Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Moon Y. F. Tay | M. Koopmans | T. Petersen | S. Wuertz | N. Gemmell | D. Djurović | S. Brar | F. Berglund | D. Larsson | C. Manaia | V. Bartkevičs | H. Hur | M. Sobsey | A. Bērziņš | B. Kocsis | J. Avsejenko | M. Streikiša | M. Y. Tay | E. Sozzi | R. Hendriksen | K. Keddy | F. Allerberger | D. Rodrigues | A. Begum | J. Meschke | J. Collard | Sukhwan Yoon | A. M. de Roda Husman | E. Lytras | M. Kuroda | G. Bosevska | A. Nitsche | J. Hrenović | R. Mdegela | C. Brinch | M. Cormican | C. Yost | I. A. Odetokun | K. Gibb | R. Zuniga-Montanez | T. Berendonk | M. Quintela-Baluja | P. Hong | Z. Daoud | V. Thamlikitkul | R. Karpíšková | R. Hasan | H. Schmitt | S. Kayama | M. Sugai | M. Kochubovski | R. Cojocaru | J. Moran-Gilad | A. Brinkmann | J. Mohammed | S. Schubert | P. Jensen | M. V. van Passel | S. Cuadros-Orellana | S. Shakoor | O. Vandenberg | J. Kjeldgaard | C. Rutgersson | A. Ahmed | W. Gaze | A. Wester | A. Ngandjio | C. Ke | Jaqueline Rocha | J. Bunce | M. Song | L. Norrgren | S. Örn | N. Solymosi | R. Boss | M. Perry | L. Malania | M. Mohsin | A. Heikinheimo | N. Beck | F. Ejobi | D. Morris | B. Njanpop-Lafourcade | P. Truska | T. Eguale | M. Alebouyeh | Pratik Kumar | F. Soria | L. O’Connor | P. Feglo | A. Bego | I. Ivanov | A. Battisti | D. Wasyl | P. Donado-Godoy | P. Power | A. Seyfarth | G. Matar | H. Kumburu | A. Di Cesare | Gianluca Corno | D. Vubil | Junzo Hisatsune | C. Kotzamanidis | D. Tabo | K. Fashae | Xiaoyang Jiao | M. Legesse | L. Raka | Kaknokrat Chonsin | O. Suthienkul | L. Hansen | B. Bouchrif | B. Karraouan | B. Levent | M. Cerdà-Cuéllar | C. Svendsen | C. Saba | F. Fani | G. Kwenda | D. Banda | A. Bastaraud | Sivachandran Parimannan | Liansheng Yu | J. Schaeffer | S. Cassar | C. A. Tagliati | Y. Hounmanou | P. Munk | T. Wittum | M. F. Valencia | Joe Brown | Lihong Zhang | C. Penny | B. Sanneh | Yongjie Yu | B. V. van Bunnik | D. Spiteri | P. Alba | Jia-yong Zhao | M. Jergović | M. Ballal | P. Collignon | D. Capone | M. Abouelnaga | H. Shin | Kristīna Kokina | F. Aarestrup | L. Samison | B. Magtibay | A. Leonard | M. R. Andrianarivelo | R. Holmstad | C. Kiiyukia | Dionisia Lambrinidis | Ilse Y. Pieters | Kareem Charlemagne | E. Paredes-Osses | Z. Z. Hossain | S. Le Guyader | Teddie Rahube | A. Nzouankeu | M. Trkov | T. R. Thorsteinsdottir | Yu-Ping Hong | Dougnon Victorien | O. Burduniuc | J. Villacís | Č. Butrimaitė-Ambrozevičienė | S. J. Santchurn | K. J. Coulibaly | Guilherme C. Oliveira | T. Oumar | C. D. Van | A. D. Adell | T. Chung | L. Lau | Kazi Jamil | A. Gassama† | Huanying Zheng | E. Diaconu | T. N. Petersen | Yith Vuthy | Eric Ng’eno | S. Fakhraldeen | C. Kurekci | M. F. Salem | R. A. Banu | Gert‐Jan Jeunen | S. Vilchez | S. Pathirage | A. M. Hatha | N. Rigamonti | A. Pereckienė | Larissa Camila Ribeiro de Souza | Frederik Duus Møller | Artan Pablo Catherine Dionisia Elizabeth Heather Jakobse Bego Power Rees Lambrinidis Neilson Gibb Co | Catherine Rees | Kris Coventry | Carlon Worrell | Angela Daniela Salazar Gutierrez | V. R. Grujić | Nataša Mazalica | Bonkoungou Isidore Juste | Thet Sopheak | Ziem A. Abah Jacques Olivier | María Cristina Martínez | Li Baisheng | Zhao Jiayong | Johan F. Bernal Morales | Zozo Nyarukweba Deogratias | Bodil Elsborg | Marliin Koolmeister | Sina Hesse | Sergio A. Lickes | Sohan Bangera | Zeinegul Shakenova | Tareq Alaati | H. Rajandas | Malcolm Vella Haber | Aleksandar Vujačić | Pushkar Pal | Fania Perez Mendoza | Jorge Huete-Pιrez | Ibrahim Raufu Adisa | Anne-Marie Sørgaard | P. Ryrfors | Natalie Weiler Gustafson | Claudia Huber Schill | Maria Luz Zamudio Rojas | Jorge Echevarria Velasquez | Kris Catangcatang | Ruby Sibulo | Felipe Campos Yauce | J. Martins | P. Álvaro | Doris Di Yoong Wen | V. Radosavljević | D. Gavačová | Katarína Pastuchová | Kerneels Esterhuyse | Mariano Gomez Lopez | R. R. D. P. Perera | N. Bandara | H. I. Premasiri | T. Van der Heijden | Bawimodom Bidjada | Somtinda Christelle Nikiema-Pessinaba | J. Thomsen | Ouidiane Obaidi | Laila Mohamed Jassim | Andrew Moore | B. Lefor | Michael Davis | Pardi Sukapanpatharam | Phuong Truong | R. Lilienthal | Sanghoon Kang | Patricia Baklayan | Doan Nguyen Minh Tran | Nguyen Do Phuc | Mark Woolhouse | J. Kalule | S. Chambers | T. Rasolofoarison | D. Graham | Elizabeth Heather Jakobsen Neilson | Arshana Amin | F. D. Møller | D. T. N. Tran | R. Perera | Liansheng Yu | Emanuele Sozzi | Bakary Sanneh | Fanny Berglund | Anne F. C. Leonard | M. Davis | Teresa Chung | F. P. Mendoza | V. Radosavljevic | Y. G. Hounmanou | N. W. Gustafson | Patricia Alba | M. L. Z. Rojas | Happiness H. Kumburu | Baisheng Li | Shizuo Kayama | David Spiteri | Patrick Munk | Thorunn R. Thorsteinsdottir | Sara Cuadros-Orellana | Y. M. Hounmanou | Jacob Moran-Gilad

[1]  M. Gillings,et al.  Assessment of global health risk of antibiotic resistance genes , 2022, Nature Communications.

[2]  Alan D. Lopez,et al.  Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis , 2022, The Lancet.

[3]  R. Kaas,et al.  Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns , 2021, Microbiology spectrum.

[4]  Christine L. Sun,et al.  Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing , 2021, bioRxiv.

[5]  Stephanie L. Hyland,et al.  A global metagenomic map of urban microbiomes and antimicrobial resistance , 2021, Cell.

[6]  E. Garner,et al.  Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant , 2021, Frontiers in Microbiology.

[7]  F. Aarestrup,et al.  A Peek into the Plasmidome of Global Sewage , 2021, bioRxiv.

[8]  Shiraz A. Shah,et al.  The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition. , 2021, Cell host & microbe.

[9]  Graham W. Taylor,et al.  Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Nature.

[10]  G. Cochrane,et al.  The European Bioinformatics Institute: empowering cooperation in response to a global health crisis , 2020, Nucleic Acids Res..

[11]  F. Aarestrup,et al.  Long-Term Temporal Stability of the Resistome in Sewage from Copenhagen , 2020, mSystems.

[12]  F. Aarestrup,et al.  Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing , 2020, medRxiv.

[13]  Moon Y. F. Tay,et al.  Setting a baseline for global urban virome surveillance in sewage , 2020, Scientific Reports.

[14]  S. Eubank,et al.  Commentary on Ferguson, et al., “Impact of Non-pharmaceutical Interventions (NPIs) to Reduce COVID-19 Mortality and Healthcare Demand” , 2020, Bulletin of Mathematical Biology.

[15]  I. Brito,et al.  Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C , 2020, Nature Communications.

[16]  Robin Patel,et al.  Molecular and clinical epidemiology of carbapenem-resistant Enterobacterales in the USA (CRACKLE-2): a prospective cohort study. , 2020, The Lancet. Infectious diseases.

[17]  O. Lund,et al.  Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering , 2020, Scientific Reports.

[18]  F. Aarestrup,et al.  Using sewage for surveillance of antimicrobial resistance , 2020, Science.

[19]  Jose V. Lopez,et al.  Host population genetics and biogeography structure the microbiome of the sponge Cliona delitrix , 2020, Ecology and evolution.

[20]  Danielle G. Lemay,et al.  The fecal resistome of dairy cattle is associated with diet during nursing , 2019, Nature Communications.

[21]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[22]  Lenwood S. Heath,et al.  NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes , 2019, Microbiome.

[23]  Jie Tan,et al.  PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning , 2019, GigaScience.

[24]  A. Shade,et al.  A global survey of arsenic-related genes in soil microbiomes , 2019, BMC Biology.

[25]  G. Cochrane,et al.  Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage , 2019, Nature Communications.

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

[27]  P. Collignon,et al.  Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis. , 2018, The Lancet. Planetary health.

[28]  Ole Lund,et al.  Rapid and precise alignment of raw reads against redundant databases with KMA , 2018, BMC Bioinformatics.

[29]  Falk Hildebrand,et al.  Structure and function of the global topsoil microbiome , 2018, Nature.

[30]  R. Dewhurst,et al.  The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle , 2017, Microbiome.

[31]  Jean M. Macklaim,et al.  Microbiome Datasets Are Compositional: And This Is Not Optional , 2017, Front. Microbiol..

[32]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[33]  A. Abate,et al.  SiC-Seq: Single-cell genome sequencing at ultra high-throughput with microfluidic droplet barcoding , 2017, Nature Biotechnology.

[34]  U. Sekar,et al.  Carbapenemase-producing Enterobacteriaceae: Risk factors for infection and impact of resistance on outcomes , 2017, International journal of applied & basic medical research.

[35]  F. Aarestrup,et al.  Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition , 2016, mSystems.

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

[37]  Sanket Patel,et al.  Interconnected microbiomes and resistomes in low-income human habitats , 2016, Nature.

[38]  M. Balouiri,et al.  Methods for in vitro evaluating antimicrobial activity: A review☆ , 2015, Journal of pharmaceutical analysis.

[39]  Jianzhong Shen,et al.  Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. , 2015, The Lancet. Infectious diseases.

[40]  Tal Galili,et al.  dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering , 2015, Bioinform..

[41]  Paul Turner,et al.  Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events , 2015, Nature Genetics.

[42]  Luis Pedro Coelho,et al.  Structure and function of the global ocean microbiome , 2015, Science.

[43]  Jianzhong Shen,et al.  Report of ribosomal RNA methylase gene erm(B) in multidrug-resistant Campylobacter coli. , 2014, The Journal of antimicrobial chemotherapy.

[44]  J. Collins,et al.  Antibiotic Treatment Expands the Resistance Reservoir and Ecological Network of the Phage Metagenome , 2013, Nature.

[45]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[46]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[47]  Otto X. Cordero,et al.  Ecology drives a global network of gene exchange connecting the human microbiome , 2011, Nature.

[48]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[49]  N. Woodford,et al.  Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study , 2010, The Lancet. Infectious diseases.

[50]  W. Whitman,et al.  The ecological coherence of high bacterial taxonomic ranks , 2010, Nature Reviews Microbiology.

[51]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[52]  J. Blanco,et al.  Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15. , 2007, The Journal of antimicrobial chemotherapy.

[53]  R. Cantón,et al.  The CTX-M β-lactamase pandemic , 2006 .

[54]  R. Cantón,et al.  The CTX-M beta-lactamase pandemic. , 2006, Current opinion in microbiology.

[55]  John W. Taylor,et al.  Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea , 2003, Science.

[56]  N. E. Jensen,et al.  Resistance to antimicrobial agents used for animal therapy in pathogenic‐, zoonotic‐ and indicator bacteria isolated from different food animals in Denmark: a baseline study for the Danish Integrated Antimicrobial Resistance Monitoring Programme (DANMAP) , 1998, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[57]  G. Ayliffe.  The progressive intercontinental spread of methicillin-resistant Staphylococcus aureus. , 1997, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[58]  P. Courvalin.  Transfer of antibiotic resistance genes between gram-positive and gram-negative bacteria , 1994, Antimicrobial Agents and Chemotherapy.

[59]  Antonio Lizana Malinconi.  Facultad de Ciencias Agrarias y Forestales , 1986 .

[60]  J. Aitchison.  Principal component analysis of compositional data , 1983 .