Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Abstract

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

Authors:
 [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [3];  [1];  [1];  [4]; ORCiD logo [1];  [1]; ORCiD logo [5];  [6]; ORCiD logo [7];  [8] more »; ORCiD logo [9] « less
+ Show Author Affiliations
  1. Genome Inst. of Singapore (Singapore)
  2. Singapore Univ. of Technology and Design (Singapore)
  3. Singapore General Hospital (Singapore); National Univ. of Singapore (Singapore). Graduate Medical School
  4. National Univ. Hospital (Singapore)
  5. Cornell Univ., Ithaca, NY (United States). Weill Medical College
  6. National Centre for Infectious Diseases (Singapore); Tan Tock Seng Hospital (Singapore); Nanyang Technological Univ. (Singapore)
  7. National Centre for Infectious Diseases (Singapore); Tan Tock Seng Hospital (Singapore); National Univ. of Singapore (Singapore)
  8. National Centre for Infectious Diseases (Singapore); Tan Tock Seng Hospital (Singapore)
  9. Genome Inst. of Singapore (Singapore); National Univ. of Singapore (Singapore)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); US Naval Medical Research Center (NMRC); WorldQuant Foundation; Bill and Melinda Gates Foundation; Alfred P. Sloan Foundation
Contributing Org.:
MetaSUB Consortium
OSTI Identifier:
1766495
Grant/Contract Number:  
AC02-05CH11231; CGAug16C005; OPP1151054; G-2015-13964
Resource Type:
Accepted Manuscript
Journal Name:
Nature Medicine
Additional Journal Information:
Journal Volume: 26; Journal Issue: 6; Journal ID: ISSN 1078-8956
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar V., Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, and Nagarajan, Niranjan. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. United States: N. p., 2020. Web. doi:10.1038/s41591-020-0894-4.
Copy to clipboard
Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar V., Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, & Nagarajan, Niranjan. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. United States. https://doi.org/10.1038/s41591-020-0894-4
Copy to clipboard
Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar V., Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, and Nagarajan, Niranjan. Mon . "Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment". United States. https://doi.org/10.1038/s41591-020-0894-4. https://www.osti.gov/servlets/purl/1766495.
Copy to clipboard
@article{osti_1766495,
title = {Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment},
author = {Chng, Kern Rei and Li, Chenhao and Bertrand, Denis and Ng, Amanda Hui Qi and Kwah, Junmei Samantha and Low, Hwee Meng and Tong, Chengxuan and Natrajan, Maanasa and Zhang, Michael Hongjie and Xu, Licheng and Ko, Karrie Kwan Ki and Ho, Eliza Xin Pei and Av-Shalom, Tamar V. and Teo, Jeanette Woon Pei and Khor, Chiea Chuen and Chen, Swaine L. and Mason, Christopher E. and Ng, Oon Tek and Marimuthu, Kalisvar and Ang, Brenda and Nagarajan, Niranjan},
abstractNote = {Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.},
doi = {10.1038/s41591-020-0894-4},
journal = {Nature Medicine},
number = 6,
volume = 26,
place = {United States},
year = {Mon Jun 08 00:00:00 EDT 2020},
month = {Mon Jun 08 00:00:00 EDT 2020}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41591-020-0894-4
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
journal, July 2019

Precision epidemiology for infectious disease control
journal, February 2019

Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis
journal, September 2018

  • Lee, Jean Y. H.; Monk, Ian R.; Gonçalves da Silva, Anders
  • Nature Microbiology, Vol. 3, Issue 10
  • DOI: 10.1038/s41564-018-0230-7

Importance of the environment in meticillin-resistant Staphylococcus aureus acquisition: the case for hospital cleaning
journal, February 2008

Versatile and open software for comparing large genomes
journal, January 2004

  • Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
  • Genome Biology, Vol. 5, Issue 2, R12
  • DOI: 10.1186/gb-2004-5-2-r12

Antibiotic resistance—the need for global solutions
journal, December 2013

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance
journal, July 2019

  • Calero-Cáceres, William; Ye, Mao; Balcázar, José Luis
  • Trends in Microbiology, Vol. 27, Issue 7
  • DOI: 10.1016/j.tim.2019.02.008

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome
journal, September 2016

  • Hartmann, Erica M.; Hickey, Roxana; Hsu, Tiffany
  • Environmental Science & Technology, Vol. 50, Issue 18
  • DOI: 10.1021/acs.est.6b00262

Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors
journal, December 2018

  • Fahimipour, Ashkaan K.; Ben Mamaar, Sarah; McFarland, Alexander G.
  • mSystems, Vol. 3, Issue 6
  • DOI: 10.1128/mSystems.00200-18

Methicillin-resistant Staphylococcus aureus colonisation: epidemiological and molecular characteristics in an acute-care tertiary hospital in Singapore
journal, July 2018

High Rate of qacA - and qacB -Positive Methicillin-Resistant Staphylococcus aureus Isolates from Chlorhexidine-Impregnated Catheter-Related Bloodstream Infections
journal, August 2012

  • Ho, Cheng-Mao; Li, Chi-Yuan; Ho, Mao-Wang
  • Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 11
  • DOI: 10.1128/AAC.00761-12

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
journal, October 2013

  • Gupta, Sushim Kumar; Padmanabhan, Babu Roshan; Diene, Seydina M.
  • Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 1
  • DOI: 10.1128/AAC.01310-13

Burden of endemic health-care-associated infection in developing countries: systematic review and meta-analysis
journal, January 2011

The Hospital Water Environment as a Reservoir for Carbapenem-Resistant Organisms Causing Hospital-Acquired Infections—A Systematic Review of the Literature
journal, February 2017

  • Kizny Gordon, Alice E.; Mathers, Amy J.; Cheong, Elaine Y. L.
  • Clinical Infectious Diseases, Vol. 64, Issue 10
  • DOI: 10.1093/cid/cix132

Healthcare Outbreaks Associated With a Water Reservoir and Infection Prevention Strategies
journal, March 2016

  • Kanamori, Hajime; Weber, David J.; Rutala, William A.
  • Clinical Infectious Diseases, Vol. 62, Issue 11
  • DOI: 10.1093/cid/ciw122

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
journal, July 2019

Environmental contamination and hospital-acquired infection: factors that are easily overlooked
journal, November 2014

  • Beggs, C.; Knibbs, L. D.; Johnson, G. R.
  • Indoor Air, Vol. 25, Issue 5
  • DOI: 10.1111/ina.12170

Impact of an Environmental Cleaning Intervention on the Presence of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococci on Surfaces in Intensive Care Unit Rooms
journal, July 2008

  • Goodman, Eric R.; Piatt, Richard; Bass, Richard
  • Infection Control & Hospital Epidemiology, Vol. 29, Issue 7
  • DOI: 10.1086/588566

A Simple and Robust Statistical Test for Detecting the Presence of Recombination
journal, February 2006

Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii , Isolated at Two Major Hospitals in Kuwait
journal, April 2018

  • Nasser, Kother; Mustafa, Abu Salim; Khan, Mohd Wasif
  • Genome Announcements, Vol. 6, Issue 16
  • DOI: 10.1128/genomeA.00264-18

Man-made microbial resistances in built environments
journal, February 2019

  • Mahnert, Alexander; Moissl-Eichinger, Christine; Zojer, Markus
  • Nature Communications, Vol. 10, Issue 1
  • DOI: 10.1038/s41467-019-08864-0

Recognizing the reagent microbiome
journal, July 2018

  • de Goffau, Marcus C.; Lager, Susanne; Salter, Susannah J.
  • Nature Microbiology, Vol. 3, Issue 8
  • DOI: 10.1038/s41564-018-0202-y

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010

Bacterial colonization and succession in a newly opened hospital
journal, May 2017

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
journal, September 2017

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing
journal, March 2019

Horizontal transfer of antibiotic resistance genes in clinical environments
journal, January 2019

  • Lerminiaux, Nicole A.; Cameron, Andrew D. S.
  • Canadian Journal of Microbiology, Vol. 65, Issue 1
  • DOI: 10.1139/cjm-2018-0275

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

  • Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
  • PeerJ, Vol. 3
  • DOI: 10.7717/peerj.985

PLSDB: a resource of complete bacterial plasmids
journal, October 2018

  • Galata, Valentina; Fehlmann, Tobias; Backes, Christina
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1050

Environmental and clinical antibiotic resistomes, same only different
journal, October 2019

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018

  • Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
  • Nature Biotechnology, Vol. 36, Issue 10
  • DOI: 10.1038/nbt.4229

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015

  • Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
  • Genome Research, Vol. 25, Issue 7
  • DOI: 10.1101/gr.186072.114

A new genomic blueprint of the human gut microbiota
journal, February 2019

Kraken: ultrafast metagenomic sequence classification using exact alignments
journal, January 2014

Metagenomics for pathogen detection in public health
journal, January 2013

  • Miller, Ruth R.; Montoya, Vincent; Gardy, Jennifer L.
  • Genome Medicine, Vol. 5, Issue 9
  • DOI: 10.1186/gm485

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance
journal, February 2018

  • Weingarten, Rebecca A.; Johnson, Ryan C.; Conlan, Sean
  • mBio, Vol. 9, Issue 1
  • DOI: 10.1128/mBio.02011-17

Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing
journal, July 2018

  • Buckner, Michelle M. C.; Ciusa, Maria Laura; Piddock, Laura J. V.
  • FEMS Microbiology Reviews, Vol. 42, Issue 6
  • DOI: 10.1093/femsre/fuy031

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
journal, May 2016

Mash: fast genome and metagenome distance estimation using MinHash
journal, June 2016

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
journal, January 2019

Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context
journal, December 2018

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree
journal, October 2018

  • Yu, Guangchuang; Lam, Tommy Tsan-Yuk; Zhu, Huachen
  • Molecular Biology and Evolution, Vol. 35, Issue 12
  • DOI: 10.1093/molbev/msy194

iNEXT: an R package for rarefaction and extrapolation of species diversity ( H ill numbers)
journal, August 2016

  • Hsieh, T. C.; Ma, K. H.; Chao, Anne
  • Methods in Ecology and Evolution, Vol. 7, Issue 12
  • DOI: 10.1111/2041-210X.12613

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
journal, November 2017

Hospital and community acquired infection and the built environment – design and testing of infection control rooms
journal, June 2007

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae
journal, September 2014

Multistate Point-Prevalence Survey of Health Care–Associated Infections
journal, March 2014

  • Magill, Shelley S.; Edwards, Jonathan R.; Bamberg, Wendy
  • New England Journal of Medicine, Vol. 370, Issue 13
  • DOI: 10.1056/NEJMoa1306801

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
journal, November 2014

Antibiotic regimens for treatment of infections due to multidrug-resistant Gram-negative pathogens: An evidence-based literature review
journal, January 2015

  • Khalili, Hossein; Izadpanah, Mandana
  • Journal of Research in Pharmacy Practice, Vol. 4, Issue 3
  • DOI: 10.4103/2279-042X.162360

MetaPhlAn2 for enhanced metagenomic taxonomic profiling
journal, September 2015

  • Truong, Duy Tin; Franzosa, Eric A.; Tickle, Timothy L.
  • Nature Methods, Vol. 12, Issue 10
  • DOI: 10.1038/nmeth.3589

PATRIC, the bacterial bioinformatics database and analysis resource
journal, November 2013

  • Wattam, Alice R.; Abraham, David; Dalay, Oral
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1099

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
journal, March 2017

  • Koren, Sergey; Walenz, Brian P.; Berlin, Konstantin
  • Genome Research, Vol. 27, Issue 5
  • DOI: 10.1101/gr.215087.116

Hand Hygiene
journal, March 2011

  • Longtin, Yves; Sax, Hugo; Allegranzi, Benedetta
  • New England Journal of Medicine, Vol. 364, Issue 13
  • DOI: 10.1056/NEJMvcm0903599

Evidence that contaminated surfaces contribute to the transmission of hospital pathogens and an overview of strategies to address contaminated surfaces in hospital settings
journal, May 2013

  • Otter, Jonathan A.; Yezli, Saber; Salkeld, James A. G.
  • American Journal of Infection Control, Vol. 41, Issue 5
  • DOI: 10.1016/j.ajic.2012.12.004

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
journal, November 2014

Microarray-based characterisation of a Panton–Valentine leukocidin-positive community-acquired strain of methicillin-resistant Staphylococcus aureus
journal, August 2006

The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing
journal, March 2013

  • Oberauner, Lisa; Zachow, Christin; Lackner, Stefan
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep01413

MVP: a microbe–phage interaction database
journal, November 2017

  • Gao, Na L.; Zhang, Chengwei; Zhang, Zhanbing
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1124

Hospital-associated microbiota and implications for nosocomial infections
journal, July 2015

Aminoglycoside-Streptothricin Resistance Gene Cluster aadE–sat4–aphA-3 Disseminated among Multiresistant Isolates of Enterococcus faecium
journal, November 2001

Fosfomycin for the treatment of infections caused by Gram-positive cocci with advanced antimicrobial drug resistance: a review of microbiological, animal and clinical studies
journal, June 2009

  • Falagas, Matthew E.; Roussos, Nikos; Gkegkes, Ioannis D.
  • Expert Opinion on Investigational Drugs, Vol. 18, Issue 7
  • DOI: 10.1517/13543780902967624

First case of E anophelis outbreak in an intensive-care unit
journal, September 2013

An environmental cleaning bundle and health-care-associated infections in hospitals (REACH): a multicentre, randomised trial
journal, April 2019

16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
journal, July 2007

  • Janda, J. M.; Abbott, S. L.
  • Journal of Clinical Microbiology, Vol. 45, Issue 9
  • DOI: 10.1128/JCM.01228-07

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014

Large-scale sequence comparisons with sourmash
journal, January 2019

Investigation of a Cluster of Sphingomonas koreensis Infections
journal, December 2018

  • Johnson, Ryan C.; Deming, Clay; Conlan, Sean
  • New England Journal of Medicine, Vol. 379, Issue 26
  • DOI: 10.1056/NEJMoa1803238
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    The availability of freshwater fish resources is maintained across a land-use gradient in Sabah, Borneo
    journal, August 2018

    • Wilkinson, Clare L.; Yeo, Darren C. J.; Tan, Heok Hui
    • Aquatic Conservation: Marine and Freshwater Ecosystems, Vol. 28, Issue 5
    • DOI: 10.1002/aqc.2920

    Conservation value of low-productivity forests measured as the amount and diversity of dead wood and saproxylic beetles
    journal, May 2018

    • Hämäläinen, Aino; Strengbom, Joachim; Ranius, Thomas
    • Ecological Applications, Vol. 28, Issue 4
    • DOI: 10.1002/eap.1705

    Islands, mainland, and terrestrial fragments: How isolation shapes plant diversity
    journal, July 2017

    • Martín-Queller, Emi; Albert, Cécile H.; Dumas, Pierre-Jean
    • Ecology and Evolution, Vol. 7, Issue 17
    • DOI: 10.1002/ece3.3150

    Table for five, please: Dietary partitioning in boreal bats
    journal, October 2018

    • Vesterinen, Eero J.; Puisto, Anna I. E.; Blomberg, Anna S.
    • Ecology and Evolution, Vol. 8, Issue 22
    • DOI: 10.1002/ece3.4559

    Drivers of tropical rainforest composition and alpha diversity patterns over a 2,520 m altitudinal gradient
    journal, April 2019

    • Veintimilla, Dario; Ngo Bieng, Marie Ange; Delgado, Diego
    • Ecology and Evolution, Vol. 9, Issue 10
    • DOI: 10.1002/ece3.5155

    Plant community responses to environmentally friendly piste management in northeast Iran
    journal, June 2019

    • Erfanian, Mohammad Bagher; Ejtehadi, Hamid; Vaezi, Jamil
    • Ecology and Evolution, Vol. 9, Issue 14
    • DOI: 10.1002/ece3.5388

    Fluvial biotopes influence macroinvertebrate biodiversity in South‐East Asian tropical streams
    journal, December 2016

    • Baker, Kate; Chadwick, Michael A.; Kahar, Rafhiah
    • Ecosphere, Vol. 7, Issue 12
    • DOI: 10.1002/ecs2.1479

    Ant diversity patterns across tropical elevation gradients: effects of sampling method and subcommunity
    journal, August 2019

    • Longino, John T.; Branstetter, Michael G.; Ward, Philip S.
    • Ecosphere, Vol. 10, Issue 8
    • DOI: 10.1002/ecs2.2798

    Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika
    journal, October 2019

    • Doble, Christopher J.; Hipperson, Helen; Salzburger, Walter
    • Environmental DNA, Vol. 2, Issue 1
    • DOI: 10.1002/edn3.43

    Plant community responses to multiple disturbances in an arid region of northeast Iran
    journal, June 2019

    • Erfanian, Mohammad Bagher; Ejtehadi, Hamid; Vaezi, Jamil
    • Land Degradation & Development, Vol. 30, Issue 13
    • DOI: 10.1002/ldr.3341

    Effects of land use on arbuscular mycorrhizal fungal communities in Estonia
    journal, January 2018

    Artificial structure density predicts fouling community diversity on settlement panels
    journal, November 2019

    Climate and land-cover change alter bumblebee species richness and community composition in subalpine areas
    journal, December 2018

    • Fourcade, Yoan; Åström, Sandra; Öckinger, Erik
    • Biodiversity and Conservation, Vol. 28, Issue 3
    • DOI: 10.1007/s10531-018-1680-1

    Dung beetle responses to successional stages in the Amazon rainforest
    journal, June 2019

    • Bitencourt, Bruna Santos; da Silva, Pedro Giovâni; Morato, Elder Ferreira
    • Biodiversity and Conservation, Vol. 28, Issue 10
    • DOI: 10.1007/s10531-019-01791-y

    A comparison of dung beetle assemblages (Coleoptera, Scarabaeoidea) collected 34 years apart in an Iberian mountain locality
    journal, January 2019

    Local and landscape habitat influences on bee diversity in agricultural landscapes in Anolaima, Colombia
    journal, January 2019

    Bumble bee (Bombus) distribution and diversity in Vermont, USA: a century of change
    journal, December 2018

    • Richardson, Leif L.; McFarland, Kent P.; Zahendra, Sara
    • Journal of Insect Conservation, Vol. 23, Issue 1
    • DOI: 10.1007/s10841-018-0113-5

    The butterflies of a Cerrado–Atlantic Forest ecotone at Laguna Blanca reveal underestimation of Paraguayan butterfly diversity and need for conservation
    journal, July 2019

    • Dickens, Jeremy K.; McMahon, Leigh; Binnie, Sarah E.
    • Journal of Insect Conservation, Vol. 23, Issue 4
    • DOI: 10.1007/s10841-019-00165-7

    Climatic variables drive temporal patterns of α and β diversities of dung beetles
    journal, September 2018

    • Ferreira, S. C.; da Silva, P. G.; Paladini, A.
    • Bulletin of Entomological Research, Vol. 109, Issue 3
    • DOI: 10.1017/S0007485318000676

    Diversity-disease relationships and shared species analyses for human microbiome-associated diseases
    journal, March 2019

    A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina
    journal, February 2020

    China’s tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis
    journal, November 2018

    High frequency of shared clonotypes in human B cell receptor repertoires
    journal, February 2019

    16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India
    journal, October 2019

    Multi-marker metabarcoding approach to study mesozooplankton at basin scale
    journal, August 2018

    A multiscale study of fungal endophyte communities of the foliar endosphere of native rubber trees in Eastern Amazon
    journal, November 2018

    Female Blow Flies As Vertebrate Resource Indicators
    journal, July 2019

    • Owings, Charity G.; Banerjee, Aniruddha; Asher, Travis M. D.
    • Scientific Reports, Vol. 9, Issue 1
    • DOI: 10.1038/s41598-019-46758-9

    Impact of coal mining on stream biodiversity in the US and its regulatory implications
    journal, April 2018

    Dissecting macroecological and macroevolutionary patterns of forest biodiversity across the Hawaiian archipelago
    journal, July 2019

    • Craven, Dylan; Knight, Tiffany M.; Barton, Kasey E.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 33
    • DOI: 10.1073/pnas.1901954116

    Global invasion history of the agricultural pest butterfly Pieris rapae revealed with genomics and citizen science
    journal, September 2019

    • Ryan, Sean F.; Lombaert, Eric; Espeset, Anne
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 40
    • DOI: 10.1073/pnas.1907492116

    Investigating microbial indicators of anthropogenic marine pollution by 16S and 18S High-Throughput Sequencing (HTS) library analysis
    journal, July 2019

    • Buccheri, Maria Antonietta; Salvo, Eliana; Coci, Manuela
    • FEMS Microbiology Letters, Vol. 366, Issue 14
    • DOI: 10.1093/femsle/fnz179

    Triclosan-Selected Host-Associated Microbiota Perform Xenobiotic Biotransformations in Larval Zebrafish
    journal, September 2019

    • Weitekamp, Chelsea A.; Phelps, Drake; Swank, Adam
    • Toxicological Sciences, Vol. 172, Issue 1
    • DOI: 10.1093/toxsci/kfz166

    Specialization and niche overlap across spatial scales: Revealing ecological factors shaping species richness and coexistence in Australian songbirds
    journal, July 2019

    • Harmáčková, Lenka; Remešová, Eva; Remeš, Vladimír
    • Journal of Animal Ecology, Vol. 88, Issue 11
    • DOI: 10.1111/1365-2656.13073

    The role of livestock intensification and landscape structure in maintaining tropical biodiversity
    journal, July 2017

    • Alvarado, Fredy; Escobar, Federico; Williams, David R.
    • Journal of Applied Ecology, Vol. 55, Issue 1
    • DOI: 10.1111/1365-2664.12957

    Comparing convenience and probability sampling for urban ecology applications
    journal, May 2018

    • Speak, Andrew; Escobedo, Francisco J.; Russo, Alessio
    • Journal of Applied Ecology, Vol. 55, Issue 5
    • DOI: 10.1111/1365-2664.13167

    Low‐intensity management benefits solitary bees in olive groves
    journal, October 2019

    • Martínez‐Núñez, Carlos; Manzaneda, Antonio J.; Isla, Jorge
    • Journal of Applied Ecology, Vol. 57, Issue 1
    • DOI: 10.1111/1365-2664.13511

    Exotic eucalypts: From demonized trees to allies of tropical forest restoration?
    journal, October 2019

    • Brancalion, Pedro H. S.; Amazonas, Nino T.; Chazdon, Robin L.
    • Journal of Applied Ecology, Vol. 57, Issue 1
    • DOI: 10.1111/1365-2664.13513

    Bacterial colonization of minerals in grassland soils is selective and highly dynamic
    journal, August 2019

    • Vieira, Selma; Sikorski, Johannes; Gebala, Aurelia
    • Environmental Microbiology, Vol. 22, Issue 3
    • DOI: 10.1111/1462-2920.14751

    Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
    journal, May 2020

    • Tsuji, Satsuki; Maruyama, Atsushi; Miya, Masaki
    • Molecular Ecology Resources, Vol. 20, Issue 5
    • DOI: 10.1111/1755-0998.13165

    How should we estimate diversity in the fossil record? Testing richness estimators using sampling‐standardised discovery curves
    journal, March 2018

    • Close, Roger A.; Evers, Serjoscha W.; Alroy, John
    • Methods in Ecology and Evolution, Vol. 9, Issue 6
    • DOI: 10.1111/2041-210x.12987

    The r package divDyn for quantifying diversity dynamics using fossil sampling data
    journal, March 2019

    • Kocsis, Ádám T.; Reddin, Carl J.; Alroy, John
    • Methods in Ecology and Evolution, Vol. 10, Issue 5
    • DOI: 10.1111/2041-210x.13161

    Choices of sampling method bias functional components estimation and ability to discriminate assembly mechanisms
    journal, April 2019

    Surveying tropical birds is much harder than you think: a primer of best practices
    journal, October 2018

    • Robinson, W. Douglas; Lees, Alexander C.; Blake, John G.
    • Biotropica, Vol. 50, Issue 6
    • DOI: 10.1111/btp.12608

    Canopy tree preference by insectivorous birds in shade‐coffee farms: Implications for migratory bird conservation
    journal, March 2019

    • Narango, Desirée L.; Tallamy, Douglas W.; Snyder, Kerry J.
    • Biotropica, Vol. 51, Issue 3
    • DOI: 10.1111/btp.12642

    Temporal variation in the influence of forest succession on caterpillar communities: A long‐term study in a tropical dry forest 
    journal, May 2019

    • Boege, Karina; Villa‐Galaviz, Edith; López‐Carretero, Antonio
    • Biotropica, Vol. 51, Issue 4
    • DOI: 10.1111/btp.12666

    Quantifying regional biodiversity in the tropics: A case study of freshwater fish in Trinidad and Tobago
    journal, August 2019

    • Jones, Faith A. M.; Rutherford, Mike G.; Deacon, Amy E.
    • Biotropica, Vol. 51, Issue 5
    • DOI: 10.1111/btp.12692

    Elevational filtering and the evolution of planthoppers (Hemiptera, Fulgoromorpha) in Papua New Guinea
    journal, March 2020

    • Chatelain, Paul; Le Cesne, Maxime; Elias, Marianne
    • Biotropica, Vol. 52, Issue 2
    • DOI: 10.1111/btp.12710

    Linking dung beetle‐mediated functions to interactions in the Atlantic Forest: Sampling design matters
    journal, March 2020

    • Raine, Elizabeth H.; Mikich, Sandra B.; Lewis, Owen T.
    • Biotropica, Vol. 52, Issue 2
    • DOI: 10.1111/btp.12722

    Interpreting beta‐diversity components over time to conserve metacommunities in highly dynamic ecosystems
    journal, May 2017

    • Ruhí, Albert; Datry, Thibault; Sabo, John L.
    • Conservation Biology, Vol. 31, Issue 6
    • DOI: 10.1111/cobi.12906

    Recreational freshwater fishing drives non-native aquatic species richness patterns at a continental scale
    journal, April 2017

    • Davis, A. J. S.; Darling, J. A.
    • Diversity and Distributions, Vol. 23, Issue 6
    • DOI: 10.1111/ddi.12557

    Turnover and nestedness in subtropical dung beetle assemblages along an elevational gradient
    journal, April 2018

    • da Silva, Pedro G.; Lobo, Jorge M.; Hensen, Maristela C.
    • Diversity and Distributions, Vol. 24, Issue 9
    • DOI: 10.1111/ddi.12763

    Bees use anthropogenic habitats despite strong natural habitat preferences
    journal, February 2019

    • Collado, Miguel Á.; Sol, Daniel; Bartomeus, Ignasi
    • Diversity and Distributions, Vol. 25, Issue 6
    • DOI: 10.1111/ddi.12899

    The biodiversity benefit of native forests and mixed‐species plantations over monoculture plantations
    journal, August 2019

    • Wang, Xiaoyang; Hua, Fangyuan; Wang, Lin
    • Diversity and Distributions, Vol. 25, Issue 11
    • DOI: 10.1111/ddi.12972

    Differential temporal beta‐diversity patterns of native and non‐native arthropod species in a fragmented native forest landscape
    journal, July 2018

    • Matthews, Thomas J.; Sadler, Jon; Carvalho, Rui
    • Ecography, Vol. 42, Issue 1
    • DOI: 10.1111/ecog.03812

    Sampling design may obscure species–area relationships in landscape‐scale field studies
    journal, October 2019

    • Bueno, Anderson Saldanha; Masseli, Gabriel S.; Kaefer, Igor L.
    • Ecography, Vol. 43, Issue 1
    • DOI: 10.1111/ecog.04568

    Comparative responses of termite functional and taxonomic diversity to land‐use change
    journal, May 2019

    • Liu, Shengjie; Lin, Xiaobing; Behm, Jocelyn E.
    • Ecological Entomology, Vol. 44, Issue 6
    • DOI: 10.1111/een.12755

    Anthropogenic disturbance equalizes diversity levels in arbuscular mycorrhizal fungal communities
    journal, April 2018

    • García de León, David; Davison, John; Moora, Mari
    • Global Change Biology, Vol. 24, Issue 6
    • DOI: 10.1111/gcb.14131

    Trade‐offs between carbon stocks and biodiversity in European temperate forests
    journal, November 2018

    • Sabatini, Francesco Maria; de Andrade, Rafael Barreto; Paillet, Yoan
    • Global Change Biology, Vol. 25, Issue 2
    • DOI: 10.1111/gcb.14503

    Congruence across taxa and spatial scales: Are we asking too much of species data?
    journal, August 2018

    • Burrascano, S.; de Andrade, R. B.; Paillet, Y.
    • Global Ecology and Biogeography, Vol. 27, Issue 8
    • DOI: 10.1111/geb.12766

    Body size, reef area and temperature predict global reef‐fish species richness across spatial scales
    journal, December 2018

    • Barneche, D. R.; Rezende, E. L.; Parravicini, V.
    • Global Ecology and Biogeography, Vol. 28, Issue 3
    • DOI: 10.1111/geb.12851

    The acoustic ecology of an Amazonian bird assemblage: the role of allometry, competition and environmental filtering in the acoustic structure
    journal, March 2019

    • Torres, Ingrid M. D.; Barreiros, Marcelo H. M.; de Araújo, Carlos B.
    • Ibis, Vol. 162, Issue 3
    • DOI: 10.1111/ibi.12720

    Livestock areas with canopy cover sustain dung beetle diversity in the humid subtropical Chaco forest
    journal, January 2019

    • Guerra Alonso, Celeste Beatriz; Zurita, Gustavo A.; Bellocq, M. Isabel
    • Insect Conservation and Diversity, Vol. 12, Issue 4
    • DOI: 10.1111/icad.12340

    A cross-continental comparison of assemblages of seed- and fruit-feeding insects in tropical rain forests: Faunal composition and rates of attack
    journal, March 2018

    • Basset, Yves; Dahl, Chris; Ctvrtecka, Richard
    • Journal of Biogeography, Vol. 45, Issue 6
    • DOI: 10.1111/jbi.13211

    Model averaging fails to improve the extrapolation capability of the island species–area relationship
    journal, June 2019

    • Matthews, Thomas J.; Aspin, Thomas W. H.
    • Journal of Biogeography
    • DOI: 10.1111/jbi.13598

    Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation
    journal, August 2017

    • Glynou, Kyriaki; Ali, Tahir; Kia, Sevda Haghi
    • Molecular Ecology, Vol. 26, Issue 18
    • DOI: 10.1111/mec.14231

    Non‐random association patterns in a plant–mycorrhizal fungal network reveal host–symbiont specificity
    journal, May 2018

    • Sepp, Siim‐Kaarel; Davison, John; Jairus, Teele
    • Molecular Ecology, Vol. 28, Issue 2
    • DOI: 10.1111/mec.14924

    Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi
    journal, July 2017

    • Pärtel, Meelis; Öpik, Maarja; Moora, Mari
    • New Phytologist, Vol. 216, Issue 1
    • DOI: 10.1111/nph.14695

    Forest biomass, soil and biodiversity relationships originate from biogeographic affinity and direct ecological effects
    journal, July 2019

    • Noreika, Norbertas; Helm, Aveliina; Öpik, Maarja
    • Oikos, Vol. 128, Issue 11
    • DOI: 10.1111/oik.06693

    Reconciling biodiversity and carbon stock conservation in an Afrotropical forest landscape
    journal, March 2018

    • Van de Perre, Frederik; Willig, Michael R.; Presley, Steven J.
    • Science Advances, Vol. 4, Issue 3
    • DOI: 10.1126/sciadv.aar6603

    High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians
    journal, June 2018

    Vascular Epiphytic Diversity in a Neotropical Transition Zone Is Driven by Environmental and Structural Heterogeneity
    journal, January 2019

    • de la Rosa-Manzano, Edilia; Mendieta-Leiva, Glenda; Guerra-Pérez, Antonio
    • Tropical Conservation Science, Vol. 12
    • DOI: 10.1177/1940082919882203

    Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort
    journal, July 2016

    The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus
    journal, July 2019

    Successional, spatial, and seasonal changes in seed rain in the Atlantic forest of southern Bahia, Brazil
    journal, December 2019

    Simple does not mean poor: grasslands and forests harbor similar ant species richness and distinct composition in highlands of southern Brazil
    journal, January 2018

    Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population
    journal, October 2018

    • Godoy-Vitorino, Filipa; Romaguera, Josefina; Zhao, Chunyu
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.02533

    Comparative Analysis of Intestine Microbiota of Four Wild Waterbird Species
    journal, August 2019

    Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon
    journal, August 2019

    Relationship between Wetland Plant Communities and Environmental Factors in the Tumen River Basin in Northeast China
    journal, March 2019

    • Zheng, Xiaojun; Fu, Jing; Ramamonjisoa, Noelikanto
    • Sustainability, Vol. 11, Issue 6
    • DOI: 10.3390/su11061559

    A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA
    journal, October 2018

    • Cahoon, A. Bruce; Huffman, Ashley G.; Krager, Megan M.
    • Metabarcoding and Metagenomics, Vol. 2
    • DOI: 10.3897/mbmg.2.26939

    Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
    text, January 2019

    • Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
    • BioMed Central
    • DOI: 10.5167/uzh-183761

    Variegated tropical landscapes conserve diverse dung beetle communities
    journal, January 2017

    • Costa, Cristiane; Oliveira, Victor Hugo F.; Maciel, Rafaella
    • PeerJ, Vol. 5
    • DOI: 10.7717/peerj.3125

    Nectar-living yeasts of a tropical host plant community: diversity and effects on community-wide floral nectar traits
    journal, January 2017

    • Canto, Azucena; Herrera, Carlos M.; Rodriguez, Rosalina
    • PeerJ, Vol. 5
    • DOI: 10.7717/peerj.3517

    Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel blaADC-257
    journal, November 2021

    • Zafer, Mai M.; Hussein, Amira F. A.; Al-Agamy, Mohamed H.
    • Frontiers in Microbiology, Vol. 12
    • DOI: 10.3389/fmicb.2021.736982
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: