-bed unit providing intensive, high-dependency and special care at City Hospital, Birmingham, UK, identifying occult transmission events and clinically important antimicrobial-resistance (AMR) genes. WGS was performed for 155 isolates collected from rectal and umbilical screening swabs over a 2 month period from 44 individual neonates. Genomic epidemiological analysis showed possible transmission events involving Escherichia coli, Enterobacter cloacae, Klebsiella oxytoca and Klebsiella pneumoniae not detected by routine screening, with eight putative clusters involving different individuals identified. Within phylogenetic clusters, the relatedness of organisms – as determined by the abundance of SNPs – varied widely, indicating that a variety of transmission routes may be implicated. While clinically important AMR genes were not present in the putative transmission clusters, our observation of suspected interspecies horizontal transfer of blaCTX-M-15 within individuals highlights the potential for their spread between organisms as well as individuals in this environment, with implications for surveillance. Our data show that WGS may reveal occult Gram-negative transmission events, demonstrating the potential of sequencing-based surveillance systems for nosocomial pathogens. Challenges remain in understanding how to utilize WGS surveillance to maximum effect in real-world settings.
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Affiliation(s)
- Vivien Price
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jonathan Swindells
- Black Country Pathology Service, Birmingham City Hospital, Dudley Road, Birmingham, West Midlands B18 7QH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Härtel C, Faust K, Fortmann I, Humberg A, Pagel J, Haug C, Kühl R, Bohnhorst B, Pirr S, Viemann D, Simon A, Zemlin M, Poralla S, Müller A, Köstlin-Gille N, Gille C, Heckmann M, Rupp J, Herting E, Göpel W. Sepsis related mortality of extremely low gestational age newborns after the introduction of colonization screening for multi-drug resistant organisms. Antimicrob Resist Infect Control 2020; 9:144. [PMID: 32843080 PMCID: PMC7449086 DOI: 10.1186/s13756-020-00804-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In 2013 German infection surveillance guidelines recommended weekly colonization screening for multidrug-resistant (MDRO) or highly epidemic organisms for neonatal intensive care units (NICUs) and extended hygiene measures based on screening results. It remains a matter of debate whether screening is worth the effort. We therefore aimed to evaluate sepsis related outcomes before and after the guideline update. METHODS The German Neonatal Network (GNN) is a prospective cohort study including data from extremely preterm infants between 22 + 0 and 28 + 6 gestational weeks born in 62 German level III NICUs. RESULTS Infants treated after guideline update (n = 8.903) had a lower mortality (12.5% vs. 13.8%, p = 0.036), reduced rates for clinical sepsis (31.4 vs. 42.8%, p < 0.001) and culture-proven sepsis (14.4% vs. 16.5%, p = 0.003) as compared to infants treated before update (n = 3.920). In a multivariate logistic regression analysis, nine pathogens of culture-proven sepsis were associated with sepsis-related death, e.g. Pseudomonas aeruginosa [OR 59 (19-180), p < 0.001)]. However, the guideline update had no significant effect on pathogen-specific case fatality, total sepsis-related mortality and culture-proven sepsis rates with MDRO. While the exposure of GNN infants to cefotaxime declined over time (31.1 vs. 40.1%, p < 0.001), the treatment rate with meropenem was increased (31.6 vs. 26.3%, p < 0.001). CONCLUSIONS The introduction of weekly screening and extended hygiene measures is associated with reduced sepsis rates, but has no effects on sepsis-related mortality and sepsis with screening-relevant pathogens. The high exposure rate to meropenem should be a target of antibiotic stewardship programs.
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Affiliation(s)
- Christoph Härtel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany. .,German Neonatal Network (GNN), Lübeck, Germany. .,Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany. .,Department of Pediatrics, University of Würzburg, Josef-Schneider-Strasse 2, D-97080, Würzburg, Germany.
| | - Kirstin Faust
- Department of Pediatrics, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Ingmar Fortmann
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Alexander Humberg
- Department of Pediatrics, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Julia Pagel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Clara Haug
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Reinhard Kühl
- German Neonatal Network (GNN), Lübeck, Germany.,Department of Pediatrics, Diakonissenkrankenhaus, Flensburg, Germany
| | - Bettina Bohnhorst
- German Neonatal Network (GNN), Lübeck, Germany.,Department of Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Pirr
- Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany.,Department of Neonatology, Hannover Medical School, Hannover, Germany
| | - Dorothee Viemann
- Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany.,Department of Neonatology, Hannover Medical School, Hannover, Germany
| | - Arne Simon
- German Neonatal Network (GNN), Lübeck, Germany.,Department of Pediatrics, Saar University Homburg, Homburg, Germany
| | - Michael Zemlin
- German Neonatal Network (GNN), Lübeck, Germany.,Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany.,Department of Pediatrics, Saar University Homburg, Homburg, Germany
| | - Silvia Poralla
- German Neonatal Network (GNN), Lübeck, Germany.,Department of Pediatrics, University of Bonn, Bonn, Germany
| | - Andreas Müller
- German Neonatal Network (GNN), Lübeck, Germany.,Department of Pediatrics, University of Bonn, Bonn, Germany
| | | | - Christian Gille
- German Neonatal Network (GNN), Lübeck, Germany.,Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany.,Department of Neonatology, Tuebingen University Children's Hospital, Tuebingen, Germany
| | - Matthias Heckmann
- German Neonatal Network (GNN), Lübeck, Germany.,Department of Neonatology and Pediatric Intensive Care, University of Greifswald, Greifswald, Germany
| | - Jan Rupp
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany.,Department of Infectious Diseases and Medical Microbiology, University of Lübeck, Lübeck, Germany
| | - Egbert Herting
- Department of Pediatrics, University of Lübeck, Lübeck, Germany.,German Neonatal Network (GNN), Lübeck, Germany.,Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany
| | - Wolfgang Göpel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany.,German Neonatal Network (GNN), Lübeck, Germany.,Priming Immunity at the beginning of life (PRIMAL) Consortium, Lübeck, Germany
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O'Connor C, Philip RK, Kelleher J, Powell J, O'Gorman A, Slevin B, Woodford N, Turton JF, McGrath E, Finnegan C, Power L, O'Connell NH, Dunne CP. The first occurrence of a CTX-M ESBL-producing Escherichia coli outbreak mediated by mother to neonate transmission in an Irish neonatal intensive care unit. BMC Infect Dis 2017; 17:16. [PMID: 28056822 PMCID: PMC5217319 DOI: 10.1186/s12879-016-2142-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/20/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) comprise part of the normal vaginal microflora. Transfer from mother to neonate can occur during delivery resulting, sometimes, in neonatal bacterial disease. Here, we aim to report the first outbreak of CTX-M ESBL-producing E. coli with evidence of mother-to-neonate transmission in an Irish neonatal intensive care unit (NICU) followed by patient-to-patient transmission. METHODS Investigation including molecular typing was conducted. Infection was defined by clinical and laboratory criteria and requirement for antimicrobial therapy with or without positive blood cultures. Colonisation was determined by isolation without relevant symptoms or indicators of infection. RESULTS Index case was an 8-day-old baby born at 34 weeks gestation who developed ESBL-producing E. coli infections at multiple body sites. Screening confirmed their mother as colonised with ESBL-producing E. coli. Five other neonates, in the NICU simultaneously with the index case, also tested positive. Of these, four were colonised while one neonate developed sepsis, requiring antimicrobial therapy. The second infected neonate's mother was also colonised by ESBL-producing E. coli. Isolates from all eight positive patients (6 neonates, 2 mothers) were compared using pulsed-field gel electrophoresis (PFGE). Two distinct ESBL-producing strains were implicated, with evidence of transmission between mothers and neonates for both strains. All isolates were confirmed as CTX-M ESBL-producers. There were no deaths associated with the outbreak. CONCLUSIONS Resources were directed towards control interventions focused on hand hygiene and antimicrobial stewardship, which ultimately proved successful. Since this incident, all neonates admitted to the NICU have been screened for ESBL-producers and expectant mothers are screened at their first antenatal appointment. To date, there have been no further outbreaks.
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Affiliation(s)
- Ciara O'Connor
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland.,Centre for Interventions in Infection, Inflammation and Immunity (4i), Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Roy K Philip
- Department of Paediatrics, University Maternity Hospital Limerick, Limerick, Ireland
| | - John Kelleher
- Department of Paediatrics, University Maternity Hospital Limerick, Limerick, Ireland
| | - James Powell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Alan O'Gorman
- Infection Prevention and Control Team, University Hospital Limerick, Limerick, Ireland
| | - Barbara Slevin
- Infection Prevention and Control Team, University Hospital Limerick, Limerick, Ireland
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London, UK
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London, UK
| | - Elaine McGrath
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Cathriona Finnegan
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Lorraine Power
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Nuala H O'Connell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland.,Centre for Interventions in Infection, Inflammation and Immunity (4i), Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Colum P Dunne
- Centre for Interventions in Infection, Inflammation and Immunity (4i), Graduate Entry Medical School, University of Limerick, Limerick, Ireland.
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Seale J, Millar M. Perinatal vertical transmission of antibiotic-resistant bacteria: a systematic review and proposed research strategy. BJOG 2014; 121:923-8. [PMID: 24674346 DOI: 10.1111/1471-0528.12746] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND Antibiotic-resistant bacteria contribute to both early- and late-onset sepsis and outbreaks in neonatal intensive care units (NICUs). The extent to which vertical transmission of these resistant bacteria contributes to colonisation or infection of vulnerable infants in NICUs is unclear. Risk factors for vertical transmission of antibiotic-resistant bacteria are not well described. OBJECTIVES To identify studies describing vertical transmission of antibiotic-resistant bacteria, risk factors for transmission and the impact of colonisation on neonatal outcomes. SEARCH STRATEGY EMBASE, CINAHL, Cochrane, PubMed, and MEDLINE databases were searched using selected terminology. Titles and abstracts were screened by two reviewers. Selected papers were reviewed in full by two individuals to ascertain whether they fulfilled the inclusion criteria. SELECTION CRITERIA Any original article investigating perinatal vertical transmission of antibiotic-resistant bacteria between a mother and neonate was included. DATA COLLECTION AND ANALYSIS Data were extracted on study design, organism, antibiotic resistance, and means of ascertaining vertical transmission. MAIN RESULTS Five papers out of 4839 titles fulfilled the inclusion criteria. Four studies were predominantly observational and one was a case report. Each demonstrated perinatal transmission. No study reported risk factors for the transmission of resistant bacteria or the impact of colonisation on neonatal outcomes. AUTHOR'S CONCLUSIONS There is an absence of research into the perinatal transmission of resistant organisms despite the potential implications of such a situation. We outline objectives that need to be addressed in future research and describe a study design to ascertain the prevalence and risk factors for vertical transmission.
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Affiliation(s)
- J Seale
- Department of Infection, Barts Health NHS Trust, London, UK
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Anthony M, Bedford-Russell A, Cooper T, Fry C, Heath PT, Kennea N, McCartney M, Patel B, Pollard T, Sharland M, Wilson P. Managing and preventing outbreaks of Gram-negative infections in UK neonatal units. Arch Dis Child Fetal Neonatal Ed 2013; 98:F549-53. [PMID: 23792354 DOI: 10.1136/archdischild-2012-303540] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
De novo guidance on the management of Gram-negative bacteria outbreaks in UK neonatal units was developed in 2012 by a Department of Health, England Antimicrobial Resistance and Healthcare Associated Infection working group. The recommendations included activation of an organisational response and establishing a control team when an outbreak is suspected; screening for the specific organism only during an outbreak; undertaking multidisciplinary reviews of cleaning routines, hand hygiene and Gram-negative bacteria transmission risks; considering deep-cleaning; cohorting colonised and infected babies preferably but not necessarily in isolation cubicles; and considering reducing beds or closing a unit to new admissions as a way of improving spacing and staff:patient ratios until the outbreak is under control. The group advised establishing mechanisms to communicate effectively across the network; informing parents of the outbreak as early as possible, and providing prewritten 'infection outbreak' information sheets. For prevention of outbreaks, the group advised meeting national staffing and cot-spacing requirements; following a Water Action Plan; using infection reduction care bundles and benchmarking; and introducing breast milk early and limiting antibiotic use.
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Affiliation(s)
- Mark Anthony
- Oxford University Hospitals NHS Trust, , Headington, Oxford, UK
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