1
|
Nurjadi D, Eichel VM, Pöschl J, Gille C, Kranig S, Heeg K, Boutin S. Monocentric observational cohort study to investigate the transmission of third-generation cephalosporin-resistant Enterobacterales in a neonatal intensive care unit in Heidelberg, Germany. Microbiol Spectr 2023; 11:e0203823. [PMID: 37737640 PMCID: PMC10581168 DOI: 10.1128/spectrum.02038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Third-generation cephalosporin-resistant Enterobacterales is a major threat for newborns in neonatal intensive care units (NICUs). The route of acquisition in a non-outbreak setting should be investigated to implement adequate infection prevention measures. To identify risk factors for colonization with and to investigate the transmission pattern of third-generation cephalosporin-resistant Enterobacterales in a NICU setting. This monocentric observational cohort study in a tertiary NICU in Heidelberg, Germany, enrolled all hospitalized neonates screened for cephalosporin-resistant Enterobacterales. Data were collected from 1 January 2018 to 31 December 2021. Weekly screening by rectal swabs for colonization with third-generation cephalosporin-resistant Enterobacterales was performed for all newborns until discharge. Whole-genome sequencing was performed for molecular characterization and transmission analysis. In total, 1,287 newborns were enrolled. The median length of stay was 20 (range 1-250) days. Eighy-eight infants (6.8%) were colonized with third-generation cephalosporin-resistant Enterobacterales. Low birth weight [<1500 g (adjusted odds ratio, 5.1; 95% CI 2.2-11.5; P < 0.001)] and longer hospitalization [per 30 days (adjusted odds ratio, 1.7; 95% CI 1.5-2.0; P < 0.001)] were associated with colonization or infection with drug-resistant Enterobacterales in a multivariate analysis. Enterobacter cloacae complex was the most prevalent third-generation cephalosporin-resistant Enterobacterales detected, 64.8% (59 of 91). Whole-genome sequencing, performed for the available 85 of 91 isolates, indicated 12 transmission clusters involving 37 patients. This cohort study suggests that transmissions of third-generation cephalosporin-resistant Enterobacterales in newborns occur frequently in a non-outbreak NICU setting, highlighting the importance of surveillance and preventive measures in this vulnerable patient group. IMPORTANCE Preterm newborns are prone to infections. Therefore, infection prevention should be prioritized in this vulnerable patient group. However, outbreaks involving drug-resistant bacteria, such as third-generation resistant Enterobacterales, are often reported. Our study aims to investigate transmission and risk factors for acquiring third-generation cephalosporin-resistant Enterobacterales in a non-outbreak NICU setting. Our data indicated that premature birth and low birth weight are significant risk factors for colonization/infection with third-generation cephalosporin-resistant Enterobacterales. Furthermore, we could identify putative transmission clusters by whole-genome sequencing, highlighting the importance of preemptive measures to prevent infections in this patient collective.
Collapse
Affiliation(s)
- Dennis Nurjadi
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- Department of Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Vanessa M. Eichel
- Department of Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Johannes Pöschl
- Department of Neonatology, Heidelberg University Hospital, Heidelberg University Children’s Hospital, Heidelberg, Germany
| | - Christian Gille
- Department of Neonatology, Heidelberg University Hospital, Heidelberg University Children’s Hospital, Heidelberg, Germany
| | - Simon Kranig
- Department of Neonatology, Heidelberg University Hospital, Heidelberg University Children’s Hospital, Heidelberg, Germany
| | - Klaus Heeg
- Department of Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- Department of Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
2
|
Decano AG, Tran N, Al-Foori H, Al-Awadi B, Campbell L, Ellison K, Mirabueno LP, Nelson M, Power S, Smith G, Smyth C, Vance Z, Woods C, Rahm A, Downing T. Plasmids shape the diverse accessory resistomes of Escherichia coli ST131. Access Microbiol 2020; 3:acmi000179. [PMID: 33997610 PMCID: PMC8115979 DOI: 10.1099/acmi.0.000179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and we examined this here using a preterm infant resistome. We found that individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.
Collapse
Affiliation(s)
- Arun Gonzales Decano
- School of Biotechnology, Dublin City University, Ireland.,Present address: School of Medicine, University of St., Andrews, UK
| | - Nghia Tran
- School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Ireland
| | | | | | | | - Kevin Ellison
- School of Biotechnology, Dublin City University, Ireland
| | - Louisse Paolo Mirabueno
- School of Biotechnology, Dublin City University, Ireland.,Present address: National Institute of Agricultural Botany - East Malling Research, Kent, UK
| | - Maddy Nelson
- School of Biotechnology, Dublin City University, Ireland
| | - Shane Power
- School of Biotechnology, Dublin City University, Ireland
| | | | - Cian Smyth
- School of Biotechnology, Dublin City University, Ireland.,Present address: Dept of Biology, Maynooth University, Dublin, Ireland
| | - Zoe Vance
- School of Genetics & Microbiology, Trinity College Dublin, Ireland
| | | | - Alexander Rahm
- School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Ireland.,Present address: GAATI Lab, Université de la Polynésie Française, Puna'auia, French Polynesia
| | - Tim Downing
- School of Biotechnology, Dublin City University, Ireland
| |
Collapse
|
3
|
Whitmer GR, Moorthy G, Arshad M. The pandemic Escherichia coli sequence type 131 strain is acquired even in the absence of antibiotic exposure. PLoS Pathog 2019; 15:e1008162. [PMID: 31856254 PMCID: PMC6922328 DOI: 10.1371/journal.ppat.1008162] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Grant R. Whitmer
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Ganga Moorthy
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
| | - Mehreen Arshad
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| |
Collapse
|
4
|
Ljungquist O, Schönbeck M, Riesbeck K, Tham J. Risk factors associated with prolonged intestinal colonization of ESBL-producing Enterobacteriaceae - a prospective cohort study. Infect Drug Resist 2019; 12:2637-2648. [PMID: 31693716 PMCID: PMC6716591 DOI: 10.2147/idr.s205163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/22/2019] [Indexed: 12/04/2022] Open
Abstract
Background Extended spectrum β-lactamase-producing Enterobacteriaceae (EPE) are responsible for a major part of the widespread antimicrobial resistance (AMR). Increased understanding of risk factors associated with intestinal colonization of EPE is crucial to implement adequate actions against AMR. The aim of this study was to define potential risk factors for prolonged intestinal colonization with EPE. A secondary aim was to analyze if patients were adequately informed about being infected or colonized by antibiotic-resistant bacteria. Methods Patients with a positive clinical EPE culture from urine, blood or feces were recruited in a region in the south of Sweden. Selective EPE fecal cultures were obtained at least three months after the initial positive culture. Prolonged intestinal colonization was defined as the prevalence of any EPE in the follow-up fecal sample. Risk factors for prolonged intestinal colonization were evaluated by using a questionnaire and by retrospective review of medical records. A univariate model and a multivariate regression analysis were performed to identify possible risk factors for intestinal EPE colonization. Results Out of 143 patients included in the study, 57% remained positive for EPE at the second sampling. In a multivariate regression model, urological intervention, history of EPE infection and travel to Africa and/or Asia within 2 years were found to be significantly associated with prolonged intestinal colonization of EPE. Before being approached by us, 50% of patients displayed inadequate knowledge of EPE infection or colonization. Conclusion In this prospective cohort study, urological intervention within 6 months and a history of EPE infection are independently associated with prolonged intestinal colonization with EPE. In contrast, travel to Africa and/or Asia within 2 years is associated with a decreased risk of prolonged intestinal colonization with EPE. There is room for improvement when it comes to patient information regarding EPE to decrease of spread.
Collapse
Affiliation(s)
- Oskar Ljungquist
- Clinical Infection Medicine, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö SE20502, Sweden.,Department of Infectious Disease, Helsingborg's Hospital, Helsingborg, Region Skåne, Sweden
| | - Marcus Schönbeck
- Clinical Infection Medicine, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö SE20502, Sweden.,Department of Infectious Disease, Helsingborg's Hospital, Helsingborg, Region Skåne, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö SE20502, Sweden
| | - Johan Tham
- Clinical Infection Medicine, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö SE20502, Sweden
| |
Collapse
|