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Wang B, Farhan MHR, Yuan L, Sui Y, Chu J, Yang X, Li Y, Huang L, Cheng G. Transfer dynamics of antimicrobial resistance among gram-negative bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176347. [PMID: 39306135 DOI: 10.1016/j.scitotenv.2024.176347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 09/09/2024] [Accepted: 09/15/2024] [Indexed: 09/26/2024]
Abstract
Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.
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Affiliation(s)
- Bangjuan Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Muhammad Haris Raza Farhan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Linlin Yuan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Sui
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinhua Chu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaohan Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Guyue Cheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
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2
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Wu X, Qi T, Zhang M, Bi J. A rare case report of Prevotella lung abscess diagnosed using third-generation metagenomic sequencing. J Int Med Res 2024; 52:3000605241271757. [PMID: 39324179 DOI: 10.1177/03000605241271757] [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: 09/27/2024] Open
Abstract
The Prevotella genus consists of obligate anaerobic Gram-negative bacteria that are symbiotic with the oral, intestinal, and vaginal mucosa. While several species of Prevotella have been implicated in pulmonary infections, identification of Prevotella as the causative agent of lung abscess is uncommon because of the requirement for stringent anaerobic culture conditions. In this report, we highlight a case of lung abscess caused by Prevotella salivae and Prevotella veroralis, underscoring the importance of third-generation metagenomic sequencing using devices from Oxford Nanopore Technologies for the precise diagnosis of specific pathogens.
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Affiliation(s)
- Xiaorui Wu
- Aerospace Center Hospital, Beijing 100049, China
| | - Tianqi Qi
- Aerospace Center Hospital, Beijing 100049, China
| | | | - Junfang Bi
- Department of Combined Traditional Chinese Medicine and West Medicine, Traditional Chinese Medicine Hospital of Shijiazhuang City, Shijiazhuang, China
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3
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Zhang Q, Ding Y, Ren Q, Zhang F, Lyu G, Lu T, Song Z, Wang Q, Cheng Y, Wang J, Gu H. Evaluation of targeted sequencing for pathogen identification in bone and joint infections: a cohort study from China. Ann Clin Microbiol Antimicrob 2024; 23:77. [PMID: 39175046 PMCID: PMC11342589 DOI: 10.1186/s12941-024-00733-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: 02/04/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
PURPOSE Bone and joint tuberculosis (BJTB) is a distinct variant of tuberculosis in which clinical diagnosis often leads to relative misdiagnosis and missed diagnoses. This study aimed to evaluate the diagnostic accuracy of the targeted nanopore sequencing (TNPseq) assay for BJTB patients in China. METHOD The study enrolled a cohort of 163 patients with suspected BJTB. Diagnostic testing was performed using the TNPseq assay on samples including punctured tissue, pus, and blood. The diagnostic accuracy of the TNPseq assay was then compared with that of the T-SPOT and Xpert MTB/RIF assays. RESULT TNPseq exhibited superior performance in terms of accuracy, demonstrating a sensitivity of 76.3% (95% CI: 71.0-81.6%) and a specificity of 98.8% (95% CI: 93.5-100%) in clinical diagnosis. When evaluated against a composite reference standard, TNPseq demonstrated a sensitivity of 74.4% (95% CI: 69.3-79.5%) and a specificity of 98.8% (95% CI: 93.7-100%). These results exceed the performance of both the T-SPOT and Xpert MTB/RIF tests. Notably, TNPseq demonstrated high specificity and accuracy in puncture specimens, with a sensitivity of 75.0% (95% CI: 70.2-79.8%) and a specificity of 98.3% (95% CI: 92.7-100%), as well as in pus samples, with a sensitivity of 83.3% (95% CI: 78.6-88.1%) and a specificity of 100% (95% CI: 100-100%). Additionally, TNPseq facilitated the detection of mixed infection scenarios, identifying 20 cases of bacterial-fungal co-infection, 17 cases of bacterial-viral co-infection, and two cases of simultaneous bacterial-fungal-viral co-infection. CONCLUSION TNPseq demonstrated great potential in the diagnosis of BJTB due to its high sensitivity and specificity. The ability of TNPseq to diagnose pathogens and detect drug resistance genes can also guide subsequent treatment. Expanding the application scenarios and scope of TNPseq will enable it to benefit more clinical treatments.
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Affiliation(s)
- Qiang Zhang
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China.
| | - Yonghua Ding
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Quanzhong Ren
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Feng Zhang
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Guoqiang Lyu
- Department of Orthopedics, The Second People's Hospital of Wenshang, Jining, 272500, People's Republic of China
| | - Tongxin Lu
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Zhen Song
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Qing Wang
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Yongxiang Cheng
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Jing Wang
- Public Health Clinical Center, Shandong University, Wen hua xi lu 44#, Jinan, 250100, Shandong Province, People's Republic of China
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui Province, People's Republic of China
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4
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Xing F, Xia Y, Lu Q, Lo SKF, Lau SKP, Woo PCY. Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report. Front Med (Lausanne) 2023; 10:1226126. [PMID: 37534314 PMCID: PMC10392123 DOI: 10.3389/fmed.2023.1226126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Nocardia species do not replicate as rapidly as other pyogenic bacteria and nocardial infections can be highly fatal, particularly in immunocompromised patients. Here, we present the first report of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis diagnosed by next-generation sequencing (NGS) using the Oxford Nanopore Technologies' MinION device. The bacterium was not identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Due to its low equipment cost, short turn-around-time, and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Yao Xia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Qianyun Lu
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan
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5
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Li B, Yan T. Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:41-89. [PMID: 37400174 DOI: 10.1016/bs.aambs.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.
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Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States.
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6
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Behling AH, Wilson BC, Ho D, Virta M, O'Sullivan JM, Vatanen T. Addressing antibiotic resistance: computational answers to a biological problem? Curr Opin Microbiol 2023; 74:102305. [PMID: 37031568 DOI: 10.1016/j.mib.2023.102305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023]
Abstract
The increasing prevalence of infections caused by antibiotic-resistant bacteria is a global healthcare crisis. Understanding the spread of resistance is predicated on the surveillance of antibiotic resistance genes within an environment. Bioinformatics and artificial intelligence (AI) methods applied to metagenomic sequencing data offer the capacity to detect known and infer yet-unknown resistance mechanisms, and predict future outbreaks of antibiotic-resistant infections. Machine learning methods, in particular, could revive the waning antibiotic discovery pipeline by helping to predict the molecular structure and function of antibiotic resistance compounds, and optimising their interactions with target proteins. Consequently, AI has the capacity to play a central role in guiding antibiotic stewardship and future clinical decision-making around antibiotic resistance.
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Affiliation(s)
- Anna H Behling
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Brooke C Wilson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Daniel Ho
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; The Maurice Wilkins Centre, The University of Auckland, Private Bag 92019, Auckland, New Zealand; Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, New South Wales, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton SO16 6YD, United Kingdom; Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore.
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand; Department of Microbiology, University of Helsinki, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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7
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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8
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Moller AG, Petit RA, Davis MH, Read TD. Development of an Amplicon Nanopore Sequencing Strategy for Detection of Mutations Conferring Intermediate Resistance to Vancomycin in Staphylococcus aureus Strains. Microbiol Spectr 2023; 11:e0272822. [PMID: 36688645 PMCID: PMC9927139 DOI: 10.1128/spectrum.02728-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections. Vancomycin intermediate S. aureus (VISA) variants can arise through de novo mutations. Here, we performed pilot experiments to develop a combined PCR/long-read sequencing-based method for detection of previously known VISA-causing mutations. Primers were designed to generate 10 amplicons covering 16 genes associated with the VISA phenotype. We sequenced amplicon pools as long reads with Oxford Nanopore adapter ligation on Flongle flow cells. We then detected mutations by mapping reads against a parental consensus or known reference sequence and comparing called variants against a database of known VISA mutations from laboratory selection. Each amplicon in the pool was sequenced to high (>1,000×) coverage, and no relationship was found between amplicon length and coverage. We also were able to detect the causative mutation (walK 646C>G) in a VISA mutant derived from the USA300 strain (N384-3 from parental strain N384). Mixing mutant (N384-3) and parental (N384) DNA at various ratios from 0 to 1 mutant suggested a mutation detection threshold of the average minor allele frequency (6.5%) at 95% confidence (two standard errors above mean mutation frequency). The study lays the groundwork for direct S. aureus antibiotic resistance genotype inference using rapid nanopore sequencing from clinical samples. IMPORTANCE Bacteremia mortality is known to increase rapidly with time after infection, making rapid diagnostics and treatment necessary. Successful treatment depends on correct administration of antibiotics based on knowledge of strain antibiotic susceptibility. Staphylococcus aureus is a major causative agent of bacteremia that is also commonly antibiotic resistant. In this work, we develop a method to accelerate detection of a complex, polygenic antibiotic resistance phenotype in S. aureus, vancomycin-intermediate resistance (VISA), through long-read genomic sequencing of amplicons representing genes most commonly mutated in VISA selection. This method both rapidly identifies VISA genotypes and incorporates the most comprehensive database of VISA genetic determinants known to date.
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Affiliation(s)
- Abraham G. Moller
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia, USA
| | - Robert A. Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Theiagen Genomics, Highlands Ranch, Colorado, USA
| | - Michelle H. Davis
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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9
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Suzuki M, Hashimoto Y, Hirabayashi A, Yahara K, Yoshida M, Fukano H, Hoshino Y, Shibayama K, Tomita H. Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing. Methods Mol Biol 2023; 2632:227-246. [PMID: 36781732 DOI: 10.1007/978-1-0716-2996-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.
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Affiliation(s)
- Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Japan
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10
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Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
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Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
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11
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Zhang H, Wang M, Han X, Wang T, Lei Y, Rao Y, Xu P, Wang Y, Gu H. The application of targeted nanopore sequencing for the identification of pathogens and resistance genes in lower respiratory tract infections. Front Microbiol 2022; 13:1065159. [PMID: 36620015 PMCID: PMC9822541 DOI: 10.3389/fmicb.2022.1065159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Lower respiratory tract infections (LRTIs) are one of the causes of mortality among infectious diseases. Microbial cultures commonly used in clinical practice are time-consuming, have poor sensitivity to unculturable and polymicrobial patterns, and are inadequate to guide timely and accurate antibiotic therapy. We investigated the feasibility of targeted nanopore sequencing (TNPseq) for the identification of pathogen and antimicrobial resistance (AMR) genes across suspected patients with LRTIs. TNPseq is a novel approach, which was improved based on nanopore sequencing for the identification of bacterial and fungal infections of clinical relevance. Methods This prospective study recruited 146 patients suspected of having LRTIs and with a median age of 61 years. The potential pathogens in these patients were detected by both TNPseq and the traditional culture workups. We compared the performance between the two methods among 146 LRTIs-related specimens. AMR genes were also detected by TNPseq to prompt the proper utilization of antibiotics. Results At least one pathogen was detected in 133 (91.1%) samples by TNPseq, but only 37 (25.3%) samples contained positive isolates among 146 cultured specimens. TNPseq possessed higher sensitivity than the conventional culture method (91.1 vs. 25.3%, P < 0.001) in identifying pathogens. It detected more samples with bacterial infections (P < 0.001) and mixed infections (P < 0.001) compared with the clinical culture tests. The most frequent AMR gene identified by TNPseq was bla TEM (n = 29), followed by bla SHV (n = 4), bla KPC (n = 2), bla CTX-M (n = 2), and mecA (n = 2). Furthermore, TNPseq discovered five possible multi-drug resistance specimens. Conclusion TNPseq is efficient to identify pathogens early, thus assisting physicians to conduct timely and precise treatment for patients with suspected LRTIs.
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Affiliation(s)
- Hongying Zhang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China,*Correspondence: Hongying Zhang ✉
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Ximei Han
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Ting Wang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Yanjuan Lei
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yu Rao
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Peisong Xu
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yunfei Wang
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,Graduate School, University of Science and Technology of China, Hefei, China,Hongcang Gu ✉
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12
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Yee R, Simner PJ. Next-Generation Sequencing Approaches to Predicting Antimicrobial Susceptibility Testing Results. Clin Lab Med 2022; 42:557-572. [PMID: 36368782 DOI: 10.1016/j.cll.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca Yee
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
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13
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Maboni G, Baptista RDP, Wireman J, Framst I, Summers AO, Sanchez S. Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA. Antibiotics (Basel) 2022; 11:1400. [PMID: 36290058 PMCID: PMC9598756 DOI: 10.3390/antibiotics11101400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Recent advances and lower costs in rapid high-throughput sequencing have engendered hope that whole genome sequencing (WGS) might afford complete resistome characterization in bacterial isolates. WGS is particularly useful for the clinical characterization of fastidious and slow-growing bacteria. Despite its potential, several challenges should be addressed before adopting WGS to detect antimicrobial resistance (AMR) genes in the clinical laboratory. Here, with three distinct ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), different approaches were compared to identify best practices for detecting AMR genes, including: total genomic DNA and plasmid DNA extractions, the solo assembly of Illumina short-reads and of Oxford Nanopore Technologies (ONT) long-reads, two hybrid assembly pipelines, and three in silico AMR databases. We also determined the susceptibility of each strain to 21 antimicrobials. We found that all AMR genes detected in pure plasmid DNA were also detectable in total genomic DNA, indicating that, at least in these three enterobacterial genera, the purification of plasmid DNA was not necessary to detect plasmid-borne AMR genes. Illumina short-reads used with ONT long-reads in either hybrid or polished assemblies of total genomic DNA enhanced the sensitivity and accuracy of AMR gene detection. Phenotypic susceptibility closely corresponded with genotypes identified by sequencing; however, the three AMR databases differed significantly in distinguishing mobile dedicated AMR genes from non-mobile chromosomal housekeeping genes in which rare spontaneous resistance mutations might occur. This study indicates that each method employed in a WGS workflow has an impact on the detection of AMR genes. A combination of short- and long-reads, followed by at least three different AMR databases, should be used for the consistent detection of such genes. Further, an additional step for plasmid DNA purification and sequencing may not be necessary. This study reveals the need for standardized biochemical and informatic procedures and database resources for consistent, reliable AMR genotyping to take full advantage of WGS in order to expedite patient treatment and track AMR genes within the hospital and community.
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Affiliation(s)
- Grazieli Maboni
- Athens Veterinary Diagnostic Laboratory, University of Georgia, Athens, GA 30602, USA
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Rodrigo de Paula Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Wireman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Isaac Framst
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Anne O. Summers
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
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14
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Hayashi K, Doi Y, Suzuki M. Rapid phylogenetic analysis using open reading frame content patterns acquired by Oxford Nanopore sequencing. J Appl Microbiol 2022; 133:3699-3707. [PMID: 36073316 DOI: 10.1111/jam.15807] [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: 06/30/2022] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
AIMS Phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole-genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time-consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real-time data analysis but the high error rate hampers its application in cgSNP-based phylogenetic analysis. Here, we developed a cgSNP-independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns. METHODS AND RESULTS WGS data of 66 Enterobacter hormaechei strains acquired by both ONT and Illumina sequencing and 162 strains obtained from NCBI database were converted to binary sequences based on the presence or absence of ORFs using BLASTn. Phylogenetic trees calculated from binary sequences (ORF trees) were compared with cgSNP trees derived from Illumina sequences. Clusters of closely related strains in the cgSNP trees formed comparable clusters in the ORF trees built with binary sequences, and the tree topologies between them were similar based on Fowlkes-Mallows index. CONCLUSIONS The ORF-based phylogenetic analysis using ONT sequencing may be useful in epidemiological investigations and offer advantages over the cgSNP-based approach. SIGNIFICANCE AND IMPACT OF THE STUDY Conversion of assembled WGS data to binary sequences based on the presence or absence of ORFs circumvents read error concerns with ONT sequencing. Since ONT sequencing generates data in real-time and does not require major investment, this ORF-based phylogenetic analysis method has the potential to enable phylogenetic and epidemiological analysis at the point of care.
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Affiliation(s)
- Kengo Hayashi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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15
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Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022; 17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.
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Affiliation(s)
- Yuan Ju
- Sichuan University, Sichuan University Library, CHINA
| | - Mengjun Pu
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Ke Sun
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Guiqin Song
- North Sichuan Medical College [Search North Sichuan Medical College]: North Sichuan Medical University, Shool of Basic Medical Sciences and Forensic Medicine, CHINA
| | - Jia Geng
- Sichuan University, State Key Laboratory of Biotherapy, No 17 Section 3 of South Renmin Rd, 610040, Chengdu, CHINA
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16
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Fuesslin V, Krautwurst S, Srivastava A, Winter D, Liedigk B, Thye T, Herrera-León S, Wohl S, May J, Fobil JN, Eibach D, Marz M, Schuldt K. Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon. Front Microbiol 2022; 13:909692. [PMID: 35814690 PMCID: PMC9257098 DOI: 10.3389/fmicb.2022.909692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.
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Affiliation(s)
- Valeria Fuesslin
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sebastian Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Doris Winter
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Britta Liedigk
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Thorsten Thye
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Silvia Herrera-León
- National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jürgen May
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Julius N. Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Daniel Eibach
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Kathrin Schuldt
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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17
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Zhang L, Huang W, Zhang S, Li Q, Wang Y, Chen T, Jiang H, Kong D, Lv Q, Zheng Y, Ren Y, Liu P, Jiang Y, Chen Y. Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing. Front Microbiol 2022; 13:858777. [PMID: 35655992 PMCID: PMC9152355 DOI: 10.3389/fmicb.2022.858777] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Yantai University, Yantai, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Department of Clinical Laboratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ying Chen
- College of Life Science, Yantai University, Yantai, China
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18
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Watanabe C, Kimizuka Y, Fujikura Y, Hamamoto T, Watanabe A, Yaguchi T, Sano T, Suematsu R, Kato Y, Miyata J, Matsukuma S, Kawana A. Mixed Infection of Cytomegalovirus and Pulmonary Nocardiosis Caused by Nocardia elegans Diagnosed Using Nanopore Sequencing Technology. Intern Med 2022; 61:1613-1617. [PMID: 34707041 PMCID: PMC9177376 DOI: 10.2169/internalmedicine.7639-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 69-year-old woman who had undergone renal transplantation and was receiving sulfamethoxazole/trimethoprim (ST) developed pulmonary nocardiosis. To our knowledge, this is the first report of the identification of Nocardia elegans using nanopore sequencing, supported by 16S rDNA capillary sequencing findings. Chest computed tomography performed after ST initiation revealed significant improvement of the pulmonary shadows compared to previous findings. We herein report the value of nanopore sequencing for rapid identification of rare pathogens, such as Nocardia elegans. Furthermore, our findings suggest that Nocardia may infect even patients receiving ST, which is currently the most effective prophylactic drug.
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Affiliation(s)
- Chie Watanabe
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yoshifumi Kimizuka
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yuji Fujikura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Takaaki Hamamoto
- Department of Laboratory Medicine, National Defense Medical College Hospital, Japan
| | - Akira Watanabe
- Division of Bio-resources, Medical Mycology Research Center, Chiba University, Japan
| | - Takashi Yaguchi
- Division of Bio-resources, Medical Mycology Research Center, Chiba University, Japan
| | - Tomoya Sano
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Ryohei Suematsu
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yoshiki Kato
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Jun Miyata
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Susumu Matsukuma
- Department of Laboratory Medicine, National Defense Medical College Hospital, Japan
- Department of Pathology and Laboratory Medicine, National Defense Medical College, Japan
| | - Akihiko Kawana
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
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19
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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Affiliation(s)
| | | | | | | | | | | | | | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (M.R.); (P.Z.); (D.J.); (X.Y.); (Y.L.); (Z.Y.)
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20
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Neffe L, Abendroth L, Bautsch W, Häussler S, Tomasch J. High plasmidome diversity of extended-spectrum beta-lactam-resistant Escherichia coli isolates collected during one year in one community hospital. Genomics 2022; 114:110368. [PMID: 35447310 DOI: 10.1016/j.ygeno.2022.110368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 04/09/2022] [Indexed: 01/14/2023]
Abstract
Plasmid-encoded antibiotic resistance encompasses many classes of currently used antibiotics. In globally distributed Escherichia coli lineages plasmids, which spread via horizontal gene transfer, are responsible for the dissemination of genes encoding extended-spectrum β-lactamases (ESBL). In this study, we combined 2nd and 3rd generation sequencing techniques to reconstruct the plasmidome of overall 97 clinical ESBL-E. coli isolates. Our results highlight the enormous plasmid diversity in respect to size, replicon-type and genetic content. Furthermore, we emphasize the diverse plasmid distribution patterns among the clinical isolates and the high intra- and extracellular mobility potential of resistance conferring genes. While the majority of resistance conferring genes were located on large plasmids of known replicon type, small cryptic plasmids seem to be underestimated resistance gene vectors. Our results contribute to a better understanding of the dissemination of resistance-conferring genes through horizontal gene transfer as well as clonal spread.
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Affiliation(s)
- Lisa Neffe
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa Abendroth
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, Hannover, Germany; Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, 2100 Copenhagen, Denmark; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30265 Hannover, Germany.
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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21
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Li Y, Jiao M, Liu Y, Ren Z, Li A. Application of Metagenomic Next-Generation Sequencing in Mycobacterium tuberculosis Infection. Front Med (Lausanne) 2022; 9:802719. [PMID: 35433724 PMCID: PMC9010669 DOI: 10.3389/fmed.2022.802719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The fight against Mycobacterium tuberculosis (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.
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Affiliation(s)
- Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengfan Jiao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zhigang Ren,
| | - Ang Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Ang Li,
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22
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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23
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2022; 10:80. [PMID: 35847383 PMCID: PMC9243550 DOI: 10.12688/f1000research.39214.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Affiliation(s)
| | - Marco Fabbri
- European Commission Joint Research Centre, Ispra, Italy
| | | | | | - Guy Van den Eede
- European Commission Joint Research Centre, Ispra, Italy
- European Commission Joint Research Centre, Geel, Belgium
| | - Erik Alm
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Catherine Carrillo
- Ottawa Laboratory – Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | | | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teresa Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, Madrid, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul Hammer
- BIOMES. NGS GmbH c/o Technische Hochschule Wildau, Wildau, Germany
| | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, Lyon, France
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Thierry Naas
- French-NRC for CPEs, Service de Bactériologie-Hygiène, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | | | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | | | - John Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Lukas M. Weber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Present address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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24
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Whittle E, Yonkus JA, Jeraldo P, Alva-Ruiz R, Nelson H, Kendrick ML, Grys TE, Patel R, Truty MJ, Chia N. Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections. mSphere 2022; 7:e0096421. [PMID: 35171692 PMCID: PMC8849348 DOI: 10.1128/msphere.00964-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Surgical site infections (SSI) are a significant burden to patients and health care systems. We evaluated the use of Nanopore sequencing (NS) to rapidly detect microbial species and antimicrobial resistance (AMR) genes present in intraoperative bile aspirates. Bile aspirates from 42 patients undergoing pancreatic head resection were included. Three methods of DNA extraction using mechanical cell lysis or protease cell lysis were compared to determine the optimum method of DNA extraction. The impact of host DNA depletion, sequence run duration, and use of different AMR gene databases was also assessed. To determine clinical value, NS results were compared to standard culture (SC) results. NS identified microbial species in all culture positive samples. Mechanical lysis improved NS detection of cultured species from 60% to 76%, enabled detection of fungal species, and increased AMR predictions. Host DNA depletion improved detection of streptococcal species and AMR correlation with SC. Selection of AMR database influenced the number of AMR hits and resistance profile of 13 antibiotics. AMR prediction using CARD and ResFinder 4.1 correctly predicted 79% and 81% of the bile antibiogram, respectively. Sequence run duration positively correlated with detection of AMR genes. A minimum of 6 h was required to characterize the biliary microbes, resulting in a turnaround time of 14 h. Rapid identification of microbial species and AMR genes can be achieved by NS. NS results correlated with SC, suggesting that NS may be useful in guiding early antimicrobial therapy postsurgery. IMPORTANCE Surgical site infections (SSI) are a significant burden to patients and health care systems. They increase mortality rates, length of hospital stays, and associated health care costs. To reduce the risk of SSI, surgical patients are administered broad-spectrum antibiotics that are later adapted to target microbial species detected at the site of surgical incision. Use of broad-spectrum antibiotics can be harmful to the patient. We wanted to develop a rapid method of detecting microbial species and their antimicrobial resistance phenotypes. We developed a method of detecting microbial species and predicting resistance phenotypes using Nanopore sequencing. Results generated using Nanopore sequencing were similar to current methods of detection but were obtained in a significantly shorter amount of time. This suggests that Nanopore sequencing could be used to tailor antibiotics in surgical patients and reduce use of broad-spectrum antibiotics.
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Affiliation(s)
- Emma Whittle
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Jennifer A. Yonkus
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Patricio Jeraldo
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Roberto Alva-Ruiz
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Heidi Nelson
- Division of Research and Optimal Patient Care, Cancer Programs, American College of Surgeonsgrid.417954.a, Chicago, Illinois, USA
| | - Michael L. Kendrick
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Thomas E. Grys
- Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Phoenix, Arizona, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Mark J. Truty
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Nicholas Chia
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
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25
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"Answers in hours": A prospective clinical study using nanopore sequencing for bile duct cultures. Surgery 2021; 171:693-702. [PMID: 34973809 DOI: 10.1016/j.surg.2021.09.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Surgical site infection is a major source of morbidity in patients undergoing pancreatic head resection and is often from organisms in intraoperative bile duct cultures. As such, many institutions use prolonged prophylactic antibiotics and tailor based on bile duct cultures. However, standard cultures take days, leaving many patients unnecessarily on prolonged antibiotics. Nanopore sequencing can provide data in hours and, thus, has the potential to improve antibiotic stewardship. The present study investigates the feasibility of nanopore sequencing in intraoperative bile samples. METHODS Patients undergoing pancreatic head resection were included. Intra-operative bile microbial profiles were determined with standard cultures and nanopore sequencing. Antibiotic recommendations were generated, and time-to-results determined for both methods. Organism yields, resistance patterns, antibiotic recommendations, and costs were compared. RESULTS Out of 42 patients, 22 (52%) had samples resulting in positive standard cultures. All positive standard cultures had microbes detected using nanopore sequencing. All 20 patients with negative standard cultures had negative nanopore sequencing. Nanopore sequencing detected more bacterial species compared to standard cultures (10.5 vs 4.4, p < 0.05) and more resistance genotypes (10.3 vs 2.7, p < 0.05). Antimicrobial recommendations based on nanopore sequencing provided coverage for standard cultures in 27 out of 44 (61%) samples, with broader coverage recommended by nanopore sequencing in 13 out of 27 (48%) of these samples. Nanopore sequencing results were faster (8 vs 98 hours) than standard cultures but had higher associated costs ($165 vs $38.49). CONCLUSION Rapid microbial profiling with nanopore sequencing is feasible with broader organism and resistance profiling compared to standard cultures. Nanopore sequencing has perfect negative predictive value and can potentially improve antibiotic stewardship; thus, a randomized control trial is under development.
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26
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Yehouenou CL, Bogaerts B, De Keersmaecker SCJ, Roosens NHC, Marchal K, Tchiakpe E, Affolabi D, Simon A, Dossou FM, Vanneste K, Dalleur O. Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019. Front Microbiol 2021; 12:752883. [PMID: 34956117 PMCID: PMC8695880 DOI: 10.3389/fmicb.2021.752883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 01/28/2023] Open
Abstract
The increasing worldwide prevalence of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli constitutes a serious threat to global public health. Surgical site infections are associated with high morbidity and mortality rates in developing countries, fueled by the limited availability of effective antibiotics. We used whole-genome sequencing (WGS) to evaluate antimicrobial resistance and the phylogenomic relationships of 19 ESBL-positive E. coli isolates collected from surgical site infections in patients across public hospitals in Benin in 2019. Isolates were identified by MALDI-TOF mass spectrometry and phenotypically tested for susceptibility to 16 antibiotics. Core-genome multi-locus sequence typing and single-nucleotide polymorphism-based phylogenomic methods were used to investigate the relatedness between samples. The broader phylogenetic context was characterized through the inclusion of publicly available genome data. Among the 19 isolates, 13 different sequence types (STs) were observed, including ST131 (n = 2), ST38 (n = 2), ST410 (n = 2), ST405 (n = 2), ST617 (n = 2), and ST1193 (n = 2). The bla CTX-M-15 gene encoding ESBL resistance was found in 15 isolates (78.9%), as well as other genes associated with ESBL, such as bla OXA-1 (n = 14) and bla TEM-1 (n = 9). Additionally, we frequently observed genes encoding resistance against aminoglycosides [aac-(6')-Ib-cr, n = 14], quinolones (qnrS1 , n = 4), tetracyclines [tet(B), n = 14], sulfonamides (sul2, n = 14), and trimethoprim (dfrA17, n = 13). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA associated with resistance to fluoroquinolones were also detected in multiple isolates. Although the phylogenomic investigation did not reveal evidence of hospital-acquired transmissions, we observed two very similar strains collected from patients in different hospitals. By characterizing a set of multidrug-resistant isolates collected from a largely unexplored environment, this study highlights the added value for WGS as an effective early warning system for emerging pathogens and antimicrobial resistance.
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Affiliation(s)
- Carine Laurence Yehouenou
- Clinical Pharmacy Research Group (CLIP), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain UCLouvain, Brussels, Belgium.,Laboratoire de Référence des Mycobactéries (LRM), Cotonou, Benin.,Faculté des Sciences de la Santé (FSS), Université d'Abomey Calavi (UAC), Cotonou, Benin
| | - Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Nancy H C Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium.,Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Edmond Tchiakpe
- Laboratory of Cell Biology and Physiology, Department of Biochemistry and Cellular Biology Faculty of Sciences and Technology and Institute of Applied Biomedical Sciences (ISBA), University of Abomey-Calavi, Cotonou, Benin.,National Reference Laboratory of Health Program Fighting Against AIDS in Benin, Health Ministry, Cotonou, Benin
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries (LRM), Cotonou, Benin.,Faculté des Sciences de la Santé (FSS), Université d'Abomey Calavi (UAC), Cotonou, Benin.,Centre National Hospitalier et Universitaire Hubert Koutoukou Maga (CNHU-HKM), Cotonou, Benin
| | - Anne Simon
- Centres hospitaliers Jolimont, prevention et contrôle des infections, Haine-Saint-Paul, Belgium
| | - Francis Moise Dossou
- Department of Surgery and Surgical Specialties, Faculty of Health Sciences, Campus universitaire champ de foire, Cotonou, Benin
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Olivia Dalleur
- Clinical Pharmacy Research Group (CLIP), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain UCLouvain, Brussels, Belgium.,Pharmacy, Clinique universitaire Saint-Luc, Université catholique de Louvain, UCLouvain, Brussels, Belgium
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27
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Fitzpatrick KJ, Rohlf HJ, Sutherland TD, Koo KM, Beckett S, Okelo WO, Keyburn AL, Morgan BS, Drigo B, Trau M, Donner E, Djordjevic SP, De Barro PJ. Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains. ACS Sens 2021; 6:4283-4296. [PMID: 34874700 DOI: 10.1021/acssensors.1c01973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
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Affiliation(s)
- Kira J. Fitzpatrick
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Hayden J. Rohlf
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Tara D. Sutherland
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Kevin M. Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, Queensland 4029, Australia
| | - Sam Beckett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Walter O. Okelo
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Anthony L. Keyburn
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, Victoria 3220, Australia
| | - Branwen S. Morgan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Steven P. Djordjevic
- Ithree Institute, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Paul J. De Barro
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health & Biosecurity, EcoSciences Precinct, Brisbane, Queensland 4001, Australia
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28
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Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods 2021; 192:106391. [PMID: 34915067 DOI: 10.1016/j.mimet.2021.106391] [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: 08/09/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
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29
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Li Y, Wang Q, Peng K, Liu Y, Xiao X, Mohsin M, Li R, Wang Z. Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin. Microb Genom 2021; 7:000667. [PMID: 34693904 PMCID: PMC8627205 DOI: 10.1099/mgen.0.000667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/06/2021] [Indexed: 02/03/2023] Open
Abstract
Abstract The emergence of plasmid-mediated tigecycline-resistant strains is posing a serious threat to food safety and human health, which has attracted worldwide attention. The tigecycline resistance gene tet (X4) has been found in diverse sources, but the distribution of tet (X4) and its genetic background in the animal farming environment is not fully understood. Thirty-two tet (X)-positive Escherichia coli strains isolated from 159 samples collected from swine farms showed resistance to tigecycline. The tet (X)-positive strains were characterized by antimicrobial susceptibility testing, conjugation assay, PCR, Illumina and long-read Nanopore sequencing, and bioinformatics analysis. A total of 11 different sequence types (STs) were identified and most of them belonged to phylogroup A, except ST641. In total, 196 possible prophage sequences were identified and some of the prophage regions were found to carry resistance genes, including tet (X4). Furthermore, our results showed possible correlations between CRISPR spacer sequences and serotypes or STs. The co-existence of tigecycline-resistant tet (A) variants and tet (X4) complicates the evolution of vital resistance genes in farming environments. Further, four reorganization plasmids carrying tet (X4) were observed, and the formation mechanism mainly involved homologous recombination. These findings contribute significantly to a better understanding of the diversity and complexity of tet (X4)-bearing plasmids, an emerging novel public health concern.
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Affiliation(s)
- Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
| | - Qian Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
| | - Yuan Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
| | - Xia Xiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, PR China
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30
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Jahan NA, Lindsey LL, Kipp EJ, Reinschmidt A, Heins BJ, Runck AM, Larsen PA. Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents. Pathogens 2021; 10:pathogens10091183. [PMID: 34578215 PMCID: PMC8471018 DOI: 10.3390/pathogens10091183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 12/26/2022] Open
Abstract
The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent–agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many mastitis pathogens circulating within five rodent species (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and a shrew (Blarina brevicauda). Interestingly, we observed a higher abundance of enteric pathogens (e.g., Salmonella) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.
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Affiliation(s)
- Nusrat A. Jahan
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (N.A.J.); (L.L.L.); (E.J.K.); (A.R.)
| | - Laramie L. Lindsey
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (N.A.J.); (L.L.L.); (E.J.K.); (A.R.)
| | - Evan J. Kipp
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (N.A.J.); (L.L.L.); (E.J.K.); (A.R.)
| | - Adam Reinschmidt
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (N.A.J.); (L.L.L.); (E.J.K.); (A.R.)
| | - Bradley J. Heins
- Department of Animal Science, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, St. Paul, MN 55108, USA;
| | - Amy M. Runck
- Department of Biology, Winona State University, Winona, MN 55987, USA;
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (N.A.J.); (L.L.L.); (E.J.K.); (A.R.)
- Correspondence:
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Extended Spectrum Beta-Lactamase (ESBL) Produced by Gram-Negative Bacteria in Trinidad and Tobago. Int J Microbiol 2021; 2021:5582755. [PMID: 34475957 PMCID: PMC8408010 DOI: 10.1155/2021/5582755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Gram-negative bacterial infections are a global health problem. The production of beta-lactamase is still the most vital factor leading to beta-lactam resistance. In Trinidad and Tobago, extended spectrum beta-lactamase (ESBL) production has been detected and reported mainly in the isolates of Klebsiella pneumoniae and Escherichia coli and constitutes a public health emergency that causes high morbidity and mortality in some patients. In this literature review, the authors cover vast information on ESBL frequency and laboratory detection using both conventional and molecular methods from clinical data. The aim is to make the reader reflect on how the actual knowledge can be used for rapid detection and understanding of the spread of antimicrobial resistance problems stemming from ESBL production among common Gram-negative organisms in the health care system.
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Hirabayashi A, Yahara K, Mitsuhashi S, Nakagawa S, Imanishi T, Ha VTT, Nguyen AV, Nguyen ST, Shibayama K, Suzuki M. Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam. PLoS One 2021; 16:e0231119. [PMID: 34319973 PMCID: PMC8318238 DOI: 10.1371/journal.pone.0231119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/21/2021] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene blaNDM, spread via plasmids among Enterobacterales in Vietnam. In this study, we characterized blaNDM-carrying plasmids in Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148-149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75-76 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.
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Affiliation(s)
- Aki Hirabayashi
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Yahara
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satomi Mitsuhashi
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Van Thi Thu Ha
- Microbiology Department, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - An Van Nguyen
- Microbiology Department, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - Son Thai Nguyen
- Microbiology Department, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Juma M, Sankaradoss A, Ndombi R, Mwaura P, Damodar T, Nazir J, Pandit A, Khurana R, Masika M, Chirchir R, Gachie J, Krishna S, Sowdhamini R, Anzala O, Meenakshi IS. Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting. Front Microbiol 2021; 12:647565. [PMID: 34385981 PMCID: PMC8353456 DOI: 10.3389/fmicb.2021.647565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background Africa has one of the highest incidences of gonorrhea. Neisseria gonorrhoeae is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing (WGS) is an efficient way of predicting AMR determinants and their spread in the population. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. Increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer MinION in remote areas lead to its adoption for routine microbial genome sequencing. To investigate whether MinION-only sequencing is sufficient for WGS and downstream analysis in resource-limited settings, we sequenced the genomes of 14 suspected N. gonorrhoeae isolates from Nairobi, Kenya. Methods Using WGS, the isolates were confirmed to be cases of N. gonorrhoeae (n = 9), and there were three co-occurrences of N. gonorrhoeae with Moraxella osloensis and N. meningitidis (n = 2). N. meningitidis has been implicated in sexually transmitted infections in recent years. The near-complete N. gonorrhoeae genomes (n = 10) were analyzed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature. Results We observe that ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC. Mutations conferring tetracycline (rpsJ) and sulfonamide (folP) resistance and plasmids encoding beta-lactamase were seen in all the strains, and tet(M)-containing plasmids were identified in nine strains. Phylogenetic analysis clustered the 10 isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Based on homology modeling of AMR targets, we see that the mutations in GyrA and ParC disrupt the hydrogen bonding with quinolone drugs and mutations in FolP may affect interaction with the antibiotic. Conclusion Here, we demonstrate the utility of mobile DNA sequencing technology in producing a consensus genome for sequence typing and detection of genetic determinants of AMR. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly, and analysis, can be used for any clinical isolate. Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis, and management of infections, especially in resource-limited settings.
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Affiliation(s)
- Meshack Juma
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Arun Sankaradoss
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Redcliff Ndombi
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Patrick Mwaura
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Tina Damodar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Junaid Nazir
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Rupsy Khurana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Moses Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Ruth Chirchir
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - John Gachie
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India.,School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Ponda, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Iyer S Meenakshi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
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34
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Murigneux V, Roberts LW, Forde BM, Phan MD, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA. MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics 2021; 22:474. [PMID: 34172000 PMCID: PMC8235852 DOI: 10.1186/s12864-021-07767-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
Background Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing. Results We evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes. Conclusions MicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07767-z.
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Affiliation(s)
- Valentine Murigneux
- QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Leah W Roberts
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia. .,Queensland Children's Hospital, Brisbane, Queensland, Australia. .,European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Hinxton, Cambridge, UK.
| | - Brian M Forde
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia.,Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia.,Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia.
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35
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Commichaux S, Javkar K, Ramachandran P, Nagarajan N, Bertrand D, Chen Y, Reed E, Gonzalez-Escalona N, Strain E, Rand H, Pop M, Ottesen A. Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads. BMC Genomics 2021; 22:389. [PMID: 34039264 PMCID: PMC8157722 DOI: 10.1186/s12864-021-07702-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. RESULTS We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. CONCLUSION The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.
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Affiliation(s)
- Seth Commichaux
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
- Biological Science Graduate Program, University of Maryland, College Park, MD, USA.
| | - Kiran Javkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, USA
| | - Padmini Ramachandran
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862, Singapore
| | - Denis Bertrand
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862, Singapore
| | - Yi Chen
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Elizabeth Reed
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | | | - Errol Strain
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA
| | - Hugh Rand
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Andrea Ottesen
- Center for Veterinary Medicine, Food and Drug Administration, Laurel, MD, USA
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Karlsson PA, Tano E, Jernberg C, Hickman RA, Guy L, Järhult JD, Wang H. Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden. Front Microbiol 2021; 12:664665. [PMID: 34054769 PMCID: PMC8155512 DOI: 10.3389/fmicb.2021.664665] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022] Open
Abstract
The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.
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Affiliation(s)
- Philip A Karlsson
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Eva Tano
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | | | - Rachel A Hickman
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden.,Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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Complete Genome Assembly of Multidrug-Resistant Yersinia enterocolitica Y72, Isolated in Sweden. Microbiol Resour Announc 2021; 10:10/19/e00264-21. [PMID: 33986087 PMCID: PMC8142573 DOI: 10.1128/mra.00264-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here, we report the complete genome sequence of a Swedish clinical strain of Yersinia enterocolitica, Y72. With emerging Yersinia outbreaks circulating in Nordic countries, the Y72 genome will provide more insights on the genetic relatedness and antibiotic resistance dissemination in future studies. Here, we report the complete genome sequence of a Swedish clinical strain of Yersinia enterocolitica, Y72. With emerging Yersinia outbreaks circulating in Nordic countries, the Y72 genome will provide more insights on the genetic relatedness and antibiotic resistance dissemination in future studies.
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38
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Xu F, Ge C, Li S, Tang S, Wu X, Luo H, Deng X, Zhang G, Stevenson A, Baker RC. Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15 +, 34 . Int J Food Microbiol 2021; 346:109167. [PMID: 33774575 DOI: 10.1016/j.ijfoodmicro.2021.109167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Our previous study demonstrated that whole genome sequencing (WGS) data generated by Oxford Nanopore Technologies (ONT) can be used for rapid and accurate prediction of selected Salmonella serotypes. However, one limitation is that established methods for WGS-based serotype prediction, utilizing data from either ONT or Illumina, cannot differentiate certain serotypes and serotype variants with the same or closely related antigenic formulae. This study aimed to evaluate nanopore sequencing and additional data analysis for identification of Salmonella enterica Choleraesuis var. Kunzendorf and S. enterica Orion var. 15+, 34+, thus overcoming this limitation. Five workflows that combined different flow cells, library construction methods and basecaller models were evaluated and compared. The workflow that consisted of the R9 flow cell, rapid sequencing library construction kit and guppy basecaller with base modified model performed best for Single Nucleotide Polymorphism (SNP) analysis. With this workflow, 99.98% of matching identity between assembled genomes from ONT and that from Illumina was achieved. Less than five high-quality SNPs differed when comparing sequencing data between ONT and Illumina. SNP typing successfully identified Choleraesuis var. Kunzendorf. While prophage prediction further differentiated Orion var. 15+, 34+ from the other two Orion variants. Our study improves the readiness of ONT as a Salmonella subtyping and source tracking tool for food industry applications.
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Affiliation(s)
- Feng Xu
- Mars Global Food Safety Center, Beijing 101407, China.
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing 101407, China.
| | - Shaoting Li
- Center for Food Safety, University of Georgia, Griffin, GA 30223, USA
| | - Silin Tang
- Mars Global Food Safety Center, Beijing 101407, China
| | - Xingwen Wu
- Mars Global Food Safety Center, Beijing 101407, China
| | - Hao Luo
- Mars Global Food Safety Center, Beijing 101407, China
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA 30223, USA
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Chen Z, Erickson DL, Meng J. Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses. Genomics 2021; 113:1366-1377. [PMID: 33716184 DOI: 10.1016/j.ygeno.2021.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/18/2021] [Accepted: 03/08/2021] [Indexed: 11/18/2022]
Abstract
Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the errors in Oxford Nanopore long-read assemblies have been developed. The impact of polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads on improving genomic analyses was evaluated using both simulated and real reads. Ten species (10 strains) were selected for simulated reads, while real reads were tested on 11 species (11 strains). Oxford Nanopore long reads were assembled with Unicycler to produce a draft assembly, followed by three rounds of polishing with Illumina short reads using two polishing tools, Pilon and NextPolish. One round of NextPolish polishing generated genome completeness and accuracy parameters similar to the reference genomes, whereas two or three rounds of Pilon polishing were needed, though contiguity remained unchanged after polishing. The polished assemblies of Escherichia coli O157:H7, Salmonella Typhimurium, and Cronobacter sakazakii with simulated reads did not provide accurate plasmid identifications. One round of NextPolish polishing was needed for accurately identifying plasmids in Staphylococcus aureus and E. coli O26:H11 with real reads, whereas one and two rounds of Pilon polishing were necessary for these two strains, respectively. Polishing failed to provide an accurate antimicrobial resistance (AMR) genotype for S. aureus with real reads. One round of polishing recovered an accurate AMR genotype for Klebsiella pneumoniae with real reads. The reference genome and draft assembly of Citrobacter braakii with real reads differed, which carried blaCMY-83 and fosA6, respectively, while both genes were present after one round of polishing. However, polishing did not improve the assembly of E. coli O26:H11 with real reads to achieve numbers of virulence genes similar to the reference genome. The draft and polished assemblies showed a phylogenetic tree topology comparable with the reference genomes. For multilocus sequence typing and pan-genome analyses, one round of NextPolish polishing was sufficient to obtain accurate results, while two or three rounds of Pilon polishing were needed. Overall, NextPolish outperformed Pilon for polishing the Oxford Nanopore long-read assemblies of bacterial pathogens, though both polishing strategies improved genomic analyses compared to the draft assemblies.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA; Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2021; 10:80. [DOI: 10.12688/f1000research.39214.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 01/12/2023] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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41
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Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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42
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Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
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Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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Zhu X, Yan S, Yuan F, Wan S. The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2020; 2020:6675206. [PMID: 33488885 PMCID: PMC7790562 DOI: 10.1155/2020/6675206] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 12/23/2022]
Abstract
Infectious diseases are major threats to human health and lead to a serious public health burden. The emergence of new pathogens and the mutation of known pathogens challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology exhibited versatile applications in pathogenic microorganism detection due to its flexible data throughput. This review article introduced the applications of nanopore sequencing in clinical microbiology and infectious diseases management, including the monitoring of emerging infectious diseases outbreak, identification of pathogen drug resistance, and disease-related microbial communities characterization.
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Affiliation(s)
- Xiaojian Zhu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shanshan Yan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| | - Fenghua Yuan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
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45
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Wee BA, Muloi DM, van Bunnik BAD. Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics. Clin Microbiol Infect 2020; 26:1612-1616. [PMID: 32979568 PMCID: PMC7721588 DOI: 10.1016/j.cmi.2020.09.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. OBJECTIVES To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. SOURCES Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli. CONTENT We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface. IMPLICATIONS A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.
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Affiliation(s)
- Bryan A Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Dishon M Muloi
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; International Livestock Research Institute, Nairobi, Kenya
| | - Bram A D van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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46
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Diagnostic tools for bacterial infections in travellers: Current and future options. Travel Med Infect Dis 2020; 37:101856. [PMID: 32841728 DOI: 10.1016/j.tmaid.2020.101856] [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: 04/03/2019] [Revised: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022]
Abstract
International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.
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47
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Latorre-Pérez A, Pascual J, Porcar M, Vilanova C. A lab in the field: applications of real-time, in situ metagenomic sequencing. Biol Methods Protoc 2020; 5:bpaa016. [PMID: 33134552 PMCID: PMC7585387 DOI: 10.1093/biomethods/bpaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/18/2023] Open
Abstract
High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
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Affiliation(s)
| | | | - Manuel Porcar
- Darwin Bioprospecting Excellence SL, Valencia, Spain
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Valencia, Spain
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Peter S, Bosio M, Gross C, Bezdan D, Gutierrez J, Oberhettinger P, Liese J, Vogel W, Dörfel D, Berger L, Marschal M, Willmann M, Gut I, Gut M, Autenrieth I, Ossowski S. Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing. mSphere 2020; 5:e00525-20. [PMID: 32817379 PMCID: PMC7440845 DOI: 10.1128/msphere.00525-20] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
Infections with multidrug-resistant bacteria often leave limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we demonstrate the application of Nanopore sequencing in a hospital setting for monitoring transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species. In 2009, we experienced an outbreak with extensively multidrug-resistant Pseudomonas aeruginosa harboring the carbapenemase-encoding blaIMP-8 gene. In 2012, the first Citrobacter freundii and Citrobacter cronae strains harboring the same gene were detected. Using Nanopore and Illumina sequencing, we conducted comparative analysis of all blaIMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platform plasmIDent for Nanopore-based characterization of clinical isolates and monitoring of ARG transfer, comprising de novo assembly of genomes and plasmids, plasmid circularization, ARG annotation, comparative genome analysis of multiple isolates, and visualization of results. Using plasmIDent, we identified a 40-kb plasmid carrying blaIMP-8 in P. aeruginosa and C. freundii, verifying the plasmid transfer. Within C. freundii, the plasmid underwent further evolution and plasmid fusion, resulting in a 164-kb megaplasmid, which was transferred to C. cronae Multiple rearrangements of the multidrug resistance gene cassette were detected in P. aeruginosa, including deletions and translocations of complete ARGs. In summary, plasmid transfer, plasmid fusion, and rearrangement of the ARG cassette mediated the rapid evolution of opportunistic pathogens in our hospital. We demonstrated the feasibility of near-real-time monitoring of plasmid evolution and ARG transfer in clinical settings, enabling successful countermeasures to contain plasmid-mediated outbreaks.IMPORTANCE Infections with multidrug-resistant bacteria represent a major threat to global health. While the spread of multidrug-resistant bacterial clones is frequently studied in the hospital setting, surveillance of the transfer of mobile genetic elements between different bacterial species was difficult until recent advances in sequencing technologies. Nanopore sequencing technology was applied to track antimicrobial gene transfer in a long-term outbreak of multidrug-resistant Pseudomonas aeruginosa, Citrobacter freundii, and Citrobacter cronae in a German hospital over 6 years. We developed a novel computational pipeline, pathoLogic, which enables de novo assembly of genomes and plasmids, antimicrobial resistance gene annotation and visualization, and comparative analysis. Applying this approach, we detected plasmid transfer between different bacterial species as well as plasmid fusion and frequent rearrangements of the antimicrobial resistance gene cassette. This study demonstrated the feasibility of near-real-time tracking of plasmid-based antimicrobial resistance gene transfer in hospitals, enabling countermeasures to contain plasmid-mediated outbreaks.
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Affiliation(s)
- Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Center, BSC, Barcelona, Spain
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Daniela Bezdan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Javier Gutierrez
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Philipp Oberhettinger
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jan Liese
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Wichard Vogel
- Medical Center, Department of Hematology, Oncology, Immunology, Rheumatology & Pulmonology, University of Tübingen, Tübingen, Germany
| | - Daniela Dörfel
- Medical Center, Department of Hematology, Oncology, Immunology, Rheumatology & Pulmonology, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Lennard Berger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ingo Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Prussing C, Snavely EA, Singh N, Lapierre P, Lasek-Nesselquist E, Mitchell K, Haas W, Owsiak R, Nazarian E, Musser KA. Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities. Front Microbiol 2020; 11:2007. [PMID: 32973725 PMCID: PMC7466660 DOI: 10.3389/fmicb.2020.02007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the bla KPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.
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Affiliation(s)
- Catharine Prussing
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Emily A. Snavely
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | | | - Kara Mitchell
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Rita Owsiak
- Maine Center for Disease Control and Prevention, Department of Health and Human Services, Augusta, ME, United States
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
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50
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Yee R, Breitwieser FP, Hao S, Opene BNA, Workman RE, Tamma PD, Dien-Bard J, Timp W, Simner PJ. Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms. Eur J Clin Microbiol Infect Dis 2020; 40:95-102. [PMID: 32783106 DOI: 10.1007/s10096-020-03996-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/23/2020] [Indexed: 11/25/2022]
Abstract
Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multidrug-resistant organisms (MDRO) are limited to specific organisms or resistance mechanisms. Metagenomic next-generation sequencing (mNGS) is a more rapid and agnostic diagnostic approach for microbiome and resistome investigations. We determined if mNGS can detect MDRO from rectal swabs in concordance with standard microbiology results. We performed and compared mNGS performance on short-read Illumina MiSeq (N = 10) and long-read Nanopore MinION (N = 5) platforms directly from rectal swabs to detect vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative organisms (CRO). We detected Enterococcus faecium (N = 8) and Enterococcus faecalis (N = 2) with associated van genes (9/10) in concordance with VRE culture-based results. We studied the microbiome and identified CRO, Pseudomonas aeruginosa (N = 1), Enterobacter cloacae (N = 1), and KPC-producing Klebsiella pneumoniae (N = 1). Nanopore real-time analysis detected the blaKPC gene in 2.3 min and provided genetic context (blaKPC harbored on pKPC_Kp46 IncF plasmid). Illumina sequencing provided accurate allelic variant determination (i.e., blaKPC-2) and strain typing of the K. pneumoniae (ST-15). We demonstrated an agnostic approach for surveillance of MDRO, examining advantages of both short- and long-read mNGS methods for AMR detection.
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Affiliation(s)
- Rebecca Yee
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Florian P Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephanie Hao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Belita N A Opene
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Pranita D Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Dien-Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles and Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Patricia J Simner
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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