1
|
Butel-Simoes G, Steinig E, Savic I, Zhanduisenov M, Papadakis G, Tran T, Moselen J, Caly L, Williamson DA, Lim CK. Optimising nucleic acid recovery from rapid antigen tests for whole genome sequencing of respiratory viruses. J Clin Virol 2024; 174:105714. [PMID: 39038394 DOI: 10.1016/j.jcv.2024.105714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Whole genome sequencing (WGS) of respiratory viruses from rapid antigen tests (RAT-WGS) is a novel approach to expanding genomic surveillance of respiratory infections. To date however, there are limited data on the genomic stability of these viruses on RATs. In this study, we investigated the effect of storage conditions and nucleic acid preservatives on the ability to enhance stability and improve recovery of respiratory virus genomes from RATs. METHODS A mixture of common respiratory viruses was used to inoculate RATs at different environmental temperatures (4°C, 20°C and 36°C), with two preservative reagents (RNALater and DNA/RNA shield) Nucleic acid was extracted from RATs at two different timepoints (72 h and seven days) and subject to real-time multiplex respiratory PCR to detect a range of respiratory viruses. WGS was performed using target-enrichment with the TWIST Comprehensive Viral Research Panel. Defined metrics from an automated in-house bioinformatic pipeline were used to assess and compare viral genome recovery under different conditions. RESULTS Nucleic acid degradation (indicated by relative change in PCR cycle threshold and WGS-based metrics) was most notable at 20 °C and 36 °C. Storage in either RNALater or DNA / RNA shield improved genome recovery for respiratory viruses across all temperature conditions, although this was most pronounced for RNALater. Subtyping of Influenza viruses demonstrated the applicability of RAT-WGS in downstream genomic epidemiological surveillance. CONCLUSIONS Under simulated conditions, RAT-WGS demonstrated that (i) viral genomes were generally stable at 4°C at 72 h and 1 week, (ii) RNALater has a more significant preservation of nucleic acids compared to DNA/RNA Shield and (iii) genome recovery can be achieved using a sequencing depth of 500,000 reads per sample in RNALater, across all respiratory viruses and conditions.
Collapse
Affiliation(s)
- G Butel-Simoes
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - E Steinig
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - I Savic
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - M Zhanduisenov
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - G Papadakis
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - T Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - J Moselen
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - L Caly
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - D A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - C K Lim
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| |
Collapse
|
2
|
Bogaerts B, Van den Bossche A, Verhaegen B, Delbrassinne L, Mattheus W, Nouws S, Godfroid M, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. J Clin Microbiol 2024; 62:e0157623. [PMID: 38441926 PMCID: PMC11077942 DOI: 10.1128/jcm.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing Escherichia coli and Listeria monocytogenes by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.
Collapse
Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | | | - Stéphanie Nouws
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Maxime Godfroid
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Stefan Hoffman
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| |
Collapse
|
3
|
Nong Y, Steinig E, Pollock GL, Taiaroa G, Carter GP, Monk IR, Pang S, Daley DA, Coombs GW, Forde BM, Harris PNA, Sherry NL, Howden BP, Pasricha S, Baines SL, Williamson DA. Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus. Commun Biol 2024; 7:349. [PMID: 38514781 PMCID: PMC10957945 DOI: 10.1038/s42003-024-06012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.
Collapse
Affiliation(s)
- Yi Nong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Doherty Applied Microbial Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Brian M Forde
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Patrick N A Harris
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Shivani Pasricha
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| |
Collapse
|
4
|
Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
Collapse
Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|
5
|
Sun F, Dong Y, Ni M, Ping Z, Sun Y, Ouyang Q, Qian L. Mobile and Self-Sustained Data Storage in an Extremophile Genomic DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206201. [PMID: 36737843 PMCID: PMC10074078 DOI: 10.1002/advs.202206201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Indexed: 06/18/2023]
Abstract
DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data storage system in the genome of the extremophile Halomonas bluephagenesis, which enables dual-mode storage, dynamic data maintenance, rapid readout, and robust recovery. The system relies on two key components: A versatile genetic toolbox for the integration of 10-100 kb scale synthetic DNA into H. bluephagenesis genome and an efficient error correction coding scheme targeting noisy nanopore sequencing reads. The storage and repeated retrieval of 5 KB data under non-laboratory conditions are demonstrated. The work highlights the potential of DNA data storage in domestic and field scenarios, and expands its application domain from archival data to frequently accessed data.
Collapse
Affiliation(s)
- Fajia Sun
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Yiming Dong
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Ming Ni
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Yuhui Sun
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Qi Ouyang
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic PhysicsPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Long Qian
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| |
Collapse
|
6
|
Foster-Nyarko E, Cottingham H, Wick RR, Judd LM, Lam MMC, Wyres KL, Stanton TD, Tsang KK, David S, Aanensen DM, Brisse S, Holt KE. Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. Microb Genom 2023; 9:mgen000936. [PMID: 36752781 PMCID: PMC9997738 DOI: 10.1099/mgen.0.000936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs. We tested the accuracy of ONT-only assemblies for common applied bacterial genomics tasks (genotyping and cluster detection, implemented via Kleborate, Kaptive and Pathogenwatch), using data from 54 unique Klebsiella pneumoniae isolates. ONT reads generated via MinION with R9.4.1 flowcells were basecalled using three alternative models [Fast, High-accuracy (HAC) and Super-accuracy (SUP), available within ONT's Guppy software], assembled with Flye and polished using Medaka. Accuracy of typing using ONT-only assemblies was compared with that of Illumina-only and hybrid ONT+Illumina assemblies, constructed from the same isolates as reference standards. The most resource-intensive ONT-assembly approach (SUP basecalling, with or without Medaka polishing) performed best, yielding reliable capsule (K) type calls for all strains (100 % exact or best matching locus), reliable multi-locus sequence type (MLST) assignment (98.3 % exact match or single-locus variants), and good detection of acquired AMR genes and mutations (88-100 % correct identification across the various drug classes). Distance-based trees generated from SUP+Medaka assemblies accurately reflected overall genetic relationships between isolates. The definition of outbreak clusters from ONT-only assemblies was problematic due to inflation of SNP counts by high base-call errors. However, ONT data could be reliably used to 'rule out' isolates of distinct lineages from suspected transmission clusters. HAC basecalling + Medaka polishing performed similarly to SUP basecalling without polishing. Therefore, we recommend investing compute resources into basecalling (SUP model), wherever compute resources and time allow, and note that polishing is also worthwhile for improved performance. Overall, our results show that MLST, K type and AMR determinants can be reliably identified with ONT-only R9.4.1 flowcell data. However, cluster detection remains challenging with this technology.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- *Correspondence: Ebenezer Foster-Nyarko,
| | - Hugh Cottingham
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Ryan R. Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Margaret M. C. Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Thomas D. Stanton
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Kara K. Tsang
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Oxford University, Oxford OX3 7LF, UK
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Oxford University, Oxford OX3 7LF, UK
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn E. Holt
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| |
Collapse
|
7
|
Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients. Antibiotics (Basel) 2022; 11:antibiotics11101364. [PMID: 36290022 PMCID: PMC9598329 DOI: 10.3390/antibiotics11101364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistant K. pneumoniae occurrence in hospitals. The situation with extended-spectrum beta-lactamase (ESBL) producing bacteria further worsened during the COVID-19 pandemic, due to an increasing number of patients in intensive care units (ICU) and extensive, while often inappropriate, use of antibiotics including carbapenems. In order to elucidate the ways and mechanisms of antibiotic resistance spreading within the K. pneumoniae population, whole genome sequencing (WGS) seems to be a promising approach, and long-read sequencing is especially useful for the investigation of mobile genetic elements carrying antibiotic resistance genes, such as plasmids. We have performed short- and long read sequencing of three carbapenem-resistant K. pneumoniae isolates obtained from COVID-19 patients in a dedicated ICU of a multipurpose medical center, which belonged to the same clone according to cgMLST analysis, in order to understand the differences in their resistance profiles. We have revealed the presence of a small plasmid carrying aph(3′)-VIa gene providing resistance to amikacin in one of these isolates, which corresponded perfectly to its phenotypic resistance profile. We believe that the results obtained will facilitate further elucidating of antibiotic resistance mechanisms for this important pathogen, and highlight the need for continuous genomic epidemiology surveillance of clinical K. pneumoniae isolates.
Collapse
|
8
|
Meumann EM, Krause VL, Baird R, Currie BJ. Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia. Trop Med Infect Dis 2022; 7:tropicalmed7080181. [PMID: 36006273 PMCID: PMC9413455 DOI: 10.3390/tropicalmed7080181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The Northern Territory (NT) is a geographically remote region of northern and central Australia. Approximately a third of the population are First Nations Australians, many of whom live in remote regions. Due to the physical environment and climate, and scale of social inequity, the rates of many infectious diseases are the highest nationally. Molecular typing and genomic sequencing in research and public health have provided considerable new knowledge on the epidemiology of infectious diseases in the NT. We review the applications of genomic sequencing technology for molecular typing, identification of transmission clusters, phylogenomics, antimicrobial resistance prediction, and pathogen detection. We provide examples where these methodologies have been applied to infectious diseases in the NT and discuss the next steps in public health implementation of this technology.
Collapse
Affiliation(s)
- Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
- Correspondence:
| | - Vicki L. Krause
- Northern Territory Centre for Disease Control, Northern Territory Government, Darwin 0810, Australia
| | - Robert Baird
- Territory Pathology, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
| |
Collapse
|