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

Gunnar Rätsch | Emmanuel Dias-Neto | Niranjan Nagarajan | Mark Hernandez | Denis Bertrand | Leming Shi | Lynn M. Schriml | Russell Y. Neches | Chenhao Li | Tamar V. Av-Shalom | Iman Hajirasouliha | Andre Kahles | Eran Elhaik | Christopher E. Mason | Youping Deng | Mikhail Karasikov | Malay Bhattacharyya | Amanda Hui Qi Ng | Oon Tek Ng | Kalisvar Marimuthu | Danilo Ercolini | Daniel J. Butler | Alina Frolova | David Danko | David C. Green | Ran Blekhman | Marius Dybwad | Hugues Richard | Harun Mustafa | Stephan Ossowski | Gregorio Iraola | Paweł P. Łabaj | Ken McGrath | Soojin Jang | Robert W. Crawford | Frank J. Kelly | Alexandra B. Graf | Dmitry Meleshko | Daniela Bezdan | Nikos C. Kyrpides | Elena Vayndorf | Francesca De Filippis | Scott W. Tighe | Le Huu Song | Emmanuel F. Mongodin | David Paez-Espino | Torsten Semmler | Sofia Ahsanuddin | Ebrahim Afshinnekoo | Eduardo Castro-Nallar | Elena M. Vayndorf | Eileen Png | Aspassia D. Chatziefthimiou | Kern Rei Chng | Chenhao Li | A. Ng | N. Nagarajan | E. Castro-Nallar | G. Rätsch | C. Mason | H. Noushmehr | I. Hajirasouliha | N. Kyrpides | Leming Shi | F. De Filippis | D. Ercolini | Youping Deng | H. Richard | E. Mongodin | C. Desnues | A. Kahles | Ran Blekhman | C. Khor | Harun Mustafa | Mikhail Karasikov | Mark Hernandez | L. Schriml | M. Dybwad | J. Hecht | D. Bertrand | D. Butler | D. Bezdan | Ebrahim Afshinnekoo | S. Ossowski | D. Meleshko | Patrick K. H. Lee | E. Elhaik | H. M. Low | Dominique Thomas | M. Bhattacharyya | Soojin Jang | G. Iraola | S. Chen | Haruo Suzuki | O. U. Sezerman | A. Frolova | J. Teo | D. Green | E. Dias-Neto | S. Tighe | T. Velavan | R. Neches | M. Zambrano | M. Leung | X. Tong | M. Sierra | K. Udekwu | J. Ugalde | David Páez-Espino | T. Semmler | O. Ng | K. Marimuthu | O. Nikolayeva | D. C. Green | L. Song | B. Ang | D. Court | Eileen Png | N. Rascovan | D. Vassilev | K. McGrath | G. Mason-Buck | Sofia Ahsanuddin | Haruo Suzuki | Dominique Thomas | Sibo Zhu | Sibo Zhu | D. Danko | M. Moraes | Christelle Desnues | Junmei Samantha Kwah | Brenda Ang | Heba Shaaban | Chiea Chuen Khor | Manuela Oliveira | C. Tong | M. Natrajan | M. H. Zhang | Licheng Xu | K. Ko | E. Ho | Tamar V Av-Shalom | David Daniela Ebrahim Sofia Chandrima Daniel J. Kern Rei Danko Bezdan Afshinnekoo Ahsanuddin Bhattac | Chandrima Bhattacharya | B. Mutai | M. Nieto-Caballero | T. Nikolayeva | Jorge L. Sanchez | H. Shaaban | Xinzhao Tong | B. Young | Josue Alicea | Ana M. Cañas | A. Chatziefthimiou | R. Crawford | Daisy Donnellan | Angela Jones | F. Kelly | Kaymisha Knights | Levy Shawn | P. Ljungdahl | Abigail Lyons | Manuela Oliveira | O. Osuolale | Orhan Özcan | Brandon Valentine | Jifeng Zhu | Houtan Noushmehr | Gabriella Mason-Buck | Chandrima Bhattacharya | Daisy Donnellan | Jochen Hecht | Abigail Lyons | Beth Mutai | Amanda Ng | Olga Nikolayeva | Tatyana Nikolayeva | Ben Young | Josue Alicea | Kaymisha Knights | Per Ljungdahl | Milton Ozorio Moraes | Marina Nieto-Caballero | Orhan Özcan | Nicolas Rascovan | Brandon Valentine | Jifeng Zhu | Klas I. Udekwu | Juan A. Ugalde | María M. Zambrano | Marcus H. Y. Leung | Hwee Meng Low | Chengxuan Tong | Maanasa Natrajan | Michael Hongjie Zhang | Licheng Xu | Karrie Kwan Ki Ko | Eliza Xin Pei Ho | Jeanette Woon Pei Teo | Jorge L. Sanchez | Maria A. Sierra | Xinzhao Tong | Angela Jones | Levy Shawn | Olayinka O. Osuolale | Osman U. Sezerman | Denise Syndercombe Court | Dimitar I. Vassilev | Thirumalaisamy P. Velavan | Swaine L. Chen | Robert Crawford | P. Lee | E. Png | Hugues Richard | Licheng Xu | L. Shawn | C. Mason | Michael Hongjie Zhang | O. Nikolayeva | You-Peng Deng | Haruo Suzuki | Dominique Thomas

[1]  Gerard D. Wright Environmental and clinical antibiotic resistomes, same only different. , 2019, Current opinion in microbiology.

[2]  Gunnar Rätsch,et al.  Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance , 2019, bioRxiv.

[3]  Niranjan Nagarajan,et al.  Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes , 2019, Nature Biotechnology.

[4]  J. Balcázar,et al.  Bacteriophages as Environmental Reservoirs of Antibiotic Resistance. , 2019, Trends in microbiology.

[5]  Luiz Irber,et al.  Large-scale sequence comparisons with sourmash , 2019, bioRxiv.

[6]  Richard J. Goater,et al.  Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread , 2019, Nature Microbiology.

[7]  N. Graves,et al.  An environmental cleaning bundle and health-care-associated infections in hospitals (REACH): a multicentre, randomised trial. , 2019, The Lancet. Infectious diseases.

[8]  T. Zhang,et al.  Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing , 2019, Microbiome.

[9]  S. Brusaferro,et al.  Impact of a probiotic-based hospital sanitation on antimicrobial resistance and HAI-associated antimicrobial consumption and costs: a multicenter study , 2019, Infection and drug resistance.

[10]  David Bogumil,et al.  Man-made microbial resistances in built environments , 2019, Nature Communications.

[11]  S. Hultgren,et al.  The Widely Used Antimicrobial Triclosan Induces High Levels of Antibiotic Tolerance In Vitro and Reduces Antibiotic Efficacy up to 100-Fold In Vivo , 2019, Antimicrobial Agents and Chemotherapy.

[12]  M. Fischer,et al.  Hospital use of antibiotics as the main driver of infections with antibiotic-resistant bacteria – a reanalysis of recent data from the European Union , 2019, bioRxiv.

[13]  Robert D. Finn,et al.  A new genomic blueprint of the human gut microbiota , 2019, Nature.

[14]  Heike Sichtig,et al.  Single-molecule sequencing detection of N6-methyladenine in microbial reference materials , 2019, Nature Communications.

[15]  Oliver G. Pybus,et al.  Precision epidemiology for infectious disease control , 2019, Nature Medicine.

[16]  Edoardo Pasolli,et al.  Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle , 2019, Cell.

[17]  Christina Backes,et al.  PLSDB: a resource of complete bacterial plasmids , 2018, Nucleic Acids Res..

[18]  Andrew D. S. Cameron,et al.  Horizontal transfer of antibiotic resistance genes in clinical environments. , 2019, Canadian journal of microbiology.

[19]  C. Deming,et al.  Investigation of a Cluster of Sphingomonas koreensis Infections , 2018, The New England journal of medicine.

[20]  Á. S. Millán Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context. , 2018 .

[21]  Jim Shaw,et al.  Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome , 2018, bioRxiv.

[22]  Alexander G. McFarland,et al.  Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors , 2018, mSystems.

[23]  Yi Guan,et al.  Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree. , 2018, Molecular biology and evolution.

[24]  Robin Patel,et al.  Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis , 2018, Nature Microbiology.

[25]  Donovan H. Parks,et al.  A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life , 2018, Nature Biotechnology.

[26]  L. Piddock,et al.  Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing , 2018, FEMS microbiology reviews.

[27]  Julian Parkhill,et al.  Recognizing the reagent microbiome , 2018, Nature Microbiology.

[28]  P. D. de Sessions,et al.  Methicillin-resistant Staphylococcus aureus colonisation: epidemiological and molecular characteristics in an acute-care tertiary hospital in Singapore , 2018, Epidemiology and Infection.

[29]  Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait , 2018, Genome Announcements.

[30]  A. Apisarnthanarak,et al.  A Systematic Review of the Burden of Multidrug-Resistant Healthcare-Associated Infections Among Intensive Care Unit Patients in Southeast Asia: The Rise of Multidrug-Resistant Acinetobacter baumannii , 2018, Infection Control & Hospital Epidemiology.

[31]  Ryan Hendrickson,et al.  KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples , 2018, mSystems.

[32]  C. Deming,et al.  Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance , 2018, mBio.

[33]  Xing-Ming Zhao,et al.  MVP: a microbe–phage interaction database , 2017, Nucleic Acids Res..

[34]  A. Katsarou,et al.  Reporting for specific materials, systems and methods , 2018 .

[35]  Jillian F Banfield,et al.  Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome , 2017, Nature Communications.

[36]  C. Tang,et al.  Bacterial diversity among four healthcare-associated institutes in Taiwan , 2017, Scientific Reports.

[37]  R. Robinson,et al.  Direct and convenient measurement of plasmid stability in lab and clinical isolates of E. coli , 2017, Scientific Reports.

[38]  Stefano Lonardi,et al.  Comprehensive benchmarking and ensemble approaches for metagenomic classifiers , 2017, Genome Biology.

[39]  Peter E. Larsen,et al.  Bacterial colonization and succession in a newly opened hospital , 2017, Science Translational Medicine.

[40]  T. Peto,et al.  The Hospital Water Environment as a Reservoir for Carbapenem-Resistant Organisms Causing Hospital-Acquired Infections—A Systematic Review of the Literature , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[41]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[42]  John Paul,et al.  Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing , 2017, The Lancet. Infectious diseases.

[43]  A. Chao,et al.  iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers) , 2016 .

[44]  Yan Li,et al.  SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation , 2016, PloS one.

[45]  Erica M. Hartmann,et al.  Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome , 2016, Environmental science & technology.

[46]  Margaret A Dudeck,et al.  Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2011–2014 , 2016, Infection Control & Hospital Epidemiology.

[47]  Eric van der Helm,et al.  Rapid resistome mapping using nanopore sequencing , 2016, bioRxiv.

[48]  W. Rutala,et al.  Healthcare Outbreaks Associated With a Water Reservoir and Infection Prevention Strategies. , 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[49]  J. O'Neill,et al.  Tackling drug-resistant infections globally: final report and recommendations , 2016 .

[50]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[51]  N. Nagarajan,et al.  OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees , 2016, Genome Biology.

[52]  F. Grenouillet,et al.  Analysis of clinical and environmental Candida parapsilosis isolates by microsatellite genotyping--a tool for hospital infection surveillance. , 2015, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[53]  Duy Tin Truong,et al.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.

[54]  L. Morawska,et al.  Environmental contamination and hospital-acquired infection: factors that are easily overlooked. , 2015, Indoor air.

[55]  Jack A Gilbert,et al.  Hospital-associated microbiota and implications for nosocomial infections. , 2015, Trends in molecular medicine.

[56]  H. Khalili,et al.  Antibiotic regimens for treatment of infections due to multidrug-resistant Gram-negative pathogens: An evidence-based literature review , 2015, Journal of research in pharmacy practice.

[57]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[58]  Matthew B. Sullivan,et al.  VirSorter: mining viral signal from microbial genomic data , 2015, PeerJ.

[59]  P. Cornejo-Juárez,et al.  The impact of hospital-acquired infections with multidrug-resistant bacteria in an oncology intensive care unit. , 2015, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

[60]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[61]  Brian D. Ondov,et al.  The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes , 2014, Genome Biology.

[62]  S. Dancer,et al.  Controlling Hospital-Acquired Infection: Focus on the Role of the Environment and New Technologies for Decontamination , 2014, Clinical Microbiology Reviews.

[63]  Jonas Korlach,et al.  Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae , 2014, Science Translational Medicine.

[64]  Justin Zobel,et al.  SRST2: Rapid genomic surveillance for public health and hospital microbiology labs , 2014, bioRxiv.

[65]  Shuifang Zhu,et al.  Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads , 2014, BMC Bioinformatics.

[66]  A. Al-Bakri,et al.  Major biologic characteristics of Acinetobacter baumannii isolates from hospital environmental and patients' respiratory tract sources. , 2014, American journal of infection control.

[67]  R. Lynfield,et al.  Multistate point-prevalence survey of health care-associated infections. , 2014, The New England journal of medicine.

[68]  N. Duran,et al.  Relationship between the resistance genes to quaternary ammonium compounds and antibiotic resistance in staphylococci isolated from surgical site infections , 2014, Medical science monitor : international medical journal of experimental and clinical research.

[69]  Yan Zhang,et al.  PATRIC, the bacterial bioinformatics database and analysis resource , 2013, Nucleic Acids Res..

[70]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[71]  H. Goossens,et al.  Antibiotic resistance—the need for global solutions , 2013, BDJ.

[72]  J. Rolain,et al.  ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes , 2013, Antimicrobial Agents and Chemotherapy.

[73]  Vincent Montoya,et al.  Metagenomics for pathogen detection in public health , 2013, Genome Medicine.

[74]  S. Kjelleberg,et al.  First case of E anophelis outbreak in an intensive-care unit , 2013, The Lancet.

[75]  Alessandra Carattoli,et al.  Plasmids and the spread of resistance. , 2013, International journal of medical microbiology : IJMM.

[76]  J. A. Salkeld,et al.  Evidence that contaminated surfaces contribute to the transmission of hospital pathogens and an overview of strategies to address contaminated surfaces in hospital settings. , 2013, American journal of infection control.

[77]  Gabriele Berg,et al.  The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing , 2013, Scientific Reports.

[78]  Rob Knight,et al.  Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs) , 2013, PloS one.

[79]  Arjun Srinivasan,et al.  Antimicrobial-Resistant Pathogens Associated with Healthcare-Associated Infections Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2009–2010 , 2013, Infection Control & Hospital Epidemiology.

[80]  Olaf Berke,et al.  A prospective study to examine the epidemiology of methicillin-resistant Staphylococcus aureus and Clostridium difficile contamination in the general environment of three community hospitals in southern Ontario, Canada , 2012, BMC Infectious Diseases.

[81]  Sven Rahmann,et al.  Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.

[82]  Denis Bertrand,et al.  FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation , 2012, WABI.

[83]  Manuel J. Gómez,et al.  Exploring Bacterial Diversity in Hospital Environments by GS-FLX Titanium Pyrosequencing , 2012, PloS one.

[84]  Chi-Yuan Li,et al.  High Rate of qacA- and qacB-Positive Methicillin-Resistant Staphylococcus aureus Isolates from Chlorhexidine-Impregnated Catheter-Related Bloodstream Infections , 2012, Antimicrobial Agents and Chemotherapy.

[85]  Hugo Sax,et al.  Ha ndhyg ien e , 2018, Medicines Management for Residential and Nursing Homes.

[86]  R. Platt,et al.  Environmental cleaning intervention and risk of acquiring multidrug-resistant organisms from prior room occupants. , 2011, Archives of internal medicine.

[87]  B. Allegranzi,et al.  Burden of endemic health-care-associated infection in developing countries: systematic review and meta-analysis , 2011, The Lancet.

[88]  William A Rutala,et al.  Role of hospital surfaces in the transmission of emerging health care-associated pathogens: norovirus, Clostridium difficile, and Acinetobacter species. , 2010, American journal of infection control.

[89]  C. Urban,et al.  In Vitro Double and Triple Bactericidal Activities of Doripenem, Polymyxin B, and Rifampin against Multidrug-Resistant Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli , 2010, Antimicrobial Agents and Chemotherapy.

[90]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[91]  M. Falagas,et al.  Fosfomycin for the treatment of infections caused by Gram-positive cocci with advanced antimicrobial drug resistance: a review of microbiological, animal and clinical studies , 2009, Expert opinion on investigational drugs.

[92]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[93]  Kazutaka Katoh,et al.  Multiple alignment of DNA sequences with MAFFT. , 2009, Methods in molecular biology.

[94]  D. Yokoe,et al.  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 , 2008, Infection Control & Hospital Epidemiology.

[95]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[96]  S. Dancer,et al.  Importance of the environment in meticillin-resistant Staphylococcus aureus acquisition: the case for hospital cleaning. , 2008, The Lancet. Infectious diseases.

[97]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[98]  S. Abbott,et al.  16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls , 2007, Journal of Clinical Microbiology.

[99]  J T Walker,et al.  Hospital and community acquired infection and the built environment – design and testing of infection control rooms , 2007, Journal of Hospital Infection.

[100]  S. Levy,et al.  Molecular Mechanisms of Antibacterial Multidrug Resistance , 2007, Cell.

[101]  S. Monecke,et al.  Microarray-based characterisation of a Panton-Valentine leukocidin-positive community-acquired strain of methicillin-resistant Staphylococcus aureus. , 2006, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[102]  R. Weinstein,et al.  Reduction in acquisition of vancomycin-resistant enterococcus after enforcement of routine environmental cleaning measures. , 2006, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[103]  D. Bryant,et al.  A Simple and Robust Statistical Test for Detecting the Presence of Recombination , 2006, Genetics.

[104]  Rita Casadio,et al.  Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings , 2005, WABI.

[105]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[106]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[107]  L. Sehulster,et al.  Guidelines for environmental infection control in health-care facilities. Recommendations of CDC and the Healthcare Infection Control Practices Advisory Committee (HICPAC). , 2003, MMWR. Recommendations and reports : Morbidity and mortality weekly report. Recommendations and reports.

[108]  W. Witte,et al.  Aminoglycoside-Streptothricin Resistance Gene Cluster aadE–sat4–aphA-3 Disseminated among Multiresistant Isolates of Enterococcus faecium , 2001, Antimicrobial Agents and Chemotherapy.

[109]  P. Bradford Extended-Spectrum β-Lactamases in the 21st Century: Characterization, Epidemiology, and Detection of This Important Resistance Threat , 2001, Clinical Microbiology Reviews.

[110]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[111]  G. Sundin,et al.  Dissemination of the strA‐strB streptomycin‐resistance genes among commensal and pathogenic bacteria from humans, animals, and plants , 1996, Molecular ecology.

[112]  T. Chang,et al.  THE CONCURRENT USE OF SULFONAMIDES AND ANTIBIOTICS IN THE TREATMENT OF INFECTIONS: IN VIVO AND IN VITRO STUDIES OF THE EFFECT OF SULFONAMIDE‐ANTIBIOTIC COMBINATIONS ON THE EMERGENCE OF DRUG RESISTANCE , 1957, Annals of the New York Academy of Sciences.