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Kohle S, Petersen TN, Vigre H, Johansson MHK, Aarestrup FM. Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity. PLoS One 2024; 19:e0300733. [PMID: 38753691 PMCID: PMC11098379 DOI: 10.1371/journal.pone.0300733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/04/2024] [Indexed: 05/18/2024] Open
Abstract
Accurate monitoring of gastro-enteric and other diseases in large populations poses a challenge for public health management. Sewage represents a larger population, is freely obtainable and non-subject to ethical approval. Metagenomic sequencing offers simultaneous, multiple-target analysis. However, no study has demonstrated the sensitivity of metagenomics for detecting bacteria in sewage. In this study, we spot-released 1013 colony-forming units (CFU) of Staphyloccus hyicus (non-pathogenetic strain 842J-88). The strain was flushed down a toilet into the sewer in the catchment area of a public wastewater treatment plant (WWTP), serving a population of 36,000 people. Raw sewage was continuously sampled at the WWTP's inlet over 30- and 60-minute intervals for a total period of seven hours. The experiment was conducted twice with one week in-between release days and under comparable weather conditions. For the metagenomics analyses, the pure single isolate of S. hyicus was sequenced, assembled and added to a large database of bacterial reference sequences. All sewage samples were analyzed by shotgun metagenome sequencing and mapped against the reference database. S. hyicus was identified in duplicate samples at both of two release days and these sequence fragment counts served as a proxy to estimate the minimum number of sick people or sensitivity required in order to observe at least one sick person at 95% probability. We found the sensitivity to be in the range 41-140 and 16-36 sick people at release days 1 and 2, respectively. The WWTP normally serves 36,000 people giving a normalized sensitivity in the range of one in 257 to 2,250 persons.
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Affiliation(s)
- Simon Kohle
- Research Group for Genomic Epidemiology, DTU-Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas N. Petersen
- Research Group for Genomic Epidemiology, DTU-Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Håkan Vigre
- Research Group for Genomic Epidemiology, DTU-Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, DTU-Food, Technical University of Denmark, Kongens Lyngby, Denmark
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Toyting J, Nuanmuang N, Utrarachkij F, Supha N, Thongpanich Y, Leekitcharoenphon P, Aarestrup FM, Sato T, Thapa J, Nakajima C, Suzuki Y. Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Microbiol Spectr 2024; 12:e0421623. [PMID: 38563788 PMCID: PMC11064549 DOI: 10.1128/spectrum.04216-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.
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Affiliation(s)
- Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Neunghatai Supha
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Yuwanda Thongpanich
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Toyotaka Sato
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
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Munk P, Yang D, Röder T, Maier L, Petersen TN, Duarte ASR, Clausen PTLC, Brinch C, Van Gompel L, Luiken R, Wagenaar JA, Schmitt H, Heederik DJJ, Mevius DJ, Smit LAM, Bossers A, Aarestrup FM. The European livestock resistome. mSystems 2024; 9:e0132823. [PMID: 38501800 PMCID: PMC11019871 DOI: 10.1128/msystems.01328-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.
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Affiliation(s)
- Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Dongsheng Yang
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Leonie Maier
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | | | | | | | - Christian Brinch
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Roosmarijn Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Dick J. J. Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Dik J. Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Lidwien A. M. Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - EFFORT ConsortiumGravelandHaitskeGonzalez-ZornBrunoMoyanoGabrielSandersPascalChauvinClaireBattistiAntonioDewulfJeroenWadepohlKatharinaWasylDariuszSkarzyńskaMagdalenaZajacMagdalenaPękala-SafińskaAgnieszkaDaskalovHristoStärkKatharina D. C.
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
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Karlsmose AK, Ivanova M, Kragh ML, Kjeldgaard JS, Otani S, Svendsen CA, Papić B, Zdovc I, Tasara T, Stephan R, Heir E, Langsrud S, Møretrø T, Dalgaard P, Fagerlund A, Hansen LT, Aarestrup FM, Leekitcharoenphon P. A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities. Infect Genet Evol 2024; 119:105582. [PMID: 38467173 DOI: 10.1016/j.meegid.2024.105582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
Listeria monocytogenes is an important human pathogen with a high mortality rate. Consumption of contaminated ready-to-eat food is the main mode of transmission to humans. Disinfectant-tolerant L. monocytogenes have emerged, which are believed to have increased persistence potential. Elucidating the mechanisms of L. monocytogenes disinfectant tolerance has been the focus of previous studies using pure cultures. A limitation of such approach is the difficulty to identify strains with reduced susceptibility due to inter-strain variation and the need to screen large numbers of strains and genes. In this study, we applied a novel metagenomic approach to detect genes associated with disinfectant tolerance in mixed L. monocytogenes planktonic communities. Two communities, consisting of 71 and 80 isolates each, were treated with the food industry disinfectants benzalkonium chloride (BC, 1.75 mg/L) or peracetic acid (PAA, 38 mg/L). The communities were subjected to metagenomic sequencing and differences in individual gene abundances between biocide-free control communities and biocide-treated communities were determined. A significant increase in the abundance of Listeria phage-associated genes was observed in both communities after treatment, suggesting that prophage carriage could lead to an increased disinfectant tolerance in mixed L. monocytogenes planktonic communities. In contrast, a significant decrease in the abundance of a high-copy emrC-harbouring plasmid pLmN12-0935 was observed in both communities after treatment. In PAA-treated community, a putative ABC transporter previously found to be necessary for L. monocytogenes resistance to antimicrobial agents and virulence, was among the genes with the highest weight for differentiating treated from control samples. The undertaken metagenomic approach in this study can be applied to identify genes associated with increased tolerance to other antimicrobials in mixed bacterial communities.
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Affiliation(s)
- Agnete Kirstine Karlsmose
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mirena Ivanova
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Laage Kragh
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jette Sejer Kjeldgaard
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christina Aaby Svendsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Even Heir
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Solveig Langsrud
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Trond Møretrø
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Paw Dalgaard
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annette Fagerlund
- Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Lisbeth Truelstrup Hansen
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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5
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Roer L, Kaya H, Tedim AP, Novais C, Coque TM, Aarestrup FM, Peixe L, Hasman H, Hammerum AM, Freitas AR. VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data. Microbiol Spectr 2024; 12:e0372423. [PMID: 38329344 PMCID: PMC10913372 DOI: 10.1128/spectrum.03724-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.
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Affiliation(s)
- Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
| | - Luísa Peixe
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M. Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana R. Freitas
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - On behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
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Martiny HM, Pyrounakis N, Petersen TN, Lukjančenko O, Aarestrup FM, Clausen PTLC, Munk P. ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets. Bioinformatics 2024; 40:btae086. [PMID: 38377397 PMCID: PMC10918635 DOI: 10.1093/bioinformatics/btae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/11/2023] [Accepted: 02/19/2024] [Indexed: 02/22/2024] Open
Abstract
MOTIVATION Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind. RESULTS In this work, we have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of ARGs. ARGprofiler tackles the challenge of deciding which reference database to use by providing the PanRes database of 14 078 unique ARGs that combines several existing collections into one. Our pipeline is designed to not only produce abundance tables of genes and microbes but also to reconstruct the flanking regions of ARGs with ARGextender. ARGextender is a bioinformatic approach combining KMA and SPAdes to recruit reads for a targeted de novo assembly. While our aim is on ARGs, the pipeline also creates Mash sketches for fast searching and comparisons of sequencing runs. AVAILABILITY AND IMPLEMENTATION The ARGprofiler pipeline is a Snakemake workflow that supports the reuse of metagenomic sequencing data and is easily installable and maintained at https://github.com/genomicepidemiology/ARGprofiler.
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Affiliation(s)
- Hannah-Marie Martiny
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Nikiforos Pyrounakis
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Thomas N Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Oksana Lukjančenko
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Philip T L C Clausen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Henrik Danms Allé, Bygning 204, Kongens Lyngby 2800, Denmark
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7
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Masirika LM, Udahemuka JC, Schuele L, Ndishimye P, Otani S, Mbiribindi JB, Marekani JM, Mambo LM, Bubala NM, Boter M, Nieuwenhuijse DF, Lang T, Kalalizi EB, Musabyimana JP, Aarestrup FM, Koopmans M, Oude Munnink BB, Siangoli FB. Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024. Euro Surveill 2024; 29:2400106. [PMID: 38487886 PMCID: PMC10941309 DOI: 10.2807/1560-7917.es.2024.29.11.2400106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024] Open
Abstract
Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases from the South Kivu province. Phylogenetic analyses reveal that the MPXV affecting the cases belongs to a novel Clade I sub-lineage. The outbreak strain genome lacks the target sequence of the probe and primers of a commonly used Clade I-specific real-time PCR.
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Affiliation(s)
- Leandre Murhula Masirika
- Centre de Recherche en Sciences Naturelles de Lwiro, DS Bukavu, South Kivu, Bukavu, Democratic Republic of the Congo
- SaBio Instituto de Investigación en Recursos Cinegéticos IREC (Universidad de Castilla-La Mancha & CSIC), Ciudad Real, Spain
| | - Jean Claude Udahemuka
- Department of Veterinary Medicine, University of Rwanda, Nyagatare, Rwanda
- Stansile Research Organization, Kigali, Rwanda
| | - Leonard Schuele
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pacifique Ndishimye
- Stansile Research Organization, Kigali, Rwanda
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Research and Innovation Centre, African Institute for Mathematical Sciences, Kigali, Rwanda
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Jean M Marekani
- Unit of Animal Production and Health, Nature Conservation and Development, Department of Biology, Faculty of Science, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Léandre Mutimbwa Mambo
- Zone de Santé de Kamituga, Kamituga, South Kivu, Bukavu, Democratic Republic of the Congo
| | | | - Marjan Boter
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudie Lang
- The Global Health Network, Oxford University, Oxford, United Kingdom
| | - Ernest Balyahamwabo Kalalizi
- SaBio Instituto de Investigación en Recursos Cinegéticos IREC (Universidad de Castilla-La Mancha & CSIC), Ciudad Real, Spain
| | - Jean Pierre Musabyimana
- Research, innovation and data science division, Rwanda Biomedical Center, Kigali, Rwanda
- Stansile Research Organization, Kigali, Rwanda
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- These authors contributed equally
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Freddy Belesi Siangoli
- These authors contributed equally
- Division Provinciale de la Santé, South Kivu, Bukavu, Democratic Republic of the Congo
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8
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Leekitcharoenphon P, Otani S, Szarvas J, Mzee T, Kumburu H, Møller FD, Aarestrup FM. The first complete genome sequence of Staphylococcus aureus ST5477. Microbiol Resour Announc 2024; 13:e0100423. [PMID: 38179915 PMCID: PMC10868164 DOI: 10.1128/mra.01004-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
This study presents the first complete genome of Staphylococcus aureus ST5477, one of the most common sequence types (ST) from bovine in eastern Africa. The genome consists of a 2,723,132-bp circular chromosome and a 3,044-bp plasmid. This strain was collected in 2017 from cow milk in Tanzania.
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Affiliation(s)
- Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Judit Szarvas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tutu Mzee
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo, Tanzania
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Kilimanjaro, Tanzania
| | - Frederik Duus Møller
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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9
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Gmeiner A, Njage PMK, Hansen LT, Aarestrup FM, Leekitcharoenphon P. Predicting Listeria monocytogenes virulence potential using whole genome sequencing and machine learning. Int J Food Microbiol 2024; 410:110491. [PMID: 38000216 DOI: 10.1016/j.ijfoodmicro.2023.110491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/06/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Contamination with food-borne pathogens, such as Listeria monocytogenes, remains a big concern for food safety. Hence, rigorous and continuous microbial surveillance is a standard procedure. At this point, however, the food industry and authorities only focus on detection of Listeria monocytogenes without characterization of individual strains into groups of more or less concern. As whole genome sequencing (WGS) gains increasing interest in the industry, this methodology presents an opportunity to obtain finer resolution of microbial traits such as virulence. Within this study, we therefore aimed to explore the use of WGS in combination with Machine Learning (ML) to predict L. monocytogenes virulence potential on a sub-species level. The WGS datasets used in this study for ML model training consisted of i) national surveillance isolates (n = 169, covering 38 MLST types) and ii) publicly available isolates acquired through the GenomeTrakr network (n = 2880, spanning 80 MLST types). We used the clinical frequency, i.e., ratio of the number of clinical isolates to total amount of isolates, as estimate for virulence potential. The predictive performance of input features from three different genomic levels (i.e., virulence genes, pan-genome genes, and single nucleotide polymorphisms (SNPs)) and six machine learning algorithms (i.e., Support Vector Machine with a linear kernel, Support Vector Machine with a radial kernel, Random Forrest, Neural Networks, LogitBoost, and Majority Voting) were compared. Our machine learning models predicted sub-species virulence potential with nested cross-validation F1-scores up to 0.88 for the majority voting classifier trained on national surveillance data and using pan-genome genes as input features. The validation of the pre-trained ML models based on 101 previously in vivo studied isolates resulted in F1-scores up to 0.76. Furthermore, we found that the more rapid and less computationally intensive raw read alignment yields comparably accurate models as de novo assembly. The results of our study suggest that a majority voting classifier trained on pan-genome genes is the best and most robust choice for the prediction of clinical frequency. Our study contributes to more rapid and precise characterization of L. monocytogenes virulence and its variation on a sub-species level. We further demonstrated a possible application of WGS data in the context of microbial hazard characterization for food safety. In the future, predictive models may assist case-specific microbial risk management in the food industry. The python code, pre-trained models, and prediction pipeline are deposited at (https://github.com/agmei/LmonoVirulenceML).
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Affiliation(s)
- Alexander Gmeiner
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark.
| | - Patrick Murigu Kamau Njage
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| | - Lisbeth Truelstrup Hansen
- National Food Institute, Technical University of Denmark, Research Group for Food Microbiology and Hygiene, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
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10
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Bogri A, Jensen EEB, Borchert AV, Brinch C, Otani S, Aarestrup FM. Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations. mSystems 2024; 9:e0101823. [PMID: 38095429 PMCID: PMC10805027 DOI: 10.1128/msystems.01018-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations. We explored whether the effect of antimicrobial treatment is detectable with metagenomic sequencing, and whether AMR genes can be spread and established in unchallenged (not treated with antibiotics) individuals following contact with treated donors, and under various frequencies of interaction. Gut and soil substrate microbiomes were investigated by metagenomic sequencing for bacterial community composition and resistome profiling. We found that tetracycline treatment altered the treated gut microbiome by decreasing bacterial diversity and increasing the abundance of tetracycline resistance genes. Untreated cockroaches that interacted with treated donors also had elevated tetracycline resistance. The levels of resistance differed depending on the magnitude and frequency of donor transfer. Additionally, treated donors showed signs of microbiome recovery due to their interaction with the untreated ones. Similar patterns were also recorded in the soil substrate microbiomes. Our results shed light on how interacting microbiomes facilitate AMR gene transmission to previously unchallenged hosts, a dynamic influenced by the interaction frequencies, using an in vivo model to validate theoretical AMR transmission models.IMPORTANCEAntimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.
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Affiliation(s)
- Amalia Bogri
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | | | - Asbjørn Vedel Borchert
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
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11
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Thorn AV, Aarestrup FM, Munk P. Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis. Microbiol Spectr 2024; 12:e0241323. [PMID: 38084973 PMCID: PMC10783016 DOI: 10.1128/spectrum.02413-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.
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Affiliation(s)
- Alix Vincent Thorn
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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12
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Lu L, Zhang F, Oude Munnink BB, Munger E, Sikkema RS, Pappa S, Tsioka K, Sinigaglia A, Dal Molin E, Shih BB, Günther A, Pohlmann A, Ziegler U, Beer M, Taylor RA, Bartumeus F, Woolhouse M, Aarestrup FM, Barzon L, Papa A, Lycett S, Koopmans MPG. West Nile virus spread in Europe: Phylogeographic pattern analysis and key drivers. PLoS Pathog 2024; 20:e1011880. [PMID: 38271294 PMCID: PMC10810478 DOI: 10.1371/journal.ppat.1011880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/04/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND West Nile virus (WNV) outbreaks in birds, humans, and livestock have occurred in multiple areas in Europe and have had a significant impact on animal and human health. The patterns of emergence and spread of WNV in Europe are very different from those in the US and understanding these are important for guiding preparedness activities. METHODS We mapped the evolution and spread history of WNV in Europe by incorporating viral genome sequences and epidemiological data into phylodynamic models. Spatially explicit phylogeographic models were developed to explore the possible contribution of different drivers to viral dispersal direction and velocity. A "skygrid-GLM" approach was used to identify how changes in environments would predict viral genetic diversity variations over time. FINDINGS Among the six lineages found in Europe, WNV-2a (a sub-lineage of WNV-2) has been predominant (accounting for 73% of all sequences obtained in Europe that have been shared in the public domain) and has spread to at least 14 countries. In the past two decades, WNV-2a has evolved into two major co-circulating clusters, both originating from Central Europe, but with distinct dynamic history and transmission patterns. WNV-2a spreads at a high dispersal velocity (88km/yr-215 km/yr) which is correlated to bird movements. Notably, amongst multiple drivers that could affect the spread of WNV, factors related to land use were found to strongly influence the spread of WNV. Specifically, the intensity of agricultural activities (defined by factors related to crops and livestock production, such as coverage of cropland, pasture, cultivated and managed vegetation, livestock density) were positively associated with both spread direction and velocity. In addition, WNV spread direction was associated with high coverage of wetlands and migratory bird flyways. CONCLUSION Our results suggest that-in addition to ecological conditions favouring bird- and mosquito- presence-agricultural land use may be a significant driver of WNV emergence and spread. Our study also identified significant gaps in data and the need to strengthen virological surveillance in countries of Central Europe from where WNV outbreaks are likely seeded. Enhanced monitoring for early detection of further dispersal could be targeted to areas with high agricultural activities and habitats of migratory birds.
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Affiliation(s)
- Lu Lu
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Feifei Zhang
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bas B. Oude Munnink
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
| | - Emmanuelle Munger
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
| | - Reina S. Sikkema
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
| | - Styliani Pappa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Katerina Tsioka
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Barbara B. Shih
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Anne Günther
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Riems, Germany
| | - Rachel A. Taylor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, United Kingdom
| | - Frederic Bartumeus
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- Centre for Research on Ecology and Forestry Applications (CREAF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Samantha Lycett
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Marion P. G. Koopmans
- Erasmus MC, Viroscience and Pandemic and Disaster Preparedness Centre, Rotterdam, the Netherlands
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13
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Bonaldo F, Avot BJP, De Cesare A, Aarestrup FM, Otani S. Foodborne Pathogen Dynamics in Meat and Meat Analogues Analysed Using Traditional Microbiology and Metagenomic Sequencing. Antibiotics (Basel) 2023; 13:16. [PMID: 38275326 PMCID: PMC10812575 DOI: 10.3390/antibiotics13010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Meat analogues play an increasing role in meeting global nutritional needs. However, while it is well known that meat possesses inherent characteristics that create favourable conditions for the growth of various pathogenic bacteria, much less is known about meat analogues. This study aimed to compare the growth and survival of Escherichia coli HEHA16, Listeria monocytogenes, Salmonella enterica Typhi, Cronobacter sakazakii, and a cocktail of these bacteria in sterile juices from minced chicken, pig, and beef, as well as pea-based and soy-based minced meat. Traditional microbiology and next-generation sequencing of those metagenomes were employed to analyse the pathogen variability, abundance, and survival after an incubation period. Our findings show that all the meat juices provided favourable conditions for the growth and proliferation of the studied bacteria, with the exception of E. coli HEHA16, which showed lower survival rates in the chicken matrix. Meat analogue juice mainly supported L. monocytogenes survival, with C. sakazakii survival supported to a lesser extent. A correlation was observed between the traditional culturing and metagenomic analysis results, suggesting that further work is needed to compare these technologies in foodborne setups. Our results indicate that plant-based meats could serve as vectors for the transmission of certain, but likely not all, foodborne pathogens, using two accurate detection methods. This warrants the need for additional research to better understand and characterise their safety implications, including their potential association with additional pathogens.
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Affiliation(s)
- Francesco Bonaldo
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano Emilia, Italy;
| | - Baptiste Jacques Philippe Avot
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (B.J.P.A.); (F.M.A.)
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano Emilia, Italy;
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (B.J.P.A.); (F.M.A.)
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (B.J.P.A.); (F.M.A.)
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14
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Lepper HC, Perry MR, Wee BA, Wills D, Nielsen H, Otani S, Simon M, Aarestrup FM, Woolhouse MEJ, van Bunnik BAD. Distinctive hospital and community resistomes in Scottish urban wastewater: Metagenomics of a paired wastewater sampling design. Sci Total Environ 2023; 902:165978. [PMID: 37544442 DOI: 10.1016/j.scitotenv.2023.165978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/08/2023]
Abstract
The wastewater microbiome contains a multitude of resistant bacteria of human origin, presenting an opportunity for surveillance of resistance in the general population. However, wastewater microbial communities are also influenced by clinical sources, such as hospitals. Identifying signatures of the community and hospital resistome in wastewater is needed for interpretation and risk analysis. In this study, we compare the resistome and microbiome of hospital, community, and mixed municipal wastewater to investigate how and why the composition of these different sites differ. We conducted shotgun metagenomic analysis on wastewater samples from eight wastewater treatment plants (WWTPs), four hospitals, and four community sites in Scotland, using a paired sampling design. Cluster analysis and source attribution random forest models demonstrated that the hospital resistome was distinct from community and WWTP resistomes. Hospital wastewater had a higher abundance and diversity of resistance genes, in keeping with evidence that hospitals act as a reservoir and enricher of resistance. However, this distinctive 'hospital' signature appeared to be weak in the resistome of downstream WWTPs, likely due to dilution. We conclude that hospital and community wastewater resistomes differ, with the hospital wastewater representing a reservoir of patient- and hospital environment-associated bacteria. However, this 'hospital' signature is transient and does not overwhelm the community signature in the resistome of the downstream WWTP influent.
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Affiliation(s)
- Hannah C Lepper
- Usher Institute, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Meghan R Perry
- Usher Institute, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom; Clinical Infection Research Group, NHS Lothian Infection Service, Edinburgh, United Kingdom.
| | - Bryan A Wee
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
| | - David Wills
- Scottish Water, Currie, Edinburgh EH14 4AP, United Kingdom.
| | - Hanne Nielsen
- National Food Institute, The Technical University of Denmark, Kemitorvet Bygning 202, 2800 Kongens Lyngby, Denmark.
| | - Saria Otani
- National Food Institute, The Technical University of Denmark, Kemitorvet Bygning 202, 2800 Kongens Lyngby, Denmark.
| | - Moray Simon
- Scottish Water, Currie, Edinburgh EH14 4AP, United Kingdom.
| | - Frank M Aarestrup
- National Food Institute, The Technical University of Denmark, Kemitorvet Bygning 202, 2800 Kongens Lyngby, Denmark.
| | - Mark E J Woolhouse
- Usher Institute, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Bram A D van Bunnik
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
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15
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Apenteng OO, Aarestrup FM, Vigre H. Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints. Sci Rep 2023; 13:20410. [PMID: 37990114 PMCID: PMC10663573 DOI: 10.1038/s41598-023-47754-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Current surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier. Here, we simulate the results of an AMR surveillance program based on metagenomics in the Danish pig population. We modelled both an increase in the occurrence of ARGs and an introduction of a new ARG in a few farms and the subsequent spread to the entire population. To make the simulation realistic, the total cost of the surveillance was constrained, and the sampling schedule was set at one pool per month with 5, 20, 50, or 100 samples. Our simulations demonstrate that a pool of 20-50 samples and a sequencing depth of 250 million fragments resulted in the shortest time to detection in both scenarios, with a time delay to detection of change of [Formula: see text]15 months in all scenarios. Compared with culture-based surveillance, our simulation indicates that there are neither significant reductions nor increases in time to detect a change using metagenomics. The benefit of metagenomics is that it is possible to monitor all known resistance in one sampling and laboratory procedure in contrast to the current monitoring that is based on the phenotypic characterisation of selected indicator bacterial species. Therefore, overall changes in AMR in a population will be detected earlier using metagenomics due to the fact that the resistance gene does not have to be transferred to and expressed by an indicator bacteria before it is possible to detect.
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Affiliation(s)
- Ofosuhene O Apenteng
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
- Section of Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Håkan Vigre
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
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16
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Njage PMK, van Bunnik B, Munk P, Marques ARP, Aarestrup FM. Association of health, nutrition, and socioeconomic variables with global antimicrobial resistance: a modelling study. Lancet Planet Health 2023; 7:e888-e899. [PMID: 37940209 DOI: 10.1016/s2542-5196(23)00213-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/22/2023] [Accepted: 09/01/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Although antimicrobial use is a key selector for antimicrobial resistance, recent studies have suggested that the ecological context in which antimicrobials are used might provide important factors for the prediction of the emergence and spread of antimicrobial resistance. METHODS We used 1547 variables from the World Bank dataset consisting of socioeconomic, developmental, health, and nutritional indicators; data from a global sewage-based study on antimicrobial resistance (abundance of antimicrobial resistance genes [ARGs]); and data on antimicrobial usage computed from the ECDC database and the IQVIA database. We characterised and built models predicting the global resistome at an antimicrobial class level. We used a generalised linear mixed-effects model to estimate the association between antimicrobial usage and ARG abundance in the sewage samples; a multivariate random forest model to build predictive models for each antimicrobial resistance class and to select the most important variables for ARG abundance; logistic regression models to test the association between the predicted country-level antimicrobial resistance abundance and the country-level proportion of clinical resistant bacterial isolates; finite mixture models to investigate geographical heterogeneities in the abundance of ARGs; and multivariate finite mixture models with covariates to investigate the effect of heterogeneity in the association between the most important variables and the observed ARG abundance across the different country subgroups. We compared our predictions with available clinical phenotypic data from the SENTRY Antimicrobial Surveillance Program from eight antimicrobial classes and 12 genera from 56 countries. FINDINGS Using antimicrobial use data from between Jan 1, 2016, and Dec 31, 2019, we found that antimicrobial usage was not significantly associated with the global ARG abundance in sewage (p=0·72; incidence rate ratio 1·02 [95% CI 0·92-1·13]), whereas country-specific World Bank's variables explained a large amount of variation. The importance of the World Bank variables differed between antimicrobial classes and countries. Generally, the estimated global ARG abundance was positively associated with the prevalence of clinical phenotypic resistance, with a strong association for bacterial groups in the human gut. The associations between bacterial groups and ARG abundance were positive and significantly different from zero for the aminoglycosides (three of the four of the taxa tested), β-lactam (all the six microbial groups), fluoroquinolones (seven of nine of the microbial groups), glycopeptide (one microbial group tested), folate pathway antagonists (four of five microbial groups), and tetracycline (two of nine microbial groups). INTERPRETATION Metagenomic analysis of sewage is a robust approach for the surveillance of antimicrobial resistance in pathogens, especially for bacterial groups associated with the human gut. Additional studies on the associations between important socioeconomic, nutritional, and health factors and antimicrobial resistance should consider the variation in these associations between countries and antimicrobial classes. FUNDING EU Horizon 2020 and Novo Nordisk Foundation.
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Affiliation(s)
| | - Bram van Bunnik
- Roslin Institute, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark.
| | - Ana Rita Pinheiro Marques
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark
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17
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Jensen EEB, Sedor V, Eshun E, Njage P, Otani S, Aarestrup FM. The resistomes of rural and urban pigs and poultry in Ghana. mSystems 2023; 8:e0062923. [PMID: 37737585 PMCID: PMC10654090 DOI: 10.1128/msystems.00629-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE To the best of our knowledge, this is the first report on the resistomes that are measured using metagenomics in livestock from Sub-Saharan Africa. We find notable differences in the microbiomes between both pigs and poultry, and those also varied markedly compared to similar samples from Europe. However, for both animal species, the same bacterial taxa drove such differences. In pigs and urban free-range poultry, we find a very low abundance of antimicrobial resistance genes (ARGs), whereas rural free-range poultry displayed similarity to the European average, and industrialized poultry exhibited higher levels. These findings show how different African livestock bacterial communities and resistomes are from their European counterparts. They also underscore the importance of continued surveillance and investigation into antimicrobial resistance across diverse ecosystems, contributing significantly to global efforts toward combating the threat of antibiotic resistance.
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Affiliation(s)
| | - Victoria Sedor
- Veterinary Services Department, Ministry of Food and Agriculture, National Food Safety Laboratory, Accra, Ghana
| | - Emmanuel Eshun
- Veterinary Services Department, Ministry of Food and Agriculture, National Food Safety Laboratory, Accra, Ghana
| | - Patrick Njage
- Technical University of Denmark, Kemitorvet, Denmark
| | - Saria Otani
- Technical University of Denmark, Kemitorvet, Denmark
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18
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Johansson MHK, Aarestrup FM, Petersen TN. Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world. PLoS One 2023; 18:e0293169. [PMID: 37856515 PMCID: PMC10586675 DOI: 10.1371/journal.pone.0293169] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.
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Affiliation(s)
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas N. Petersen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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19
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Leekitcharoenphon P, Vigre H, Kaas RS, Aarestrup FM. Trends in Salmonella Dublin over time in Denmark from food and animal related isolates. Infect Genet Evol 2023; 113:105475. [PMID: 37394050 DOI: 10.1016/j.meegid.2023.105475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
Salmonella enterica serovar Dublin is highly adapted to cattle and a relatively rare cause of human infections. In Denmark S. Dublin has been endemic in the cattle population for many years. A national surveillance program in the cattle population was established at herd-level to reduce the occurrence of S. Dublin. In this study, we analyzed 421 S. Dublin genomes from cattle and food in order to determine the trend of S. Dublin's population size over time in Denmark and the impact of intervention in the cattle industry on the bacterial population size. A phylogenetic tree based on SNPs exhibited two major clades and one small cluster. All isolates were ST10. The temporal phylogenetic tree for the S. Dublin isolates showed that the most recent common ancestor was estimated to be in ∼1980 for the two major clades. An effective population size over time based on a Bayesian skyline plot showed that the population size of S. Dublin decreased significantly between 2014 and 2019 in both major clades. This result was concordant with the decrease of infected human cases by S. Dublin in Denmark. The strengthening of a surveillance program in Denmark could be the cause for the reduction of S. Dublin's effective population size. This study showed that whole genome sequencing combined with computer intensive phylogenetic analysis estimating the effective size of the S. Dublin's population over time is a strongly relevant measure with respect to assessing the impact of control measures aiming to reduce the bacterial population in the reservoir and the risk for human infection.
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Affiliation(s)
- Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Håkan Vigre
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Rolf Sommer Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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20
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Nuanmuang N, Leekitcharoenphon P, Njage PMK, Gmeiner A, Aarestrup FM. An Overview of Antimicrobial Resistance Profiles of Publicly Available Salmonella Genomes with Sufficient Quality and Metadata. Foodborne Pathog Dis 2023; 20:405-413. [PMID: 37540138 PMCID: PMC10510693 DOI: 10.1089/fpd.2022.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Salmonella enterica (S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR. This study aimed to evaluate the current usefulness of public WGS data for Salmonella surveillance and to investigate the associations between serovars, antibiotic resistance genes (ARGs), and metadata. Out of 191,306 Salmonella genomes deposited in European Nucleotide Archive and NCBI databases, 47,452 WGS with sufficient minimum metadata (country, year, and source) of S. enterica were retrieved from 116 countries and isolated between 1905 and 2020. For in silico analysis of the WGS data, KmerFinder, SISTR, and ResFinder were used for species, serovars, and AMR identification, respectively. The results showed that the five common isolation sources of S. enterica are human (29.10%), avian (22.50%), environment (11.89%), water (9.33%), and swine (6.62%). The most common ARG profiles for each class of antimicrobials are β-lactam (blaTEM-1B; 6.78%), fluoroquinolone [(parC[T57S], qnrB19); 0.87%], folate pathway antagonist (sul2; 8.35%), macrolide [mph(A); 0.39%], phenicol (floR; 5.94%), polymyxin B (mcr-1.1; 0.09%), and tetracycline [tet(A); 12.95%]. Our study reports the first overview of ARG profiles in publicly available Salmonella genomes from online databases. All data sets from this study can be searched at Microreact.
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Affiliation(s)
- Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Murigu Kamau Njage
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Alexander Gmeiner
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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21
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Pajand O, Rahimi H, Badmasti F, Gholami F, Alipour T, Darabi N, Aarestrup FM, Leekitcharoenphon P. Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring bla NDM-1: a comparative genomic analysis of carbapenem resistant strains. J Biomed Sci 2023; 30:73. [PMID: 37626377 PMCID: PMC10464136 DOI: 10.1186/s12929-023-00960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Certain clonal complexes (CCs) of Klebsiella pneumoniae such as CC147 (ST147 and ST392) are major drivers of blaNDM dissemination across the world. ST147 has repeatedly reported from our geographical region, but its population dynamics and evolutionary trajectories need to be further studied. METHODS Comparative genomic analysis of 51 carbapenem-nonsusceptible strains as well as three hypervirulent K. pneumoniae (hvKp) recovered during 16-months of surveillance was performed using various bioinformatics tools. We investigated the genetic proximity of our ST147 strains with publicly available corresponding genomes deposited globally and from neighbor countries in our geographic region. RESULTS While IncL/M plasmid harboring blaOXA-48 was distributed among divergent clones, blaNDM-1 was circulated by twenty of the 25 CC147 dominant clone and were mostly recovered from the ICU. The NDM-1 core structure was bracketed by a single isoform of mobile genetic elements (MGEs) [ΔISKpn26-NDM-TnAs3-ΔIS3000-Tn5403] and was located on Col440I plasmid in 68.7% of ST392. However, various arrangements of MGEs including MITESen1/MITESen1 composite transposon or combination of MITESen1/ISSen4/IS903B/IS5/ISEhe3 on IncFIb (pB171) were identified in ST147. It seems that ST392 circulated blaNDM-1 in 2018 before being gradually replaced by ST147 from the middle to the end of sample collection in 2019. ST147 strains possessed the highest number of resistance markers and showed high genetic similarity with four public genomes that harbored blaNDM-1 on the same replicon type. Mainly, there was a convergence between clusters and isolated neighboring countries in the minimum-spanning tree. A conserved arrangement of resistance markers/MGEs was linked to methyltransferase armA which was embedded in class 1 integron in 8 isolates of ST147/ST48 high-risk clones. CONCLUSION Our findings highlight the dynamic nature of blaNDM-1 transmission among K. pneumoniae in Iran that occurs both clonally and horizontally via various combinations of MGEs. This is the first analysis of Iranian ST147/NDM + clone in the global context.
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Affiliation(s)
- Omid Pajand
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
- Clinical Research Development Unit, Kowsar Educational, Research and Therapeutic Hospital, Semnan University of Medical Sciences, Semnan, Iran
- Abnormal Uterine Bleeding Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Hamzeh Rahimi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Faeze Gholami
- Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Tahereh Alipour
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Narges Darabi
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
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22
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Jespersen ML, Munk P, Johansen J, Kaas RS, Webel H, Vigre H, Nielsen HB, Rasmussen S, Aarestrup FM. Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering. Commun Biol 2023; 6:700. [PMID: 37422584 PMCID: PMC10329687 DOI: 10.1038/s42003-023-05083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of 757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches. Applying these methods, we recovered 3353 near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different MAG species and found that within-species genomic variation was in 36% of the investigated species (12/33) coherent with regional separation. Additionally, we found that variation of organelle genes correlated less with geography compared to metabolic and membrane genes, suggesting that the global differences of these species are caused by regional environmental selection rather than dissemination limitations. From the combination of the large and globally distributed dataset and in-depth analysis, we present a wide investigation of global within-species phylogeny of sewage bacteria. The global differences found here emphasize the need for worldwide data sets when making global conclusions.
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Affiliation(s)
- Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Rolf Sommer Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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23
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Kumburu HH, Shayo M, van Zwetslaar M, Njau J, Kuchaka DJ, Ignas IP, Wadugu B, Kasworm R, Masaki LJ, Hallgren MB, Clausen PT, Mmbaga BT, Aarestrup FM, Sonda TB. Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: A case report. Heliyon 2023; 9:e17439. [PMID: 37539288 PMCID: PMC10395014 DOI: 10.1016/j.heliyon.2023.e17439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/29/2023] [Accepted: 06/16/2023] [Indexed: 08/05/2023] Open
Abstract
In resource-limited settings, patients are often first presented to clinical settings when seriously ill and access to proper clinical microbial diagnostics is often very limited or non-existing. On February 16th, 2022 we were on a field trip to test a completely field-deployable metagenomics sequencing set-up, that includes DNA purification, sequencing, and bioinformatics analyses using bioinformatics tools installed on a laptop for water samples, just outside Moshi, Tanzania. On our way to the test site, we were contacted by the nearby Machame hospital regarding a child seriously ill with diarrhea and not responding to treatment. Within the same day, we conducted an onsite metagenomics examination of a fecal sample from the child, and Campylobacter jejuni was identified as the causative agent. The treatment was subsequently changed, with almost immediate improvement, and the child was discharged on February 21st.
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Affiliation(s)
- Happiness H. Kumburu
- Kilimanjaro Christian Medical Centre (KCMC), Tanzania
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
- Kilimanjaro Christian Medical University College (KCMUCo), 2240 Moshi Kilimanajro, Tanzania
| | - Mariana Shayo
- Kilimanjaro Christian Medical University College (KCMUCo), 2240 Moshi Kilimanajro, Tanzania
| | - Marco van Zwetslaar
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
| | - Judith Njau
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
| | - Davis J. Kuchaka
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
- The Nelson Mandela African Institution of Science and Technology (NM-AIST), Tanzania
| | - Ignas P. Ignas
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
| | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
| | | | | | | | | | - Blandina Theophil Mmbaga
- Kilimanjaro Christian Medical Centre (KCMC), Tanzania
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
- Kilimanjaro Christian Medical University College (KCMUCo), 2240 Moshi Kilimanajro, Tanzania
| | | | - Tolbert B. Sonda
- Kilimanjaro Christian Medical Centre (KCMC), Tanzania
- Kilimanjaro Clinical Research Institute (KCRI), Sokoine Road, P. O. Box. 2236, Moshi, Tanzania
- Kilimanjaro Christian Medical University College (KCMUCo), 2240 Moshi Kilimanajro, Tanzania
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Mzee T, Kumburu H, Kazimoto T, Leekitcharoenphon P, van Zwetselaar M, Masalu R, Mlaganile T, Sonda T, Wadugu B, Mushi I, Aarestrup FM, Matee M. Molecular Characterization of Staphylococcus aureus Isolated from Raw Milk and Humans in Eastern Tanzania: Genetic Diversity and Inter-Host Transmission. Microorganisms 2023; 11:1505. [PMID: 37375007 DOI: 10.3390/microorganisms11061505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 06/29/2023] Open
Abstract
Staphylococcus aureus is a common cause of infection in humans and animals, including bovine mastitis, globally. The objective of this study was to genetically characterize a collection of S. aureus isolates recovered from milk and nasal swabs from humans with and without animal contact (bovine = 43, human = 12). Using whole genome sequencing (NextSeq550), isolates were sequence typed, screened for antimicrobial resistance and virulence genes and examined for possible inter-species host transmission. Multi locus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogeny revealed 14 different sequence types, including the following six novel sequence types: ST7840, 7841, 7845, 7846, 7847, and 7848. The SNP tree confirmed that MLST clustering occurred most commonly within CC97, CC5477, and CC152. ResFinder analysis revealed five common antibiotic resistance genes, namely tet(K), blaZ, dfrG, erm©, and str, encoding for different antibiotics. mecA was discovered in one human isolate only. Multidrug resistance was observed in 25% of the isolates, predominantly in CC152 (7/8) and CC121 (3/4). Known bovine S. aureus (CC97) were collected in humans and known human S. aureus lineages (CC152) were collected in cattle; additionally, when these were compared to bovine-isolated CC97 and human-isolated CC152, respectively, no genetic distinction could be observed. This is suggestive of inter-host transmission and supports the need for surveillance of the human-animal interface.
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Affiliation(s)
- Tutu Mzee
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo P.O. Box 74, Tanzania
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam P.O. Box 35179, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Theckla Kazimoto
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo P.O. Box 74, Tanzania
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK 2800 Kgs. Lyngby, Denmark
| | | | - Rose Masalu
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam P.O. Box 35179, Tanzania
| | - Tarsis Mlaganile
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo P.O. Box 74, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Ignass Mushi
- Kilimanjaro Clinical Research Institute, Moshi P.O. Box 2236, Tanzania
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK 2800 Kgs. Lyngby, Denmark
| | - Mecky Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
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Izquierdo-Lara RW, Heijnen L, Oude Munnink BB, Schapendonk CME, Elsinga G, Langeveld J, Post J, Prasad DK, Carrizosa C, Been F, van Beek J, Schilperoort R, Vriend R, Fanoy E, de Schepper EIT, Sikkema RS, Molenkamp R, Aarestrup FM, Medema G, Koopmans MPG, de Graaf M. Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance. Sci Total Environ 2023; 873:162209. [PMID: 36796689 PMCID: PMC9927792 DOI: 10.1016/j.scitotenv.2023.162209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/04/2023]
Abstract
Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.
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Affiliation(s)
- Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Jeroen Langeveld
- Partners4urbanwater, Nijmegen, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Johan Post
- Partners4urbanwater, Nijmegen, the Netherlands
| | - Divyae K Prasad
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christian Carrizosa
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Frederic Been
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Rianne Vriend
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Ewout Fanoy
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands.
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Duarte ASR, Marques AR, Andersen VD, Korsgaard HB, Mordhorst H, Møller FD, Petersen TN, Vigre H, Hald T, Aarestrup FM. Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018. Euro Surveill 2023; 28:2200678. [PMID: 37199989 PMCID: PMC10197494 DOI: 10.2807/1560-7917.es.2023.28.20.2200678] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023] Open
Abstract
BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.
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Affiliation(s)
- Ana Sofia R Duarte
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Ana Rita Marques
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Vibe D Andersen
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Helle B Korsgaard
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Hanne Mordhorst
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Frederik D Møller
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Thomas N Petersen
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Håkan Vigre
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Tine Hald
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
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Bogri A, Otani S, Aarestrup FM, Brinch C. Interplay between strain fitness and transmission frequency determines prevalence of antimicrobial resistance. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.981377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The steep rise of infections caused by bacteria that are resistant to antimicrobial agents threatens global health. However, the association between antimicrobial use and the prevalence of resistance is not straightforward. Therefore, it is necessary to quantify the importance of additional factors that affect this relationship. We theoretically explore how the prevalence of resistance is affected by the combination of three factors: antimicrobial use, bacterial transmission, and fitness cost of resistance. We present a model that combines within-host, between-hosts and between-populations dynamics, built upon the competitive Lotka-Volterra equations. We developed the model in a manner that allows future experimental validation of the findings with single isolates in the laboratory. Each host may carry two strains (susceptible and resistant) that represent the host’s commensal microbiome and are not the target of the antimicrobial treatment. The model simulates a population of hosts who are treated periodically with antibiotics and transmit bacteria to each other. We show that bacterial transmission results in strain co-existence. Transmission disseminates resistant bacteria in the population, increasing the levels of resistance. Counterintuitively, when the cost of resistance is low, high transmission frequencies reduce resistance prevalence. Transmission between host populations leads to more similar resistance levels, increasing the susceptibility of the population with higher antimicrobial use. Overall, our results indicate that the interplay between bacterial transmission and strain fitness affects the prevalence of resistance in a non-linear way. We then place our results within the context of ecological theory, particularly on temporal niche partitioning and metapopulation rescue, and we formulate testable experimental predictions for future research.
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28
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Andersen VD, Møller FD, Jensen MS, Aarestrup FM, Vigre H. The quantitative effect of antimicrobial usage in Danish pig farms on the abundance of antimicrobial resistance genes in slaughter pigs. Prev Vet Med 2023; 214:105899. [PMID: 36940534 DOI: 10.1016/j.prevetmed.2023.105899] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/21/2023]
Abstract
Research has long established the connection between antimicrobial use (AMU) and antimicrobial resistance (AMR) in production animals, and shown that the ceasing of AMU reduces AMR. Our previous study of Danish slaughter-pig production found a quantitative relationship between lifetime AMU and abundance of antimicrobial resistance genes (ARGs). This study aimed to generate further quantitative knowledge on how changes in AMU in farms influence the abundance of ARGs both with immediate effect and over time. The study included 83 farms that were visited from 1 to 5 times. From each visit, a pooled faecal sample was produced. The abundance of ARGs was obtained by metagenomics. We used two-level linear mixed models for estimating the effect of AMU on the abundance of ARGs against six antimicrobial classes. The lifetime AMU of each batch was calculated from usage during their three rearing periods; as piglets, weaners and slaughter pigs (rearing pathway). AMU at farm level was estimated as the mean lifetime AMU of the sampled batches from each farm. At batch level, AMU was measured as the deviation between the batch-specific lifetime AMU and the general mean lifetime AMU at the farm. For peroral tetracycline and macrolide use there was a significant quantitative linear effect on the abundance of ARGs in batches within individual farms, indicating an immediate effect of changed AMU from batch to batch within farms. These estimated effects between batches within farms were approximately 1/2-1/3 of the effect estimated between farms. For all antimicrobial classes, the effect of the mean farm-level AMU and the abundance of ARGs present in the faeces of slaughter pigs was significant. This effect was identified only for peroral use, except for lincosamides, where the effect was for parenteral use. The results also indicated that the abundance of ARGs against a specific antimicrobial class also increased by the peroral usage of one or several other antimicrobial classes, except for ARGs against beta-lactams. These effects were generally lower than the AMU effect of the specific antimicrobial class. Overall, the farm peroral mean lifetime AMU affected the abundance of ARGs at antimicrobial class level and abundance of ARGs of other classes. However, the difference of AMU of the slaughter-pig batches affected only the abundance of ARGs at the same antimicrobial class level in the same antimicrobial class. The results do not exclude that parenteral usage of antimicrobials may have an effect on the abundance of ARGs.
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Affiliation(s)
- V D Andersen
- The National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - F D Møller
- The National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - M S Jensen
- The National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - F M Aarestrup
- The National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - H Vigre
- The National Food Institute, Technical University of Denmark, Lyngby, Denmark.
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29
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM, Gibb K, Coventry K, Collignon P, Cassar S, Allerberger F, Begum A, Hossain ZZ, Worrell C, Vandenberg O, Pieters I, Victorien DT, Gutierrez ADS, Soria F, Grujić VR, Mazalica N, Rahube TO, Tagliati CA, Rodrigues D, Oliveira G, de Souza LCR, Ivanov I, Juste BI, Oumar T, Sopheak T, Vuthy Y, Ngandjio A, Nzouankeu A, Olivier ZAAJ, Yost CK, Kumar P, Brar SK, Tabo DA, Adell AD, Paredes-Osses E, Martinez MC, Cuadros-Orellana S, Ke C, Zheng H, Baisheng L, Lau LT, Chung T, Jiao X, Yu Y, JiaYong Z, Morales JFB, Valencia MF, Donado-Godoy P, Coulibaly KJ, Hrenovic J, Jergović M, Karpíšková R, Deogratias ZN, Elsborg B, Hansen LT, Jensen PE, Abouelnaga M, Salem MF, Koolmeister M, Legesse M, Eguale T, Heikinheimo A, Le Guyader S, Schaeffer J, Villacis JE, Sanneh B, Malania L, Nitsche A, Brinkmann A, Schubert S, Hesse S, Berendonk TU, Saba CKS, Mohammed J, Feglo PK, Banu RA, Kotzamanidis C, Lytras E, Lickes SA, Kocsis B, Solymosi N, Thorsteinsdottir TR, Hatha AM, Ballal M, Bangera SR, Fani F, Alebouyeh M, Morris D, O’Connor L, Cormican M, Moran-Gilad J, Battisti A, Diaconu EL, Corno G, Di Cesare A, Alba P, Hisatsune J, Yu L, Kuroda M, Sugai M, Kayama S, Shakenova Z, Kiiyukia C, Ng’eno E, Raka L, Jamil K, Fakhraldeen SA, Alaati T, Bērziņš A, Avsejenko J, Kokina K, Streikisa M, Bartkevics V, Matar GM, Daoud Z, Pereckienė A, Butrimaite-Ambrozeviciene C, Penny C, Bastaraud A, Rasolofoarison T, Collard JM, Samison LH, Andrianarivelo MR, Banda DL, Amin A, Rajandas H, Parimannan S, Spiteri D, Haber MV, Santchurn SJ, Vujacic A, Djurovic D, Bouchrif B, Karraouan B, Vubil DC, Pal P, Schmitt H, van Passel M, Jeunen GJ, Gemmell N, Chambers ST, Mendoza FP, Huete-Pιrez J, Vilchez S, Ahmed AO, Adisa IR, Odetokun IA, Fashae K, Sørgaard AM, Wester AL, Ryrfors P, Holmstad R, Mohsin M, Hasan R, Shakoor S, Gustafson NW, Schill CH, Rojas MLZ, Velasquez JE, Magtibay BB, Catangcatang K, Sibulo R, Yauce FC, Wasyl D, Manaia C, Rocha J, Martins J, Álvaro P, Di Yoong Wen D, Shin H, Hur HG, Yoon S, Bosevska G, Kochubovski M, Cojocaru R, Burduniuc O, Hong PY, Perry MR, Gassama A, Radosavljevic V, Tay MYF, Zuniga-Montanez R, Wuertz S, Gavačová D, Pastuchová K, Truska P, Trkov M, Keddy K, Esterhuyse K, Song MJ, Quintela-Baluja M, Lopez MG, Cerdà-Cuéllar M, Perera RRDP, Bandara NKBKRGW, Premasiri HI, Pathirage S, Charlemagne K, Rutgersson C, Norrgren L, Örn S, Boss R, Van der Heijden T, Hong YP, Kumburu HH, Mdegela RH, Hounmanou YMG, Chonsin K, Suthienkul O, Thamlikitkul V, de Roda Husman AM, Bidjada B, Njanpop-Lafourcade BM, Nikiema-Pessinaba SC, Levent B, Kurekci C, Ejobi F, Kalule JB, Thomsen J, Obaidi O, Jassim LM, Moore A, Leonard A, Graham DW, Bunce JT, Zhang L, Gaze WH, Lefor B, Capone D, Sozzi E, Brown J, Meschke JS, Sobsey MD, Davis M, Beck NK, Sukapanpatharam P, Truong P, Lilienthal R, Kang S, Wittum TE, Rigamonti N, Baklayan P, Van CD, Tran DMN, Do Phuc N, Kwenda G, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2023; 14:178. [PMID: 36635285 PMCID: PMC9837105 DOI: 10.1038/s41467-023-35890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Patrick Munk
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christian Brinch
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N. Petersen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S. Hendriksen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S. Kjeldgaard
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - D. G. Joakim Larsson
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M. Aarestrup
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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Ostenfeld LJ, Munk P, Aarestrup FM, Otani S. Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome. PLoS One 2023; 18:e0283676. [PMID: 36996123 PMCID: PMC10062541 DOI: 10.1371/journal.pone.0283676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Microbial communities have huge impacts on their ecosystems and local environments spanning from marine and soil communities to the mammalian gut. Bacteriophages (phages) are important drivers of population control and diversity in the community, but our understanding of complex microbial communities is halted by biased detection techniques. Metagenomics have provided a method of novel phage discovery independent of in vitro culturing techniques and have revealed a large proportion of understudied phages. Here, five jumbophage genomes, that were previously assembled in silico from pig faecal metagenomes, are detected and observed directly in their natural environment using a modified phageFISH approach, and combined with methods to decrease bias against large-sized phages (e.g., jumbophages). These phages are uncultured with unknown hosts. The specific phages were detected by PCR and fluorescent in situ hybridisation in their original faecal samples as well as across other faecal samples. Co-localisation of bacterial signals and phage signals allowed detection of the different stages of phage life cycle. All phages displayed examples of early infection, advanced infection, burst, and free phages. To our knowledge, this is the first detection of jumbophages in faeces, which were investigated independently of culture, host identification, and size, and based solely on the genome sequence. This approach opens up opportunities for characterisation of novel in silico phages in vivo from a broad range of gut microbiomes.
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Affiliation(s)
- Line Jensen Ostenfeld
- Research group for Genomic Epidemiology, National Food Institute, Copenhagen, Denmark
| | - Patrick Munk
- Research group for Genomic Epidemiology, National Food Institute, Copenhagen, Denmark
| | - Frank M Aarestrup
- Research group for Genomic Epidemiology, National Food Institute, Copenhagen, Denmark
| | - Saria Otani
- Research group for Genomic Epidemiology, National Food Institute, Copenhagen, Denmark
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31
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Aytan-Aktug D, Grigorjev V, Szarvas J, Clausen PTLC, Munk P, Nguyen M, Davis JJ, Aarestrup FM, Lund O. SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies. Microbiol Spectr 2022; 10:e0264122. [PMID: 36377945 PMCID: PMC9769690 DOI: 10.1128/spectrum.02641-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.
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Affiliation(s)
- Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Vladislav Grigorjev
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2022; 13:7251. [PMID: 36456547 PMCID: PMC9715550 DOI: 10.1038/s41467-022-34312-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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Affiliation(s)
- Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S Kjeldgaard
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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33
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Teseo S, Otani S, Brinch C, Leroy S, Ruiz P, Desvaux M, Forano E, Aarestrup FM, Sapountzis P. A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle. Microbiome 2022; 10:155. [PMID: 36155629 PMCID: PMC9511753 DOI: 10.1186/s40168-022-01357-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/24/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries. RESULTS Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes. CONCLUSIONS Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.
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Affiliation(s)
- S Teseo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - S Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - C Brinch
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - S Leroy
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - P Ruiz
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - M Desvaux
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - E Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - F M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - P Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France.
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Sengeruan LP, van Zwetselaar M, Kumburu H, Aarestrup FM, Kreppel K, Sauli E, Sonda T. Plasmid characterization in bacterial isolates of public health relevance in a tertiary healthcare facility in Kilimanjaro, Tanzania. J Glob Antimicrob Resist 2022; 30:384-389. [DOI: 10.1016/j.jgar.2022.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022] Open
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Reda RM, Maricchiolo G, Quero GM, Basili M, Aarestrup FM, Pansera L, Mirto S, Abd El-Fattah AH, Alagawany M, Abdel Rahman AN. Rice protein concentrate as a fish meal substitute in Oreochromis niloticus: Effects on immune response, intestinal cytokines, Aeromonas veronii resistance, and gut microbiota composition. Fish Shellfish Immunol 2022; 126:237-250. [PMID: 35654384 DOI: 10.1016/j.fsi.2022.05.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The potential of rice protein concentrate (RPC) to substitute fishmeal (FM) protein in the diet of Oreochromis niloticus was assessed in a five-month-long feeding trial. Fishmeal protein was replaced by RPC at rates of 0% (control), 25%, 50%, and 75% (RPC0, RPC25, RPC50, and RPC75, respectively). RPC25 had no significant effect on antioxidant capacity (total antioxidant capacity; superoxide dismutase, catalase, and glutathione peroxidase activities) and immune indices (lysozyme, nitric oxide, antiprotease, and bactericidal activities) after one, two, and five months of feeding, while the values for these parameters were significantly lower in the RPC75 group compared to those in the RPC0 group. The RPC25 group showed higher mRNA levels of the intestinal cytokines IL-1β, IL-10β, TGF-β, and TNF-α than the control group. In fish affected by Aeromonas veronii, the highest significant cumulative mortality was recorded in the RPC75 group, followed by the RPC50, RPC25, and control groups. Gut microbiome analyses showed a reduction in microbial diversity in response to the addition of RPC, regardless of the RPC content, and the composition of the community of the RPC samples differed from that of the control. RPC-enriched diets resulted in higher relative abundances of Bacteroidetes and Fusobacteria in the gut compared to that in the gut of the control fish. In summary, RPC can be used to replace up to 25% of the FM protein in the diet of O. niloticus, while improving the antioxidant capacity, immunocompetence, and disease resistance of the fish.
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Affiliation(s)
- Rasha M Reda
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt.
| | - Giulia Maricchiolo
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (IRBIM-CNR), Messina, Italy
| | - Grazia Marina Quero
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Marco Basili
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Frank M Aarestrup
- Department of Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Lidia Pansera
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (IRBIM-CNR), Messina, Italy
| | - Simone Mirto
- Institute of Anthropic Impact and Sustainability in Marine Environment, National Research Council (CNR-IAS), Palermo, Italy
| | - Amir H Abd El-Fattah
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt
| | - Mahmoud Alagawany
- Department of Poultry, Faculty of Agriculture, Zagazig University, P.O. Box 44511, Zagazig, Egypt
| | - Afaf N Abdel Rahman
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt
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Rebelo AR, Bortolaia V, Leekitcharoenphon P, Hansen DS, Nielsen HL, Ellermann-Eriksen S, Kemp M, Røder BL, Frimodt-Møller N, Søndergaard TS, Coia JE, Østergaard C, Westh H, Aarestrup FM. One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings. Front Microbiol 2022; 13:804627. [PMID: 35756053 PMCID: PMC9226621 DOI: 10.3389/fmicb.2022.804627] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings. We collected all bacterial isolates processed by all Danish Clinical Microbiology Laboratories in 1 day. We randomly selected 500 isolates without any preselection of species. We performed AST through standard broth microdilution (BMD) for 488 isolates (n = 6,487 phenotypic AST results) and compared results with in silico antibiograms obtained through WGS (Illumina NextSeq) followed by bioinformatics analyses using ResFinder 4.0 (n = 5,229 comparisons). A higher proportion of AMR was observed for Gram-negative bacteria (10.9%) than for Gram-positive bacteria (6.1%). Comparison of BMD with WGS data yielded a concordance of 91.7%, with discordant results mainly due to phenotypically susceptible isolates harboring genetic AMR determinants. These cases correspond to 6.2% of all isolate-antimicrobial combinations analyzed and to 6.8% of all phenotypically susceptible combinations. We detected fewer cases of phenotypically resistant isolates without any known genetic resistance mechanism, particularly 2.1% of all combinations analyzed, which corresponded to 26.4% of all detected phenotypic resistances. Most discordances were observed for specific combinations of species-antimicrobial: macrolides and tetracycline in streptococci, ciprofloxacin and β-lactams in combination with β-lactamase inhibitors in Enterobacterales, and most antimicrobials in Pseudomonas aeruginosa. WGS has the potential to be used for surveillance and routine clinical microbiology. However, in clinical microbiology settings and especially for certain species and antimicrobial agent combinations, further developments in AMR gene databases are needed to ensure higher concordance between in silico predictions and expected phenotypic AMR profiles.
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Affiliation(s)
- Ana Rita Rebelo
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Michael Kemp
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Bent Løwe Røder
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark
| | | | | | - John Eugenio Coia
- Department of Clinical Microbiology, Hospital of South West Jutland, Esbjerg, Denmark
| | - Claus Østergaard
- Department of Clinical Microbiology, Vejle Hospital, Vejle, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Janes VA, Matamoros S, Munk P, Clausen PTLC, Koekkoek SM, Koster LAM, Jakobs ME, de Wever B, Visser CE, Aarestrup FM, Lund O, de Jong MD, Bossuyt PMM, Mende DR, Schultsz C. Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study. The Lancet Microbe 2022; 3:e588-e597. [DOI: 10.1016/s2666-5247(22)00088-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 03/11/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022] Open
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Poulsen CS, Ekstrøm CT, Aarestrup FM, Pamp SJ. Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes. Microbiol Spectr 2022; 10:e0009022. [PMID: 35289669 PMCID: PMC9045301 DOI: 10.1128/spectrum.00090-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/22/2022] [Indexed: 11/20/2022] Open
Abstract
Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here, we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a PCR step (Nextera), and two were PCR free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at -80°C) were assessed. All DNA isolations were performed in duplicate, totaling 80 samples, excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generating comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously. IMPORTANCE Previous research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities. These findings suggest that library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure. Overall, we recommend that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions. Furthermore, if we are to obtain a more holistic insight from microbiome data generated around the world, we will need to provide more detailed sample metadata, including information about the different sample processing procedures, together with the DNA sequencing data at the public repositories.
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Affiliation(s)
- Casper S. Poulsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Claus T. Ekstrøm
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sünje J. Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Aytan-Aktug D, Clausen PTLC, Szarvas J, Munk P, Otani S, Nguyen M, Davis JJ, Lund O, Aarestrup FM. PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest. mSystems 2022; 7:e0118021. [PMID: 35382558 PMCID: PMC9040769 DOI: 10.1128/msystems.01180-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning-specifically, random forests. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level; the models achieved Matthews correlation coefficients of 0.662 and 0.867 at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool is available online through the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/). IMPORTANCE Antimicrobial resistance is a global health threat to humans and animals, causing high mortality and morbidity while effectively ending decades of success in fighting against bacterial infections. Plasmids confer extra genetic capabilities to the host organisms through accessory genes that can encode antimicrobial resistance and virulence. In addition to lateral inheritance, plasmids can be transferred horizontally between bacterial taxa. Therefore, detection of the host range of plasmids is crucial for understanding and predicting the dissemination trajectories of extrachromosomal genes and bacterial evolution as well as taking effective countermeasures against antimicrobial resistance.
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Affiliation(s)
- Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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40
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Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R, Deplano A, Vandendriessche S, Černá Bolfíková B, Hulva P, Arendrup MC, Hare RK, Barnadas C, Stegger M, Sieber RN, Skov RL, Petersen A, Angen Ø, Rasmussen SL, Espinosa-Gongora C, Aarestrup FM, Lindholm LJ, Nykäsenoja SM, Laurent F, Becker K, Walther B, Kehrenberg C, Cuny C, Layer F, Werner G, Witte W, Stamm I, Moroni P, Jørgensen HJ, de Lencastre H, Cercenado E, García-Garrote F, Börjesson S, Hæggman S, Perreten V, Teale CJ, Waller AS, Pichon B, Curran MD, Ellington MJ, Welch JJ, Peacock SJ, Seilly DJ, Morgan FJE, Parkhill J, Hadjirin NF, Lindsay JA, Holden MTG, Edwards GF, Foster G, Paterson GK, Didelot X, Holmes MA, Harrison EM, Larsen AR. Emergence of methicillin resistance predates the clinical use of antibiotics. Nature 2022; 602:135-141. [PMID: 34987223 PMCID: PMC8810379 DOI: 10.1038/s41586-021-04265-w] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics1. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development.
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Affiliation(s)
- Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Stien Vandendriessche
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University, Prague, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Maiken C Arendrup
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus K Hare
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Céline Barnadas
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert L Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sophie L Rasmussen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Wildlife Conservation Research Unit (WildCRU), Department of Zoology, University of Oxford, Tubney, UK
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura J Lindholm
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Frederic Laurent
- Bacteriology Department and French National Reference Center for Staphylococci, Hospices Civils de Lyon, University of Lyon, Lyon, France
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Birgit Walther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig University Giessen, Giessen, Germany
| | - Christiane Cuny
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Wolfgang Witte
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | | | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Fernando García-Garrote
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
- Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sara Hæggman
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Andrew S Waller
- Animal Health Trust, Newmarket, UK
- Intervacc AB, Stockholm, Stockholm, Sweden
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bruno Pichon
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fiona J E Morgan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | | | - Giles F Edwards
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | | | - Gavin K Paterson
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anders R Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
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Florensa AF, Kaas RS, Clausen PTLC, Aytan-Aktug D, Aarestrup FM. ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom 2022; 8. [PMID: 35072601 PMCID: PMC8914360 DOI: 10.1099/mgen.0.000748] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important health threats globally. The ability to accurately identify resistant bacterial isolates and the individual antimicrobial resistance genes (ARGs) is essential for understanding the evolution and emergence of AMR and to provide appropriate treatment. The rapid developments in next-generation sequencing technologies have made this technology available to researchers and microbiologists at routine laboratories around the world. However, tools available for those with limited experience with bioinformatics are lacking, especially to enable researchers and microbiologists in low- and middle-income countries (LMICs) to perform their own studies. The CGE-tools (Center for Genomic Epidemiology) including ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/) was developed to provide freely available easy to use online bioinformatic tools allowing inexperienced researchers and microbiologists to perform simple bioinformatic analyses. The main purpose was and is to provide these solutions for people involved in frontline diagnosis especially in LMICs. Since its original publication in 2012, ResFinder has undergone a number of improvements including improvement of the code and databases, inclusion of point mutations for selected bacterial species and predictions of phenotypes also for selected species. As of 28 September 2021, 820 803 analyses have been performed using ResFinder from 61 776 IP-addresses in 171 countries. ResFinder clearly fulfills a need for several people around the globe and we hope to be able to continue to provide this service free of charge in the future. We also hope and expect to provide further improvements including phenotypic predictions for additional bacterial species.
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Affiliation(s)
| | - Rolf Sommer Kaas
- National Food Institute, Technical University of Denmark, DK-2800 kgs. Lyngby, Denmark
| | | | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, DK-2800 kgs. Lyngby, Denmark
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Poulsen CS, Kaas RS, Aarestrup FM, Pamp SJ. Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns. Microbiol Spectr 2021; 9:e0138721. [PMID: 34612701 DOI: 10.1101/2021.05.24.445395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, -80°C; freezer, -20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We provide recommendations for sample storage and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a data set that could also be used for benchmarking algorithms to identify and correct for unwanted batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing be published together with DNA sequencing data at the International Nucleotide Sequence Database Collaboration (ENA/EBI, NCBI, DDBJ) or other repositories.
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Affiliation(s)
- Casper Sahl Poulsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Rolf Sommer Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
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Poulsen CS, Kaas RS, Aarestrup FM, Pamp SJ. Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns. Microbiol Spectr 2021; 9:e0138721. [PMID: 34612701 PMCID: PMC8510183 DOI: 10.1128/spectrum.01387-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/11/2022] Open
Abstract
Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, -80°C; freezer, -20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We provide recommendations for sample storage and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a data set that could also be used for benchmarking algorithms to identify and correct for unwanted batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing be published together with DNA sequencing data at the International Nucleotide Sequence Database Collaboration (ENA/EBI, NCBI, DDBJ) or other repositories.
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Affiliation(s)
- Casper Sahl Poulsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rolf Sommer Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Abstract
The majority of emerging infectious diseases originate in animals. Current routine surveillance is focused on known diseases and clinical syndromes, but the increasing likelihood of emerging disease outbreaks shows the critical importance of early detection of unusual illness or circulation of pathogens - prior to human disease manifestation. In this Viewpoint, we focus on one key pillar of preparedness—the need for early warning surveillance at the human, animal, environmental interface. The COVID-19 pandemic has revolutionized the scale of sequencing of pathogen genomes, and the current investments in global genomic surveillance offer great potential for a novel, truly integrated Disease X (with epidemic or pandemic potential) surveillance arm provided we do not make the mistake of developing them solely for the case at hand. Generic tools include metagenomic sequencing as a catch-all technique, rather than detection and sequencing protocols focusing on what we know. Developing agnostic or more targeted metagenomic sequencing to assess unusual disease in humans and animals, combined with random sampling of environmental samples capturing pathogen circulation is technically challenging, but could provide a true early warning system. Rather than rebuilding and reinforcing the pre-existing silo's, a real step forward would be to take the lessons learned and bring in novel essential partnerships in a One Health approach to preparedness.
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Affiliation(s)
| | - Marc Bonten
- Utrecht University Medical Centre, Utrecht, The Netherlands
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Perry MR, Lepper HC, McNally L, Wee BA, Munk P, Warr A, Moore B, Kalima P, Philip C, de Roda Husman AM, Aarestrup FM, Woolhouse MEJ, van Bunnik BAD. Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family. Front Microbiol 2021; 12:703560. [PMID: 34566912 PMCID: PMC8461093 DOI: 10.3389/fmicb.2021.703560] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/10/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater. Methods: Sewage was collected over a 24-h period from multiple wastewater collection points (CPs) representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. ARG abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates. Results: Microbiota and ARG composition varied between CPs and overall ARG abundance was higher in hospital wastewater than in community influent. ARG and microbiota compositions were correlated (Procrustes analysis, p=0.014). Total antimicrobial usage was not associated with higher ARG abundance in wastewater. However, there was a small positive association between resistance genes and antimicrobial usage matched to ARG phenotype (IRR 1.11, CI 1.06-1.16, p<0.001). Furthermore, analyzing carbapenem and vancomycin resistance separately indicated that counts of ARGs to these antimicrobials were positively associated with their increased usage [carbapenem rate ratio (RR) 1.91, 95% CI 1.01-3.72, p=0.07, and vancomycin RR 10.25, CI 2.32-49.10, p<0.01]. Overall, ARG abundance within hospital wastewater did not reflect resistance patterns in clinical isolates from concurrent hospital inpatients. However, for clinical isolates of the family Enterococcaceae and Staphylococcaceae, there was a positive relationship with wastewater ARG abundance [odds ratio (OR) 1.62, CI 1.33-2.00, p<0.001, and OR 1.65, CI 1.21-2.30, p=0.006 respectively]. Conclusion: We found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation, we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.
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Affiliation(s)
- Meghan R. Perry
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Hannah C. Lepper
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Luke McNally
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Bryan A. Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Amanda Warr
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Barbara Moore
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
| | - Pota Kalima
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
| | - Carol Philip
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
| | | | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Nieuwenhuijse DF, Oude Munnink BB, Phan MVT, Munk P, Venkatakrishnan S, Aarestrup FM, Cotten M, Koopmans MPG. Author Correction: Setting a baseline for global urban virome surveillance in sewage. Sci Rep 2021; 11:17446. [PMID: 34433858 PMCID: PMC8387382 DOI: 10.1038/s41598-021-95934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Matthew Cotten
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
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Mashe T, Leekitcharoenphon P, Mtapuri-Zinyowera S, Kingsley RA, Robertson V, Tarupiwa A, Kock MM, Makombe EP, Chaibva BV, Manangazira P, Phiri I, Nyadundu S, Chigwena CT, Mufoya LP, Thilliez G, Midzi S, Mwamakamba LW, Hamblion EL, Matheu J, Jensen JD, Aarestrup FM, Hendriksen RS, Ehlers MM. Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019. J Antimicrob Chemother 2021; 76:1160-1167. [PMID: 33347558 DOI: 10.1093/jac/dkaa519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control. OBJECTIVES To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics. METHODS A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis. RESULTS A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs. CONCLUSIONS This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.
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Affiliation(s)
- Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Pimlapas Leekitcharoenphon
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK.,University of East Anglia, Norwich, UK
| | - V Robertson
- Medical Microbiology, University of Zimbabwe, Zimbabwe
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Tshwane Academic Divisions, Pretoria, South Africa
| | - Evidence P Makombe
- Gweru Provincial Hospital, Ministry of Health and Child Care, Gweru, Zimbabwe
| | | | - Portia Manangazira
- Ministry of Health and Child Care, Epidemiology and Disease Control, Zimbabwe
| | - Isaac Phiri
- Ministry of Health and Child Care, Epidemiology and Disease Control, Zimbabwe
| | - Simon Nyadundu
- Provincial Medical Directorate Offices, Midlands Province, Ministry of Health and Child Care, Gweru, Zimbabwe
| | | | | | | | | | - Lusubilo W Mwamakamba
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | - Esther L Hamblion
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | | | - Jacob D Jensen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Tshwane Academic Divisions, Pretoria, South Africa
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48
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Ingham AC, Kielsen K, Mordhorst H, Ifversen M, Aarestrup FM, Müller KG, Pamp SJ. Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation. Microbiome 2021; 9:148. [PMID: 34183060 PMCID: PMC8240369 DOI: 10.1186/s40168-021-01100-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/20/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (aGvHD). It is unknown if, when, and under which conditions a re-establishment of microbial and immunological homeostasis occurs. It is also unclear whether microbiota long-term dynamics occur at other body sites than the gut such as the mouth or nose. Moreover, it is not known whether the patients' microbiota prior to HSCT holds clues to whether the patient would suffer from severe complications subsequent to HSCT. Here, we take a holobiont perspective and performed an integrated host-microbiota analysis of the gut, oral, and nasal microbiota in 29 children undergoing allo-HSCT. RESULTS The bacterial diversity decreased in the gut, nose, and mouth during the first month and reconstituted again 1-3 months after allo-HSCT. The microbial community composition traversed three phases over 1 year. Distinct taxa discriminated the microbiota temporally at all three body sides, including Enterococcus spp., Lactobacillus spp., and Blautia spp. in the gut. Of note, certain microbial taxa appeared already changed in the patients prior to allo-HSCT as compared with healthy children. Acute GvHD occurring after allo-HSCT could be predicted from the microbiota composition at all three body sites prior to HSCT. The reconstitution of CD4+ T cells, TH17, and B cells was associated with distinct taxa of the gut, oral, and nasal microbiota. CONCLUSIONS This study reveals for the first time bacteria in the mouth and nose that may predict aGvHD. Monitoring of the microbiota at different body sites in HSCT patients and particularly through involvement of samples prior to transplantation may be of prognostic value and could assist in guiding personalized treatment strategies. The identification of distinct bacteria that have a potential to predict post-transplant aGvHD might provide opportunities for an improved preventive clinical management, including a modulation of microbiomes. The host-microbiota associations shared between several body sites might also support an implementation of more feasible oral and nasal swab sampling-based analyses. Altogether, the findings suggest that the microbiota and host factors together could provide actionable information to guiding precision medicine. Video Abstract.
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Affiliation(s)
- Anna Cäcilia Ingham
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
- Present address: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Katrine Kielsen
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Hanne Mordhorst
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marianne Ifversen
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Gottlob Müller
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.
- Present address: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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49
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Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2021; 75:3491-3500. [PMID: 32780112 PMCID: PMC7662176 DOI: 10.1093/jac/dkaa345] [Citation(s) in RCA: 1320] [Impact Index Per Article: 440.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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Affiliation(s)
- Valeria Bortolaia
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rolf S Kaas
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France.,University of Rennes 1, INSERM U1230, Rennes, France
| | - Alain Philippon
- Faculty of Medicine Paris Descartes, Bacteriology, Paris, France
| | - Rosa L Allesoe
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Ana Rita Rebelo
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Alfred Ferrer Florensa
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Linda Fagelhauer
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Bernd Neumann
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Guido Werner
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Jennifer K Bender
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Minh Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Muna F Anjum
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | | | | | - Ana Amaro
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Lurdes Clemente
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Joël Mossong
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Ole Lund
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
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Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 2021; 76:101-109. [PMID: 33009809 PMCID: PMC7729385 DOI: 10.1093/jac/dkaa390] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 11/17/2022] Open
Abstract
Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.
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Affiliation(s)
- Markus H K Johansson
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Supathep Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas N Petersen
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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