Evidence map›Paper›PMID 37693518›Full record

ArticlemedRxiv : the preprint server for health sciences2023

Genomic Epidemiologic Investigation of a Multispecies Hospital Outbreak of NDM-5-Producing Enterobacterales Infections.

Nathan J Raabe, Abby L Valek, Marissa P Griffith, Emma Mills, Kady Waggle, Vatsala Rangachar Srinivasa, Ashley M Ayres, Claire Bradford, Hannah Creager, Lora L Pless and 4 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 2 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors at 2 institutions in 2 countries.

Nathan J RaabeMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Abby L ValekDepartment of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA.
Marissa P GriffithMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Emma MillsDivision of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA.
Kady WaggleMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Vatsala Rangachar SrinivasaMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Ashley M AyresDepartment of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA.
Claire BradfordDepartment of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213, USA.
Hannah CreagerDepartment of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street Pittsburgh, PA 15213.
Lora L PlessMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Alexander J SundermannMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Daria Van TyneDivision of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA.
Graham M SnyderDivision of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, 818 Scaife Hall, Pittsburgh, Pennsylvania 15261, USA.
Lee H HarrisonMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
University of Pittsburgh · USUPMC Presbyterian · US

Funding

Wellcome Trust
6 · The paper itself

Abstract

Background: New Delhi metallo-β-lactamase (NDM) represents an emergent mechanism of carbapenem resistance associated with high mortality and limited antimicrobial treatment options. Because the Methods: Initial outbreak detection of NDM-producing Enterobacterales identified at an acute care hospital occurred via traditional IP&C methods and was supplemented by real-time WGS surveillance, which was performed weekly using the Illumina platform. To resolve NDM-encoding plasmids, we performed long-read Oxford Nanopore sequencing and constructed hybrid assemblies using Illumina and Nanopore sequencing data. Reports of relatedness between NDM-producing organisms and reactive WGS for suspected outbreaks were shared with the IP&C team for assessment and intervention. Findings: We observed a multispecies outbreak of NDM-5-producing Enterobacterales isolated from 15 patients between February 2021 and February 2023. The 19 clinical and surveillance isolates sequenced included seven bacterial species and each encoded the same NDM-5 plasmid, which showed high homology to NDM plasmids previously observed in Asia. WGS surveillance and epidemiologic investigation characterized ten horizontal plasmid transfer events and six bacterial transmission events between patients housed in varying hospital units. Transmission prevention focused on enhanced observation and adherence to basic infection prevention measures. Interpretation: Our investigation revealed a complex, multispecies outbreak of NDM that involved multiple plasmid transfer and bacterial transmission events, increasing the complexity of outbreak identification and transmission prevention. Our investigation highlights the utility of combining traditional IP&C and prospective genomic methods in identifying and containing plasmid-associated outbreaks. Funding: This work was funded in part by the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH) (R01AI127472) (R21AI1783691).

Indexed as

New-Delhi metallo-β-lactamaseOutbreak InvestigationPlasmidWhole genome sequencing

Identifiers

PMID37693518
PMCPMC10491379
OpenAlexW4386357600

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.