Evidence map›Paper›PMID 35379360›Full record

ArticleGenome medicine2022

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.

Rauf Salamzade, Abigail L Manson, Bruce J Walker, Thea Brennan-Krohn, Colin J Worby, Peijun Ma, Lorrie L He, Terrance P Shea, James Qu, Sinéad B Chapman and 20 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.

0numbers the graph read from it
0cells of the map it votes in
27citing papers in PubMed
2.8field-weighted citation impact, top 7% of its field
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

27 citing papers in PubMed, 40 citations in OpenAlex.

  1. Article
  2. Article
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  4. ConfrontingInfection and drug resistance · 2026
    Review
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  16. Article
  17. Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2024
    Article
  18. Genomic Characterization of a Carbapenem-ResistantInfection and drug resistance · 2024
    Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors at 6 institutions in 2 countries.

Rauf SalamzadeInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Abigail L MansonInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Bruce J WalkerInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Thea Brennan-KrohnDepartment of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
Colin J WorbyInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Peijun MaInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Lorrie L HeInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Terrance P SheaInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
James QuInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Sinéad B ChapmanInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Whitney HoweInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Sarah K YoungInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Jenna I WursterDepartment of Ophthalmology, Department of Microbiology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, 240 Charles St., Boston, MA, 02114, USA.
Mary L DelaneyDivision of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Sanjat KanjilalDivision of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Andrew B OnderdonkDivision of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Cassiana E BittencourtDepartment of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA, 92868, USA.
Gabrielle M GussinDivision of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA, 92617, USA.
Diane KimDivision of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA, 92617, USA.
Ellena M PetersonDepartment of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA, 92868, USA.
Mary Jane FerraroMassachusetts General Hospital, Boston, MA, 02114, USA.
David C HooperMassachusetts General Hospital, Boston, MA, 02114, USA.
Erica S ShenoyMassachusetts General Hospital, Boston, MA, 02114, USA.
Christina A CuomoInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Lisa A CosimiInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Susan S HuangDivision of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA, 92617, USA.
James E KirbyDepartment of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
Virginia M PierceMassachusetts General Hospital, Boston, MA, 02114, USA.
Roby P BhattacharyyaInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Ashlee M EarlInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. aearl@broadinstitute.org.ORCID 0000-0001-7857-9145
Broad Institute · USUniversity of California, Irvine · USMassachusetts General Hospital · USBrigham and Women's Hospital · USBeth Israel Deaconess Medical Center · USMassachusetts Eye and Ear Infirmary · US

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI EARL, ASHLEE MIRIAM · 2014 to 2024
$66.5M
INFECTIOUS DISEASE AND BASIC MICROBIOLOGICAL MECHANISMST32AI007061 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI Marcia B Goldberg · 1985 to 2026
$12.1M
Pediatric Infectious Diseases Research TrainingT32HD055148 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI WESSELS, MICHAEL R · 2008 to 2018
$2.7M
Plasmid Eviction to Restore Susceptibility in Carbapenem-Resistant EnterobacteriaceaeR33AI119114 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI KIRBY, JAMES E · 2017 to 2019
$1.5M
Antimicrobial Synergy for Carbapenem-Resistant Enterobacteriaceae - Administrative SupplementK08AI132716 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI BRENNAN-KROHN, THEA · 2018 to 2022
$916k
NIAID NIH HHS K08 AI132716NIAID NIH HHS R33 AI119114NIAID NIH HHS T32 AI007061NIAID NIH HHS U19 AI110818NICHD NIH HHS T32 HD055148NIH HHS 1K08AI132716NIH HHS R33AI119114NIH HHS T32AI007061NIH HHS T32HD055148NIH HHS U19AI110818
6 · The paper itself

Abstract

backgroundCarbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms.

methodsTo overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years.

resultsOur CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment.

conclusionsCollectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

Indexed as

CarbapenemsGene Transfer, HorizontalAnti-Bacterial AgentsHumansPlasmidsProspective StudiesAnti-Bacterial AgentsCarbapenems

Identifiers

PMID35379360
PMCPMC8981930
OpenAlexW4226064126

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Registered trials

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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.