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Hareza DA, Cosgrove SE, Simner PJ, Harris AD, Bergman Y, Conzemius R, Jacobs E, Beisken S, Tamma PD. Is Carbapenem Therapy Necessary for the Treatment of Non-CTX-M Extended-Spectrum β-Lactamase-Producing Enterobacterales Bloodstream Infections? Clin Infect Dis 2024; 78:1103-1110. [PMID: 37972276 PMCID: PMC11093655 DOI: 10.1093/cid/ciad703] [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: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Investigations into antibiotics for extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) bloodstream infections (BSIs) have focused on blaCTX-M genes. Patient outcomes from non-CTX-M-producing ESBL-E BSIs and optimal treatment are unknown. METHODS A multicenter observational study investigating 500 consecutive patients with ceftriaxone-resistant Enterobacterales BSIs during 2018-2022 was conducted. Broth microdilution and whole-genome sequencing confirmed antibiotic susceptibilities and ESBL gene presence, respectively. Inverse probability weighting (IPW) using propensity scores ensured patients with non-CTX-M and CTX-M ESBL-E BSIs were similar before outcome evaluation. RESULTS 396 patients (79.2%) were confirmed to have an ESBL-E BSI. ESBL gene family prevalence was as follows: blaCTX-M (n = 370), blaSHV (n = 16), blaOXY (n = 12), and blaVEB (n = 5). ESBL gene identification was not limited to Escherichia coli and Klebsiella species. In the IPW cohort, there was no difference in 30-day mortality or ESBL-E infection recurrence between the non-CTX-M and CTX-M groups (odds ratio [OR], 0.99; 95% confidence interval [CI], .87-1.11; P = .83 and OR, 1.10; 95% CI, .85-1.42; P = .47, respectively). In an exploratory analysis limited to the non-CTX-M group, 86% of the 21 patients who received meropenem were alive on day 30; none of the 5 patients who received piperacillin-tazobactam were alive on day 30. CONCLUSIONS Our findings suggest that non-CTX-M and CTX-M ESBL-E BSIs are equally concerning and associated with similar clinical outcomes. Meropenem may be associated with improved survival in patients with non-CTX-M ESBL-E BSIs, underscoring the potential benefit of comprehensive molecular diagnostics to enable early antibiotic optimization for ESBL-E BSIs beyond just blaCTX-M genes.
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Affiliation(s)
- Dariusz A Hareza
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sara E Cosgrove
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anthony D Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Emily Jacobs
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Pranita D Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Costales C, Dien Bard J. The Report Says What?: How the Medical Microbiologist can aid in the Interpretation of Next-Generation Sequencing Results. Clin Lab Med 2024; 44:75-84. [PMID: 38280799 DOI: 10.1016/j.cll.2023.10.006] [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: 01/29/2024]
Abstract
The applications of next-generation sequencing (NGS) in the clinical microbiology laboratory are expanding at a rapid pace. The medical microbiologist thus plays a key role in translating the results of these emerging technologies to the practicing clinician. Here we discuss the factors to consider to successfully develop standardized reporting for microbial targeted or metagenomic NGS testing in the clinical laboratory.
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Affiliation(s)
- Cristina Costales
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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3
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Vidal-García M, Urrutikoetxea-Gutiérrez M, Forero Niampira JC, Basaras M, Cisterna R, Díaz de Tuesta Del Arco JL. Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing. Future Microbiol 2023; 18:1309-1317. [PMID: 37850345 DOI: 10.2217/fmb-2023-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 10/19/2023] Open
Abstract
Aim: This study aimed to assess the ultra-fast method using MinION™ sequencing for rapid identification of β-lactamase-producing Klebsiella pneumoniae clinical isolates from positive blood cultures. Methods: Spiked-blood positive blood cultures were extracted using the ultra-fast method and automated DNA extraction for MinION sequencing. Raw reads were analyzed for β-lactamase resistance genes. Multilocus sequence typing and β-lactamase variant characterization were performed after assembly. Results: The ultra-fast method identified clinically relevant β-lactamase resistance genes in less than 1 h. Multilocus sequence typing and β-lactamase variant characterization required 3-6 h. Sequencing quality showed no direct correlation with pore number or DNA concentration. Conclusion: Nanopore sequencing, specifically the ultra-fast method, is promising for the rapid diagnosis of bloodstream infections, facilitating timely identification of multidrug-resistant bacteria in clinical samples.
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Affiliation(s)
- Matxalen Vidal-García
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Mikel Urrutikoetxea-Gutiérrez
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Juan C Forero Niampira
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Miren Basaras
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Ramón Cisterna
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - José L Díaz de Tuesta Del Arco
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
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4
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Rose R, Nolan DJ, Ashcraft D, Feehan AK, Velez-Climent L, Huston C, Lain B, Rosenthal S, Miele L, Fogel GB, Pankey G, Garcia-Diaz J, Lamers SL. Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates. BMC Microbiol 2023; 23:225. [PMID: 37596530 PMCID: PMC10436404 DOI: 10.1186/s12866-023-02975-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbapenem resistance in carbapenem-resistant Enterobacterales (CRE); however, the majority of these studies used short-read platforms (e.g. Illumina) to generate sequence data. In this study, our objective was to determine whether Oxford Nanopore Technologies (ONT) long-read WGS would improve detection of carbapenem AMR genes with respect to short-read only WGS for nine clinical CRE samples. We measured the minimum inhibitory breakpoint (MIC) using two phenotype assays (MicroScan and ETEST) for six antibiotics, including two carbapenems (meropenem and ertapenem) and four non-carbapenems (gentamicin, ciprofloxacin, cefepime, and trimethoprim/sulfamethoxazole). We generated short-read data using the Illumina NextSeq and long-read data using the ONT MinION. Four assembly methods were compared: ONT-only assembly; ONT-only assembly plus short-read polish; ONT + short-read hybrid assembly plus short-read polish; short-read only assembly. RESULTS Consistent with previous studies, our results suggest that the hybrid assembly produced the highest quality results as measured by gene completeness and contig circularization. However, ONT-only methods had minimal impact on the detection of AMR genes and plasmids compared to short-read methods, although, notably, differences in gene copy number differed between methods. All four assembly methods showed identical presence/absence of the blaKPC-2 carbapenemase gene for all samples. The two phenotype assays showed 100% concordant results for the non-carbapenems, but only 65% concordance for the two carbapenems. The presence/absence of AMR genes was 100% concordant with AMR phenotypes for all four non-carbapenem drugs, although only 22%-50% sensitivity for the carbapenems. CONCLUSIONS Overall, these findings suggest that the lack of complete correspondence between CRE AMR genotype and phenotype for carbapenems, while concerning, is independent of sequencing platform/assembly method.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA.
- FoxSeq, LLC, Thibodaux, LA, USA.
| | - David J Nolan
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Amy K Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | - Benjamin Lain
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Simon Rosenthal
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Lucio Miele
- Translational Science and Genetics at Louisiana State University Health Science Center, New Orleans, LA, USA
| | | | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
- FoxSeq, LLC, Thibodaux, LA, USA
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Simner PJ, Bergman Y, Conzemius R, Jacobs E, Tekle T, Beisken S, Tamma PD. An NDM-Producing Escherichia coli Clinical Isolate Exhibiting Resistance to Cefiderocol and the Combination of Ceftazidime-Avibactam and Aztreonam: Another Step Toward Pan-β-Lactam Resistance. Open Forum Infect Dis 2023; 10:ofad276. [PMID: 37416757 PMCID: PMC10319620 DOI: 10.1093/ofid/ofad276] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/15/2023] [Indexed: 07/08/2023] Open
Abstract
Background Cefiderocol and ceftazidime-avibactam plus aztreonam (CZA-ATM) are preferred treatment regimens for New Delhi metallo-β-lactamase (NDM)-producing infections. Methods We report the case of a US patient who traveled to India to receive a renal transplant. He subsequently experienced pyelonephritis by an NDM-producing Escherichia coli. Broth microdilution and the broth disk elution method indicated resistance to all β-lactams, including cefiderocol and CZA-ATM. Whole-genome sequencing investigations were undertaken to identify resistance mechanisms. Results An E. coli isolate belonging to sequence type (ST) 167 containing a blaNDM-5 gene was identified on a plasmid of the IncFIA/IncFIB/IncFIC replicon groups. When compared with the genome of another ST167 E. coli clinical isolate containing blaNDM-5 and exhibiting susceptibility to cefiderocol and CZA-ATM, a 12-base pair insertion in ftsI, translating to a 4-amino acid duplication in PBP3, was identified. Moreover, a blaCMY-59 gene was harbored on an IncI-γ replicon type, and frameshift mutations were identified in the cirA iron transport gene. Conclusions This is the first clinical case of a US patient harboring an NDM-producing isolate exhibiting resistance to all available β-lactam agents. The isolate's unexpected resistance to cefiderocol and CZA-ATM was likely due to a combination of (1) a modified PBP3 (increased MICs to both regimens), (2) truncated iron-binding protein (increased cefiderocol MIC), and (3) a blaCMY gene (reduced CZA-ATM activity). E. coli ST167 clinical isolates harboring blaNDM-5 genes are a recognized international high-risk clone. When coupled with the additional mechanisms identified in our patient's isolate, which is not uncommon for this high-risk clone, pan-β-lactam resistance may occur.
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Affiliation(s)
- Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Emily Jacobs
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tsigereda Tekle
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Pranita D Tamma
- Correspondence: Pranita D. Tamma, MD, MHS, Johns Hopkins University School of Medicine, 200 N. Wolfe Street, Room 3149, Baltimore, MD 21287 ()
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6
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Lascols C, Cherney B, Conley AB, Rishishwar L, Crawford MA, Morse SA, Fisher DJ, Anderson K, Hodge DR, Pillai SP, Hughes MA, Khan E, Sue D. Investigation of multidrug-resistant plasmids from carbapenemase-producing Klebsiella pneumoniae clinical isolates from Pakistan. Front Microbiol 2023; 14:1192097. [PMID: 37455731 PMCID: PMC10340517 DOI: 10.3389/fmicb.2023.1192097] [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: 03/22/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Objectives The study aim was to investigate multidrug-resistant (MDR) plasmids from a collection of 10 carbapenemase-producing Klebsiella pneumoniae clinical isolates identified within the same healthcare institution in Pakistan. Full characterization of the MDR plasmids including structure, typing characteristics, and AMR content as well as determination of their plasmid-based antimicrobial susceptibility profiles were carried out. Methods Plasmids were isolated from 10 clinical isolates of Klebsiella pneumoniae, and from a corresponding set of Escherichia coli transconjugants, then sequenced using Nanopore/Illumina technology to generate plasmid hybrid assemblies. Full characterization of MDR plasmids, including determination of next generation sequencing (NGS)-based AMR profiles, plasmid incompatibility groups, and types, was carried out. The structure of MDR plasmids was analyzed using the Galileo AMR platform. For E. coli transconjugants, the NGS-based AMR profiles were compared to NGS-predicted AMR phenotypes and conventional broth microdilution (BMD) antimicrobial susceptibility testing (AST) results. Results All carbapenemase-producing K. pneumoniae isolates (carrying either blaNDM-1, or/and blaOXA-48) carried multiple AMR plasmids encoding 34 antimicrobial resistance genes (ARGs) conferring resistance to antimicrobials from 6 different classes. The plasmid incompatibility groups and types identified were: IncC (types 1 and 3), IncFIA (type 26) IncFIB, IncFII (types K1, K2, K7, and K9), IncHI1B, and IncL. None of the blaNDM-1 and blaESBL-plasmids identified in this study were previously described. Most blaNDM-1-plasmids shared identical AMR regions suggesting potential genetic material/plasmid exchange between K. pneumoniae isolates of this collection. The majority of NGS-based AMR profiles from the E. coli transconjugants correlated well with both NGS-based predicted and conventional AST results. Conclusion This study highlights the complexity and diversity of the plasmid-based genetic background of carbapenemase-producing clinical isolates from Pakistan. This study emphasizes the need for characterization of MDR plasmids to determine their complete molecular background and monitor AMR through plasmid transmission between multi-resistant bacterial pathogens.
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Affiliation(s)
- Christine Lascols
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention, Atlanta, GA, United States
| | - Blake Cherney
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | - Matthew A. Crawford
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | | | - Debra J. Fisher
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Kevin Anderson
- Science and Technology Directorate, U.S. Department of Homeland Security, Washington, DC, United States
| | - David R. Hodge
- Science and Technology Directorate, U.S. Department of Homeland Security, Washington, DC, United States
| | - Segaran P. Pillai
- Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Molly A. Hughes
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Erum Khan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - David Sue
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention, Atlanta, GA, United States
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7
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Harris M, Fasolino T, Ivankovic D, Davis NJ, Brownlee N. Genetic Factors That Contribute to Antibiotic Resistance through Intrinsic and Acquired Bacterial Genes in Urinary Tract Infections. Microorganisms 2023; 11:1407. [PMID: 37374909 DOI: 10.3390/microorganisms11061407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The overprescribing and misuse of antibiotics have led to the rapid development of multidrug-resistant bacteria, such as those that cause UTIs. UTIs are the most common outpatient infections and are mainly caused by Escherichia coli and Klebsiella spp., although some Gram-positive bacteria, such as Pseudomonas aeruginosa, have been isolated in many cases. The rise of antimicrobial-resistant bacteria is a major public health concern, as it is predicted to lead to increased healthcare costs and poor patient outcomes and is expected to be the leading cause of global mortality by 2050. Antibiotic resistance among bacterial species can arise from a myriad of factors, including intrinsic and acquired resistance mechanisms, as well as mobile genetic elements, such as transposons, integrons, and plasmids. Plasmid-mediated resistance is of major concern as drug-resistance genes can quickly and efficiently spread across bacterial species via horizontal gene transfer. The emergence of extended-spectrum β-lactamases (ESBLs) such as NDM-1, OXA, KPC, and CTX-M family members has conferred resistance to many commonly used antibiotics in the treatment of UTIs, including penicillins, carbapenems, cephalosporins, and sulfamethoxazole. This review will focus on plasmid-mediated bacterial genes, especially those that encode ESBLs, and how they contribute to antibiotic resistance. Early clinical detection of these genes in patient samples will provide better treatment options and reduce the threat of antibiotic resistance.
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Affiliation(s)
- Mohammed Harris
- Department of Healthcare Genetics and Genomics, Clemson University, Clemson, SC 29634, USA
| | - Tracy Fasolino
- Department of Healthcare Genetics and Genomics, Clemson University, Clemson, SC 29634, USA
| | - Diana Ivankovic
- Department of Healthcare Genetics and Genomics, Clemson University, Clemson, SC 29634, USA
| | - Nicole J Davis
- Department of Healthcare Genetics and Genomics, Clemson University, Clemson, SC 29634, USA
| | - Noel Brownlee
- Department of Healthcare Genetics and Genomics, Clemson University, Clemson, SC 29634, USA
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8
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Tamma PD, Bergman Y, Jacobs EB, Lee JH, Lewis S, Cosgrove SE, Simner PJ. Comparing the activity of novel antibiotic agents against carbapenem-resistant Enterobacterales clinical isolates. Infect Control Hosp Epidemiol 2023; 44:762-767. [PMID: 35822340 DOI: 10.1017/ice.2022.161] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE We compared the activity of 8 novel β-lactam and tetracycline-derivative antibiotics against a cohort of clinical carbapenem-resistant Enterobacterales (CRE) isolates and investigated the incremental susceptibility benefit of the addition of an aminoglycoside, fluoroquinolone, or polymyxin to the β-lactam agents to assist with empiric antibiotic decision making. METHODS A collection of consecutive CRE clinical isolates from unique patients at 3 US hospitals (2016-2021) was assembled. Broth microdilution was performed to obtain antimicrobial susceptibility testing results. Mechanisms of carbapenem resistance were investigated through short-read and long-read whole-genome sequencing. RESULTS Of the 603 CRE isolates, 276 (46%) were carbapenemase producing and 327 (54%) were non-carbapenemase producing, respectively. The organisms most frequently identified were Klebsiella pneumoniae (38%), Enterobacter cloacae complex (26%), and Escherichia coli (16%). We obtained the following percent susceptibility to novel β-lactam agents: ceftazidime-avibactam (95%), meropenem-vaborbactam (92%), imipenem-relebactam (84%), and cefiderocol (92%). Aminoglycosides and the polymyxins provided greater incremental coverage as second agents, compared to fluoroquinolones. Amikacin and plazomicin exhibited the greatest additive value. Ceftazidime-avibactam, meropenem-vaborbactam, and cefiderocol were active against 94% of the 220 KPC-producing isolates. Cefiderocol was active against 83% of the 29 NDM-producing isolates. Ceftazidime-avibactam had 100% activity against the 9 OXA-48-like-producing isolates. Tigecycline had the highest activity compared to other tetracyclines against KPC, NDM, or OXA-48-like-producing isolates. CONCLUSION Selection among novel agents requires a nuanced understanding of the molecular epidemiology of CRE. This work provides insights into the comparative activity of novel agents and the additive value of a second antibiotic for empiric antibiotic decision making.
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Affiliation(s)
- Pranita D Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily B Jacobs
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jae Hyoung Lee
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shawna Lewis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sara E Cosgrove
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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9
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Edalatmand A, McArthur AG. CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database. Database (Oxford) 2023; 2023:7133783. [PMID: 37079891 PMCID: PMC10118295 DOI: 10.1093/database/baad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
Scientific literature is published at a rate that makes manual data extraction a highly time-consuming task. The Comprehensive Antibiotic Resistance Database (CARD) utilizes literature to curate information on antimicrobial resistance genes and to enable time-efficient triage of publications we have developed a classification algorithm for identifying publications describing first reports of new resistance genes. Trained on publications contained in the CARD, CARD*Shark downloads, processes and identifies publications recently added to PubMed that should be reviewed by biocurators. With CARD*Shark, we can minimize the monthly scope of articles a biocurator reviews from hundreds of articles to a few dozen, drastically improving the speed of curation while ensuring no relevant publications are overlooked. Database URL http://card.mcmaster.ca.
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Affiliation(s)
- Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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10
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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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11
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Chen T, Zhang L, Huang W, Zong H, Li Q, Zheng Y, Lv Q, Kong D, Ren Y, Jiang Y, Li Y, Liu P. Detection of Pathogens and Antimicrobial Resistance Genes in Ventilator-Associated Pneumonia by Metagenomic Next-Generation Sequencing Approach. Infect Drug Resist 2023; 16:923-936. [PMID: 36814827 PMCID: PMC9939671 DOI: 10.2147/idr.s397755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
Background The early identification of pathogens and their antibiotic resistance are essential for the management and treatment of patients affected by ventilator-associated pneumonia (VAP). However, microbiological culture may be time-consuming and has a limited culturability of many potential pathogens. In this study, we developed a rapid nanopore-based metagenomic next-generation sequencing (mNGS) diagnostic assay for detection of VAP pathogens and antimicrobial resistance genes (ARGs). Patients and Methods Endotracheal aspirate (ETA) samples from 63 patients with suspected VAP were collected between November 2021 and July 2022. Receiver operating characteristic (ROC) curves were established to compare the pathogen identification performance of the target pathogen reads, reads percent of microbes (RPM) and relative abundance (RA). The evaluation of the accuracy of mNGS was performed comparing with the gold standard and the composite standard, respectively. Then, the ARGs were analyzed by mNGS. Results ROC curves showed that RA has the highest diagnostic value and the corresponding threshold was 9.93%. The sensitivity and specificity of mNGS test were 91.3% and 78.3%, respectively, based on the gold standard, while the sensitivity and specificity of mNGS test were 97.4% and 100%, respectively, based on the composite standard. A total of 13 patients were virus-positive based on mNGS results, while the coinfection rate increased from 27% to 46% compared to the rate obtained based on clinical findings. The mNGS test also performed well at predicting antimicrobial resistance phenotypes. Patients with a late-onset VAP had a significantly greater proportion of ARGs in their respiratory microbiome compared to those with early-onset VAP (P = 0.041). Moreover, the median turnaround time of mNGS was 4.43 h, while routine culture was 72.00 h. Conclusion In this study, we developed a workflow that can accurately detect VAP pathogens and enable prediction of antimicrobial resistance phenotypes within 5 h of sample receipt by mNGS.
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Affiliation(s)
- Ting Chen
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Huijun Zong
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Yan Li
- The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, People’s Republic of China,Department of Critical Care Medicine, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100071, People’s Republic of China,Correspondence: Yan Li, The PLA 307 Clinical College of Anhui Medical University, The Fifth Clinical Medical College of Anhui Medical University, Hefei, 230032, People’s Republic of China, Email
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, People’s Republic of China,Peng Liu, Beijing Institute of Microbiology and Epidemiology, Dongdajie Road 20, Beijing, 100071, People’s Republic of China, Tel +86-010-66948487, Email
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12
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Validation and Application of Long-Read Whole-Genome Sequencing for Antimicrobial Resistance Gene Detection and Antimicrobial Susceptibility Testing. Antimicrob Agents Chemother 2023; 67:e0107222. [PMID: 36533931 PMCID: PMC9872642 DOI: 10.1128/aac.01072-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing applications are increasingly used for detection and characterization of antimicrobial-resistant pathogens in clinical settings. Oxford Nanopore Technologies (ONT) sequencing offers advantages for clinical use compared with other sequencing methodologies because it enables real-time basecalling, produces long sequencing reads that increase the ability to correctly assemble DNA fragments, provides short turnaround times, and requires relatively uncomplicated sample preparation. A drawback of ONT sequencing, however, is its lower per-read accuracy than short-read sequencing. We sought to identify best practices in ONT sequencing protocols. As some variability in sequencing results may be introduced by the DNA extraction methodology, we tested three DNA extraction kits across three independent laboratories using a representative set of six bacterial isolates to investigate accuracy and reproducibility of ONT technology. All DNA extraction techniques showed comparable performance; however, the DNeasy PowerSoil Pro kit had the highest sequencing yield. This kit was subsequently applied to 42 sequentially collected bacterial isolates from blood cultures to assess Ares Genetics's pipelines for predictive whole-genome sequencing antimicrobial susceptibility testing (WGS-AST) performance compared to phenotypic triplicate broth microdilution results. WGS-AST results ranged across the organisms and resulted in an overall categorical agreement of 95% for penicillins, 82.4% for cephalosporins, 76.7% for carbapenems, 86.9% for fluoroquinolones, and 96.2% for aminoglycosides. Very major errors/major errors were 0%/16.7% (penicillins), 11.7%/3.6% (cephalosporins), 0%/24.4% (carbapenems), 2.5%/7.7% (fluoroquinolones), and 0%/4.1% (aminoglycosides), respectively. This work showed that, although additional refinements are necessary, ONT sequencing demonstrates potential as a method to perform WGS-AST on cultured isolates for patient care.
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13
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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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14
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Shropshire WC, Konovalova A, McDaneld P, Gohel M, Strope B, Sahasrabhojane P, Tran CN, Greenberg D, Kim J, Zhan X, Aitken S, Bhatti M, Savidge TC, Treangen TJ, Hanson BM, Arias CA, Shelburne SA. Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections. mSystems 2022; 7:e0047622. [PMID: 36036505 PMCID: PMC9601100 DOI: 10.1128/msystems.00476-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 01/25/2023] Open
Abstract
Noncarbapenemase-producing carbapenem-resistant Enterobacterales (non-CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem-resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole-genome sequencing was used to elucidate carbapenem nonsusceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem nonsusceptible Enterobacterales (CNSE) mechanisms (i.e., isolates with carbapenem intermediate resistance phenotypes or greater) through a combination of phylogenetic analysis, antimicrobial resistance gene detection/copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%), whereas 25.3% (20/79) were Enterobacterales with intermediate susceptibility to carbapenems (CIE), and 22.8% (18/79) were carbapenemase-producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum β-lactamase (ESBL) genes (Wilcoxon Test; P-value < 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6×; n = 17) and K. pneumoniae (median CNV = 3.2×, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene (i.e., ompC/ompF or ompK36/ompK35). Completely resolved CNSE genomes revealed that IS26 and ISEcp1 structures harboring blaCTX-M variants along with other antimicrobial resistance elements were associated with gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE-mediated β-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS26 translocatable units, or segmental duplication, typically due to ISEcp1 transposition units. Non-CP-CRE strains were the most common cause of CRE bacteremia with carbapenem nonsusceptibility driven by concurrent porin loss and MGE-mediated amplification of blaCTX-M genes. IMPORTANCE Carbapenem-resistant Enterobacterales (CRE) are considered urgent antimicrobial resistance (AMR) threats. The vast majority of CRE research has focused on carbapenemase-producing Enterobacterales (CPE) even though noncarbapenemase-producing CRE (non-CP-CRE) comprise 50% or more of isolates in some surveillance studies. Thus, carbapenem resistance mechanisms in non-CP-CRE remain poorly characterized. To address this problem, we applied a combination of short- and long-read sequencing technologies to a cohort of CRE bacteremia isolates and used these data to unravel complex mobile genetic element structures mediating β-lactamase gene amplification. By generating complete genomes of 65 carbapenem nonsusceptible Enterobacterales (CNSE) covering a genetically diverse array of isolates, our findings both generate novel insights into how non-CP-CRE overcome carbapenem treatments and provide researchers scaffolds for characterization of their own non-CP-CRE isolates. Improved recognition of mechanisms driving development of non-CP-CRE could assist with design and implementation of future strategies to mitigate the impact of these increasingly recognized AMR pathogens.
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Affiliation(s)
- W. C. Shropshire
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - A. Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - P. McDaneld
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - M. Gohel
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - B. Strope
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - P. Sahasrabhojane
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - C. N. Tran
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - D. Greenberg
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - J. Kim
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - X. Zhan
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - S. Aitken
- Division of Pharmacy, Michigan Medicine at University of Michigan, Ann Arbor, Michigan, USA
| | - M. Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - T. C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - T. J. Treangen
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - B. M. Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - C. A. Arias
- Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - S. A. Shelburne
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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15
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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:antibiotics11101400. [PMID: 36290058 PMCID: PMC9598756 DOI: 10.3390/antibiotics11101400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [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
- Correspondence:
| | - 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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16
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Zhang R, Yang T, Zhang Q, Liu D, Elhadidy M, Ding T. Whole-genome sequencing: a perspective on sensing bacterial risk for food safety. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Simner PJ, Mostafa HH, Bergman Y, Ante M, Tekle T, Adebayo A, Beisken S, Dzintars K, Tamma PD. Progressive Development of Cefiderocol Resistance in Escherichia coli During Therapy is Associated With an Increase in blaNDM-5 Copy Number and Gene Expression. Clin Infect Dis 2022; 75:47-54. [PMID: 34618008 PMCID: PMC9402677 DOI: 10.1093/cid/ciab888] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND As cefiderocol is increasingly being prescribed in clinical practice, it is critical that we understand key mechanisms contributing to acquired resistance to this agent. METHODS We describe a patient with acute lymphoblastic leukemia and a New Delhi metallo-ß-lactamase (NDM)-5-producing Escherichia coli intra-abdominal infection in whom resistance to cefiderocol evolved approximately 2 weeks after the start of treatment. Through whole-genome sequencing (WGS), messenger RNA expression studies, and ethylenediaminetetraacetic acid inhibition analysis, we investigated the role of increased NDM-5 production and genetic mutations contributing to the development of cefiderocol resistance, using 5 sequential clinical E. coli isolates obtained from the patient. RESULTS In all 5 isolates, blaNDM-5 genes were identified. The minimum inhibitory concentrations for cefiderocol were 2, 4, and >32 μg/mL for isolates 1-2, 3, and 4-5, respectively. WGS showed that isolates 1-3 contained a single copy of the blaNDM-5 gene, whereas isolates 4 and 5 had 5 and 10 copies of the blaNDM-5 gene, respectively, on an IncFIA/FIB/IncFII plasmid. These findings were correlated with those of blaNDM-5 messenger RNA expression analysis, in which isolates 4 and 5 expressed blaNDM-5 1.7- and 2.8-fold, respectively, compared to, isolate 1. Synergy testing with the combination of ceftazidime-avibactam and aztreonam demonstrated expansion of the zone of inhibition between the disks for all isolates. The patient was successfully treated with this combination and remained infection free 1 year later. CONCLUSIONS The findings in our patient suggest that increased copy numbers of blaNDM genes through translocation events are used by Enterobacterales to evade cefiderocol-mediated cell death. The frequency of increased blaNDM-5 expression in contributing to cefiderocol resistance needs investigation.
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Affiliation(s)
- Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Tsigereda Tekle
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ayomikun Adebayo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Kathryn Dzintars
- Department of Pharmacy, Johns Hopkins Hospital, Baltimore, Maryland, USAand
| | - Pranita D Tamma
- Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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18
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Conzemius R, Bergman Y, Májek P, Beisken S, Lewis S, Jacobs EB, Tamma PD, Simner PJ. Automated antimicrobial susceptibility testing and antimicrobial resistance genotyping using Illumina and Oxford Nanopore Technologies sequencing data among Enterobacteriaceae. Front Microbiol 2022; 13:973605. [PMID: 36003946 PMCID: PMC9393496 DOI: 10.3389/fmicb.2022.973605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequencing (WGS) enables the molecular characterization of bacterial pathogens. We compared the accuracy of the Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for the determination of AMR classes and antimicrobial susceptibility testing (AST) among 181 clinical Enterobacteriaceae isolates. Sequencing reads for each isolate were uploaded to AREScloud (Ares Genetics) to determine the presence of AMR markers and the predicted WGS-AST profile. The profiles of both sequencing platforms were compared to broth microdilution (BMD) AST. Isolates were delineated by resistance to third-generation cephalosporins and carbapenems as well as the presence of AMR markers to determine clinically relevant AMR classes. The overall categorical agreement (CA) was 90% (Illumina) and 88% (ONT) across all antimicrobials, 96% for the prediction of resistance to third-generation cephalosporins for both platforms, and 94% (Illumina) and 91% (ONT) for the prediction of resistance to carbapenems. Carbapenem resistance was overestimated on ONT with a major error of 16%. Sensitivity for the detection of carbapenemases, extended-spectrum β-lactamases, and plasmid-mediated ampC genes was 98, 95, and 70% by ONT compared to the Illumina dataset as the reference. Our results highlight the potential of the ONT platform’s use in clinical microbiology laboratories. When combined with robust bioinformatics methods, WGS-AST predictions may be a future approach to guide effective antimicrobial decision-making.
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Affiliation(s)
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | | | - Shawna Lewis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Emily B. Jacobs
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Pranita D. Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Patricia J. Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Patricia J. Simner,
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19
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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20
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Golden AR, Karlowsky JA, Walkty A, Baxter MR, Denisuik AJ, McCracken M, Mulvey MR, Adam HJ, Bay D, Zhanel GG. Comparison of phenotypic antimicrobial susceptibility testing results and WGS-derived genotypic resistance profiles for a cohort of ESBL-producing Escherichia coli collected from Canadian hospitals: CANWARD 2007-18. J Antimicrob Chemother 2021; 76:2825-2832. [PMID: 34378044 DOI: 10.1093/jac/dkab268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/05/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine whether the genotypic resistance profile inferred from WGS could accurately predict phenotypic resistance for ESBL-producing Escherichia coli isolated from patient samples in Canadian hospital laboratories. METHODS As part of the ongoing CANWARD study, 671 E. coli were collected and phenotypically confirmed as ESBL producers using CLSI M100 disc testing criteria. Isolates were sequenced using the Illumina MiSeq platform, resulting in 636 high-quality genomes for comparison. Using a rules-based approach, the genotypic resistance profile was compared with the phenotypic resistance interpretation generated using the CLSI broth microdilution method for ceftriaxone, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole. RESULTS The most common genes associated with non-susceptibility to ceftriaxone, gentamicin and trimethoprim/sulfamethoxazole were CTX-M-15 (n = 391), aac(3)-IIa + aac(6')-Ib-cr (n = 121) and dfrA17 + sul1 (n = 169), respectively. Ciprofloxacin non-susceptibility was most commonly attributed to alterations in both gyrA (S83L + D87N) and parC (S80I + E84V), with (n = 187) or without (n = 197) aac(6')-Ib-cr. Categorical agreement (susceptible or non-susceptible) between actual and predicted phenotype was 95.6%, 98.9%, 97.6% and 88.8% for ceftriaxone, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole, respectively. Only ciprofloxacin results (susceptible or non-susceptible) were predicted with major error (ME) and very major error (VME) rates of <3%: ciprofloxacin (ME, 1.5%; VME, 1.1%); gentamicin (ME, 0.8%-31.7%; VME, 4.8%); ceftriaxone (ME, 81.8%; VME, 3.0%); and trimethoprim/sulfamethoxazole (ME, 0.9%-23.0%; VME, 5.2%-8.5%). CONCLUSIONS Our rules-based approach for predicting a resistance phenotype from WGS performed well for ciprofloxacin, with categorical agreement of 98.9%, an ME rate of 1.5% and a VME rate of 1.1%. Although high categorical agreements were also obtained for gentamicin, ceftriaxone and trimethoprim/sulfamethoxazole, ME and/or VME rates were ≥3%.
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Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Department of Clinical Microbiology, Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Andrew Walkty
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Department of Clinical Microbiology, Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Andrew J Denisuik
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Melissa McCracken
- National Microbiology Laboratory-Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2 Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,National Microbiology Laboratory-Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2 Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Department of Clinical Microbiology, Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Denice Bay
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
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21
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Fawcett WJ, Klein AA. Anaesthesia and peri-operative medicine over the next 25 years. Anaesthesia 2021; 76:1416-1420. [PMID: 34333762 DOI: 10.1111/anae.15552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/31/2022]
Affiliation(s)
- W J Fawcett
- Department of Anaesthesia, Royal Surrey County NHS Foundation Trust, Guildford, UK
| | - A A Klein
- Department of Anaesthesia and Intensive Care, Royal Papworth Hospital, Cambridge, UK
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22
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Mahfouz N, Ferreira I, Beisken S, von Haeseler A, Posch AE. Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. J Antimicrob Chemother 2021; 75:3099-3108. [PMID: 32658975 PMCID: PMC7566382 DOI: 10.1093/jac/dkaa257] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/04/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
Background Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance. Methods We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates. Results CARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%). Conclusions We show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.
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Affiliation(s)
- Norhan Mahfouz
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria
| | - Inês Ferreira
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria.,Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Stephan Beisken
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna 1030, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Andreas E Posch
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria
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23
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Gene-Gene Interactions Dictate Ciprofloxacin Resistance in Pseudomonas aeruginosa and Facilitate Prediction of Resistance Phenotype from Genome Sequence Data. Antimicrob Agents Chemother 2021; 65:e0269620. [PMID: 33875431 DOI: 10.1128/aac.02696-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ciprofloxacin is one of the most widely used antibiotics for treating Pseudomonas aeruginosa infections. However, P. aeruginosa acquires mutations that confer ciprofloxacin resistance, making treatment more difficult. Resistance is multifactorial, with mutations in multiple genes influencing the resistance phenotype. However, the contributions of individual mutations and mutation combinations to the amounts of ciprofloxacin that P. aeruginosa can tolerate are not well understood. Engineering P. aeruginosa strain PAO1 to contain mutations in any one of the resistance-associated genes gyrA, nfxB, rnfC, parC, and parE showed that only gyrA mutations increased the MIC for ciprofloxacin. Mutations in parC and parE increased the MIC of a gyrA mutant, making the bacteria ciprofloxacin resistant. Mutations in nfxB and rnfC increased the MIC, conferring resistance, only if both were mutated in a gyrA background. Mutations in all of gyrA, nfxB, rnfC, and parC/E further increased the MIC. These findings reveal an epistatic network of gene-gene interactions in ciprofloxacin resistance. We used this information to predict ciprofloxacin resistance/susceptibility for 274 isolates of P. aeruginosa from their genome sequences. Antibiotic susceptibility profiles were predicted correctly for 84% of the isolates. The majority of isolates for which prediction was unsuccessful were ciprofloxacin resistant, demonstrating the involvement of additional as yet unidentified genes and mutations in resistance. Our data show that gene-gene interactions can play an important role in antibiotic resistance and can be successfully incorporated into models predicting resistance phenotype.
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24
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Jacobs MR, Colson JD, Rhoads DD. Recent advances in rapid antimicrobial susceptibility testing systems. Expert Rev Mol Diagn 2021; 21:563-578. [PMID: 33926351 DOI: 10.1080/14737159.2021.1924679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged. AREAS COVERED Advances in rapid phenotypic and molecular-based AST systems. EXPERT OPINION AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.
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Affiliation(s)
- Michael R Jacobs
- Emeritus Professor of Pathology and Emeritus Medical Director, Clinical Microbiology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jordan D Colson
- Microbiology Fellow, Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel D Rhoads
- Section Head of Microbiology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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25
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Zhou M, Wu Y, Kudinha T, Jia P, Wang L, Xu Y, Yang Q. Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing. Front Genet 2021; 12:620009. [PMID: 33841495 PMCID: PMC8024499 DOI: 10.3389/fgene.2021.620009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Bloodstream infection is a major cause of morbidity and mortality worldwide. We explored whether MinION nanopore sequencing could accelerate diagnosis, resistance, and virulence profiling prediction in simulated blood samples and blood cultures. One milliliter of healthy blood samples each from direct spike (sample 1), anaerobic (sample 2), and aerobic (sample 3) blood cultures with initial inoculation of ∼30 CFU/ml of a clinically isolated Klebsiella pneumoniae strain was subjected to DNA extraction and nanopore sequencing. Hybrid assembly of Illumina and nanopore reads from pure colonies of the isolate (sample 4) was used as a reference for comparison. Hybrid assembly of the reference genome identified a total of 39 antibiotic resistance genes and 77 virulence genes through alignment with the CARD and VFDB databases. Nanopore correctly detected K. pneumoniae in all three blood samples. The fastest identification was achieved within 8 h from specimen to result in sample 1 without blood culture. However, direct sequencing in sample 1 only identified seven resistance genes (20.6%) but 28 genes in samples 2–4 (82.4%) compared to the reference within 2 h of sequencing time. Similarly, 11 (14.3%) and 74 (96.1%) of the virulence genes were detected in samples 1 and 2–4 within 2 h of sequencing time, respectively. Direct nanopore sequencing from positive blood cultures allowed comprehensive pathogen identification, resistance, and virulence genes prediction within 2 h, which shows its promising use in point-of-care clinical settings.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yarong Wu
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia.,Pathology West, NSW Health Pathology, Orange, NSW, Australia
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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26
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Sherif M, Palmieri M, Mirande C, El-Mahallawy H, Rashed HG, Abd-El-Reheem F, El-Manakhly AR, Abdel-Latif RAR, Aboulela AG, Saeed LY, Abdel-Rahman S, Elsayed E, van Belkum A, El-Kholy A. Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study. Eur J Clin Microbiol Infect Dis 2021; 40:1451-1460. [PMID: 33559021 DOI: 10.1007/s10096-021-04177-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was blaCTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were blaNDM-1 (n = 13), blaNDM-5 (n = 1), blaOXA-48 (n = 12), blaOXA-181 (n = 2), and blaKPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.
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Affiliation(s)
- May Sherif
- Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mattia Palmieri
- bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France
| | - Caroline Mirande
- bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France
| | - Hadir El-Mahallawy
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hebatallah G Rashed
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Fadwa Abd-El-Reheem
- Department of Clinical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Arwa Ramadan El-Manakhly
- Department of Microbiology and Infection Control, Dar-Al-Fouad Hospital, 6th of October City, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Russian University in Cairo, Cairo, Egypt
| | | | | | - Laila Yosef Saeed
- Department of Clinical Pathology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Soheir Abdel-Rahman
- Department of Clinical Pathology, Faculty of Medicine, Banha University, Banha, Egypt
| | - Eman Elsayed
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France
| | - Amani El-Kholy
- Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt.
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27
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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: 85] [Impact Index Per Article: 28.3] [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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28
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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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29
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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30
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Lepuschitz S, Weinmaier T, Mrazek K, Beisken S, Weinberger J, Posch AE. Analytical Performance Validation of Next-Generation Sequencing Based Clinical Microbiology Assays Using a K-mer Analysis Workflow. Front Microbiol 2020; 11:1883. [PMID: 32849463 PMCID: PMC7422695 DOI: 10.3389/fmicb.2020.01883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) enables clinical microbiology assays such as molecular typing of bacterial isolates which is now routinely applied for infection control and epidemiology. Additionally, feasibility for NGS-based identification of antimicrobial resistance (AMR) markers as well as genetic prediction of antibiotic susceptibility testing results has been demonstrated. Various bioinformatics approaches enabling NGS-based clinical microbiology assays exist, but standardized, computationally efficient and scalable sample-to-results workflows including validated quality control parameters are still lacking. Bioinformatics analysis workflows based on k-mers have been shown to allow for fast and efficient analysis of large genomics data sets as obtained from microbial sequencing applications. We here demonstrate applicability of k-mer based clinical microbiology assays for whole-genome sequencing (WGS) including variant calling, taxonomic identification, bacterial typing as well as AMR marker detection. The wet-lab and dry-lab workflows were developed and validated in line with Clinical Laboratory Improvement Act (CLIA) guidelines for laboratory-developed tests (LDTs) on multi-drug resistant ESKAPE pathogens. The developed k-mer based workflow demonstrated ≥99.39% repeatability, ≥99.09% reproducibility and ≥99.76% accuracy for variant calling and applied assays as determined by intra-day and inter-day triplicate measurements. The limit of detection (LOD) across assays was found to be at 20× sequencing depth and 15× for AMR marker detection. Thorough benchmarking of the k-mer based workflow revealed analytical performance criteria are comparable to state-of-the-art alignment based workflows across clinical microbiology assays. Diagnostic sensitivity and specificity for multilocus sequence typing (MLST) and phylogenetic analysis were 100% for both approaches. For AMR marker detection, sensitivity and specificity were 95.29 and 99.78% for the k-mer based workflow as compared to 95.17 and 99.77% for the alignment-based approach. Summarizing, results illustrate that k-mer based analysis workflows enable a broad range of clinical microbiology assays, potentially not only for WGS-based typing and AMR gene detection but also genetic prediction of antibiotic susceptibility testing results.
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31
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Mitchell SL, Simner PJ. Next-Generation Sequencing in Clinical Microbiology: Are We There Yet? Clin Lab Med 2020; 39:405-418. [PMID: 31383265 DOI: 10.1016/j.cll.2019.05.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Next-generation sequencing (NGS) applications have been transitioning from research tools to diagnostic methods and are becoming more commonplace in clinical microbiology laboratories. These applications include (1) whole-genome sequencing, (2) targeted next-generation sequencing methods, and (3) metagenomic next-generation sequencing. The introduction of these methods into the clinical microbiology laboratory has led to the theoretic question of "Will NGS-based methods supplant traditional methods for strain typing, identification, and antimicrobial susceptibility prediction?" The authors address this question and discuss where we are at now with clinical NGS applications for infectious diseases, what does the future hold, and at what cost?
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Affiliation(s)
- Stephanie L Mitchell
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, 4401 Penn Avenue, Main Hospital, Floor B, #269, Pittsburgh, PA 15224, 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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32
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Abstract
The rise of antimicrobial resistance is a leading medical threat, motivating efforts to forecast both its evolutionary dynamics and its genetic causes. Aminoglycosides are a major class of antibiotics that disrupt translation, but resistance may occur by a number of mechanisms. Here, we show the repeated evolution of resistance to the aminoglycoside tobramycin in both P. aeruginosa and A. baumannii via mutations in fusA1, encoding elongation factor G, and ptsP, encoding the nitrogen-specific phosphotransferase system. Laboratory evolution and whole-population genome sequencing were used to identify these targets, but mutations at identical amino acid positions were also found in published genomes of diverse bacterial species and clinical isolates. We also identified other resistance mechanisms associated with growth in biofilms that likely interfere with drug binding or uptake. Characterizing the evolution of multiple species in the presence of antibiotics can identify new, repeatable causes of resistance that may be predicted and counteracted by alternative treatment. Different species exposed to a common stress may adapt by mutations in shared pathways or in unique systems, depending on how past environments have molded their genomes. Understanding how diverse bacterial pathogens evolve in response to an antimicrobial treatment is a pressing example of this problem, where discovery of molecular parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in environments containing antibiotics, combined with periodic whole-population genome sequencing, can be used to identify many contending routes to antimicrobial resistance. We separately propagated two clinically relevant Gram-negative pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii, in increasing concentrations of tobramycin in two different environments each: planktonic and biofilm. Independently of the pathogen, the populations adapted to tobramycin selection by parallel evolution of mutations in fusA1, encoding elongation factor G, and ptsP, encoding phosphoenolpyruvate phosphotransferase. As neither gene is a direct target of this aminoglycoside, mutations to either are unexpected and underreported causes of resistance. Additionally, both species acquired antibiotic resistance-associated mutations that were more prevalent in the biofilm lifestyle than in the planktonic lifestyle; these mutations were in electron transport chain components in A. baumannii and lipopolysaccharide biosynthesis enzymes in P. aeruginosa populations. Using existing databases, we discovered site-specific parallelism of fusA1 mutations that extends across bacterial phyla and clinical isolates. This study suggests that strong selective pressures, such as antibiotic treatment, may result in high levels of predictability in molecular targets of evolution, despite differences between organisms’ genetic backgrounds and environments.
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33
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Molecular Typing, Characterization of Antimicrobial Resistance, Virulence Profiling and Analysis of Whole-Genome Sequence of Clinical Klebsiella pneumoniae Isolates. Antibiotics (Basel) 2020; 9:antibiotics9050261. [PMID: 32429555 PMCID: PMC7277670 DOI: 10.3390/antibiotics9050261] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae is one of the most important pathogens concerned with multidrug resistance in healthcare-associated infections. The treating of infections caused by this bacterium is complicated due to the emergence and rapid spreading of carbapenem-resistant strains, which are associated with high mortality rates. Recently, several hypervirulent and carbapenemase-producing isolates were reported that make the situation even more complicated. In order to better understand the resistance and virulence mechanisms, and, in turn, to develop effective treatment strategies for the infections caused by multidrug-resistant K. pneumoniae, more comprehensive genomic and phenotypic data are required. Here, we present the first detailed molecular epidemiology report based on second and third generation (long-read) sequencing for the clinical isolates of K. pneumoniae in the Russian Federation. The data include three schemes of molecular typing, phenotypic and genotypic antibiotic resistance determination, as well as the virulence and plasmid profiling for 36 K. pneumoniae isolates. We have revealed 2 new multilocus sequence typing (MLST)-based sequence types, 32 multidrug-resistant (MDR) isolates and 5 colistin-resistant isolates in our samples. Three MDR isolates belonged to a very rare ST377 type. The whole genome sequences and additional data obtained will greatly facilitate further investigations in the field of antimicrobial resistance studies.
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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Innovative and rapid antimicrobial susceptibility testing systems. Nat Rev Microbiol 2020; 18:299-311. [PMID: 32055026 DOI: 10.1038/s41579-020-0327-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope.
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Pitt ME, Nguyen SH, Duarte TPS, Teng H, Blaskovich MAT, Cooper MA, Coin LJM. Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing. Gigascience 2020; 9:giaa002. [PMID: 32016399 PMCID: PMC6998412 DOI: 10.1093/gigascience/giaa002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/17/2019] [Accepted: 01/10/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify appropriate antibiotics to treat these bacterial infections. The MinION device can sequence native DNA and RNA in real time, providing an opportunity to compare the utility of DNA and RNA for prediction of antibiotic susceptibility. However, the effectiveness of bacterial direct RNA sequencing and base-calling has not previously been investigated. This study interrogated the genome and transcriptome of 4 extensively drug-resistant (XDR) K. pneumoniae clinical isolates; however, further antimicrobial susceptibility testing identified 3 isolates as pandrug-resistant (PDR). RESULTS The majority of acquired resistance (≥75%) resided on plasmids including several megaplasmids (≥100 kb). DNA sequencing detected most resistance genes (≥70%) within 2 hours of sequencing. Neural network-based base-calling of direct RNA achieved up to 86% identity rate, although ≤23% of reads could be aligned. Direct RNA sequencing (with ∼6 times slower pore translocation) was able to identify (within 10 hours) ≥35% of resistance genes, including those associated with resistance to aminoglycosides, β-lactams, trimethoprim, and sulphonamide and also quinolones, rifampicin, fosfomycin, and phenicol in some isolates. Direct RNA sequencing also identified the presence of operons containing up to 3 resistance genes. Polymyxin-resistant isolates showed a heightened transcription of phoPQ (≥2-fold) and the pmrHFIJKLM operon (≥8-fold). Expression levels estimated from direct RNA sequencing displayed strong correlation (Pearson: 0.86) compared to quantitative real-time PCR across 11 resistance genes. CONCLUSION Overall, MinION sequencing rapidly detected the XDR/PDR K. pneumoniae resistome, and direct RNA sequencing provided accurate estimation of expression levels of these genes.
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Affiliation(s)
- Miranda E Pitt
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia
| | - Son H Nguyen
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
| | - Tânia P S Duarte
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
| | - Haotian Teng
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland, 4072, Australia
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia
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VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning. PLoS Comput Biol 2020; 16:e1007511. [PMID: 31929521 PMCID: PMC7015433 DOI: 10.1371/journal.pcbi.1007511] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 02/12/2020] [Accepted: 10/25/2019] [Indexed: 01/30/2023] Open
Abstract
Antimicrobial resistance (AMR) is an increasing threat to public health. Current methods of determining AMR rely on inefficient phenotypic approaches, and there remains incomplete understanding of AMR mechanisms for many pathogen-antimicrobial combinations. Given the rapid, ongoing increase in availability of high-density genomic data for a diverse array of bacteria, development of algorithms that could utilize genomic information to predict phenotype could both be useful clinically and assist with discovery of heretofore unrecognized AMR pathways. To facilitate understanding of the connections between DNA variation and phenotypic AMR, we developed a new bioinformatics tool, variant mapping and prediction of antibiotic resistance (VAMPr), to (1) derive gene ortholog-based sequence features for protein variants; (2) interrogate these explainable gene-level variants for their known or novel associations with AMR; and (3) build accurate models to predict AMR based on whole genome sequencing data. We curated the publicly available sequencing data for 3,393 bacterial isolates from 9 species that contained AMR phenotypes for 29 antibiotics. We detected 14,615 variant genotypes and built 93 association and prediction models. The association models confirmed known genetic antibiotic resistance mechanisms, such as blaKPC and carbapenem resistance consistent with the accurate nature of our approach. The prediction models achieved high accuracies (mean accuracy of 91.1% for all antibiotic-pathogen combinations) internally through nested cross validation and were also validated using external clinical datasets. The VAMPr variant detection method, association and prediction models will be valuable tools for AMR research for basic scientists with potential for clinical applicability. Antimicrobial resistance (AMR) is a global health threat. The current method to determine AMR is inefficient and complete understanding of the mechanisms of AMR is lacking. With the increased feasibility of sequencing bacterial genomes, it is now easier, faster and cheaper to have genomic insights into AMR. In this manuscript, we propose a novel bioinformatic tool for variant mapping and prediction of antibiotic resistance (VAMPr). We curated 3,393 bacterial genomes from 9 bacterial species that contained AMR phenotypes for 29 antibiotics. We used protein orthology and detected 14,615 variants. Combined with AMR phenotypes, we built 93 association and prediction models. The association model confirms known genetic AMR mechanisms, and the prediction models achieved high accuracies. Together, our work will be valuable for AMR research for basic scientists with the potential for clinical applicability.
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Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing. J Clin Microbiol 2019; 58:e01315-19. [PMID: 31619531 PMCID: PMC6935936 DOI: 10.1128/jcm.01315-19] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.
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Affiliation(s)
- Lauren M Petersen
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Wayne E Moschetti
- Dartmouth-Hitchcock Medical Center, Department of Orthopaedics and Sports Medicine, Lebanon, New Hampshire, USA
| | - Colleen M Kershaw
- Dartmouth-Hitchcock Medical Center, Department of Infectious Disease and International Health, Lebanon, New Hampshire, USA
| | - Gregory J Tsongalis
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
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Biofilms facilitate cheating and social exploitation of β-lactam resistance in Escherichia coli. NPJ Biofilms Microbiomes 2019; 5:36. [PMID: 31814991 PMCID: PMC6884583 DOI: 10.1038/s41522-019-0109-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/30/2019] [Indexed: 11/27/2022] Open
Abstract
Gram-negative bacteria such as Escherichia coli commonly resist β-lactam antibiotics using plasmid-encoded β-lactamase enzymes. Bacterial strains that express β-lactamases have been found to detoxify liquid cultures and thus to protect genetically susceptible strains, constituting a clear laboratory example of social protection. These results are not necessarily general; on solid media, for instance, the rapid bactericidal action of β-lactams largely prevents social protection. Here, we tested the hypothesis that the greater tolerance of biofilm bacteria for β-lactams would facilitate social interactions. We used a recently isolated E. coli strain, capable of strong biofilm formation, to compare how cooperation and exploitation in colony biofilms and broth culture drives the dynamics of a non-conjugative plasmid encoding a clinically important β-lactamase. Susceptible cells in biofilms were tolerant of ampicillin—high doses and several days of exposure were required to kill them. In support of our hypothesis, we found robust social protection of susceptible E. coli in biofilms, despite fine-scale physical separation of resistant and susceptible cells and lower rates of production of extracellular β-lactamase. In contrast, social interactions in broth were restricted to a relatively narrow range of ampicillin doses. Our results show that β-lactam selection pressure on Gram-negative biofilms leads to cooperative resistance characterized by a low equilibrium frequency of resistance plasmids, sufficient to protect all cells.
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Sun H, Chan CW, Wang Y, Yao X, Mu X, Lu X, Zhou J, Cai Z, Ren K. Reliable and reusable whole polypropylene plastic microfluidic devices for a rapid, low-cost antimicrobial susceptibility test. LAB ON A CHIP 2019; 19:2915-2924. [PMID: 31369010 DOI: 10.1039/c9lc00502a] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using an antimicrobial susceptibility test (AST) as an example, this work demonstrates a practical method to fabricate microfluidic chips entirely from polypropylene (PP) and the benefits for potential commercial use. Primarily caused by the misuse and abuse of antibiotics, antimicrobial resistance (AMR) is a major threat to modern medicine. The AST is a promising technique to help with the optimal use of antibiotics for reducing AMR. However, current phenotypic ASTs suffer from long turnaround time, while genotypic ASTs suffer from low reliability, and both are unaffordable for routine use. New microfluidics based AST methods are rapid but still unreliable as well as costly due to the PDMS chip material. Herein, we demonstrate a convenient method to fabricate whole PP microfluidic chips with high resolution and fidelity. Unlike PDMS chips, the whole PP chips showed better reliability due to their inertness; they are solvent-compatible and can be conveniently reused and recycled, which largely decreases the cost, and are environmentally friendly. We specially designed 3D chambers that allow for quick cell loading without valving/liquid exchange; this new hydrodynamic design satisfies the shear stress requirement for on-chip bacterial culture, which, compared to reported designs for similar purposes, allows for a simpler, more rapid, and high-throughput operation. Our system allows for reliable tracking of individual cells and acquisition of AST results within 1-3 hours, which is among the group of fastest phenotypic methods. The PP chips are more reliable and affordable than PDMS chips, providing a practical solution to improve current culture-based AST and benefiting the fight against AMR through helping doctors prescribe effective, narrow-spectrum antibiotics; they will also be broadly useful for other applications wherein a reliable, solvent-resistant, anti-fouling, and affordable microfluidic chip is needed.
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Affiliation(s)
- Han Sun
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Chiu-Wing Chan
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Yisu Wang
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Xiao Yao
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Xuan Mu
- Department of Biomedical Engineering, Tufts University, 4 Colby, Medford, MA 02155, USA.
| | - Xuedong Lu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jianhua Zhou
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, Department of Biomedical Engineering, School of Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China. and State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Waterloo Rd, Kow-loon, Hong Kong, China
| | - Kangning Ren
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China. and HKBU Institute of Research and Continuing Education, Shenzhen, China and State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Waterloo Rd, Kow-loon, Hong Kong, China
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Chen C, Zhang Y, Yu SL, Zhou Y, Yang SY, Jin JL, Chen S, Cui P, Wu J, Jiang N, Zhang WH. Tracking Carbapenem-Producing Klebsiella pneumoniae Outbreak in an Intensive Care Unit by Whole Genome Sequencing. Front Cell Infect Microbiol 2019; 9:281. [PMID: 31440476 PMCID: PMC6694789 DOI: 10.3389/fcimb.2019.00281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/23/2019] [Indexed: 11/24/2022] Open
Abstract
The presence of carbapenem-producing Klebsiella pneumoniae (CP-Kp) is a serious threat to the control of nosocomial infections. Plasmid-mediated horizontal transfer of the resistance gene makes it difficult to control hospital-acquired CP- Kp infections. Nine CP- Kp strains were isolated during an outbreak in the intensive care unit of Shanghai Huashan hospital in east China. We conducted a retrospective study to identify the origin and route of transmission of this CP-Kp outbreak. Whole-genome sequencing (WGS) analysis was performed on 9 clinical isolates obtained from 8 patients, and the results were compared to clinical and epidemiological records. All isolates were ST11 CP-Kp. Single-nucleotide polymorphisms and the presence and structure of plasmids indicated that this CP-Kp outbreak had different origins. These 9 isolates were partitioned into two clades according to genetic distance. Four plasmids, CP002474.1, CP006799.1, CP018455.1, and CP025459.1, were detected among the 9 isolates. The plasmid phylogeny and antibiotic resistance (AR) gene profile results were consistent with the sequencing results. We found that two clades of CP-Kp were responsible for this nosocomial outbreak and demonstrated the transmission route from two index patients. Plasmid carriage and phylogeny are a useful tool for identifying clades involved in disease transmission.
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Affiliation(s)
- Chen Chen
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Sheng-Lei Yu
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Si-Yu Yang
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Jia-Lin Jin
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Shu Chen
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hong Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital of Fudan University, Shanghai, China
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Raymond B. Five rules for resistance management in the antibiotic apocalypse, a road map for integrated microbial management. Evol Appl 2019; 12:1079-1091. [PMID: 31297143 PMCID: PMC6597870 DOI: 10.1111/eva.12808] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Resistance to new antimicrobials can become widespread within 2-3 years. Resistance problems are particularly acute for bacteria that can experience selection as both harmless commensals and pathogenic hospital-acquired infections. New drugs, although welcome, cannot tackle the antimicrobial resistance crisis alone: new drugs must be partnered with more sustainable patterns of use. However, the broader experience of resistance management in other disciplines, and the assumptions on which resistance rests, is not widely appreciated in clinical and microbiological disciplines. Improved awareness of the field of resistance management could improve clinical outcomes and help shape novel solutions. Here, the aim is to develop a pragmatic approach to developing a sustainable integrated means of using antimicrobials, based on an interdisciplinary synthesis of best practice, recent theory and recent clinical data. This synthesis emphasizes the importance of pre-emptive action and the value of reducing the supply of genetic novelty to bacteria under selection. The weight of resistance management experience also cautions against strategies that over-rely on the fitness costs of resistance or low doses. The potential (and pitfalls) of shorter courses, antibiotic combinations and antibiotic mixing or cycling are discussed in depth. Importantly, some of variability in the success of clinical trials of mixing approaches can be explained by the number and diversity of drugs in a trial, as well as whether trials encompass single wards or the wider transmission network that is a hospital. Consideration of the importance of data, and of the initially low frequency of resistance, leads to a number of additional recommendations. Overall, reduction in selection pressure, interference with the transmission of problematic genotypes and multidrug approaches (combinations, mixing or cycling) are all likely to be required for sustainability and the protection of forthcoming drugs.
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Comparing Patient Risk Factor-, Sequence Type-, and Resistance Locus Identification-Based Approaches for Predicting Antibiotic Resistance in Escherichia coli Bloodstream Infections. J Clin Microbiol 2019; 57:JCM.01780-18. [PMID: 30894438 PMCID: PMC6535602 DOI: 10.1128/jcm.01780-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/12/2019] [Indexed: 01/02/2023] Open
Abstract
Rapid diagnostic tests for antibiotic resistance that identify the presence or absence of antibiotic resistance genes/loci are increasingly being developed. However, these approaches usually neglect other sources of predictive information which could be identified over shorter time periods, including patient epidemiologic risk factors for antibiotic resistance and markers of lineage. Using a data set of 414 Escherichia coli isolates recovered from separate episodes of bacteremia at a single academic institution in Toronto, Ontario, Canada, between 2010 and 2015, we compared the potential predictive ability of three approaches (epidemiologic risk factor-, pathogen sequence type [ST]-, and resistance gene identification-based approaches) for classifying phenotypic resistance to three antibiotics representing classes of broad-spectrum antimicrobial therapy (ceftriaxone [a 3rd-generation cephalosporin], ciprofloxacin [a fluoroquinolone], and gentamicin [an aminoglycoside]). We used logistic regression models to generate model receiver operating characteristic (ROC) curves. Predictive discrimination was measured using apparent and corrected (bootstrapped) areas under the curves (AUCs). Epidemiologic risk factor-based models based on two simple risk factors (prior antibiotic exposure and recent prior susceptibility of Gram-negative bacteria) provided a modest predictive discrimination, with AUCs ranging from 0.65 to 0.74. Sequence type-based models demonstrated strong discrimination (AUCs, 0.83 to 0.94) across all three antibiotic classes. The addition of epidemiologic risk factors to sequence type significantly improved the ability to predict resistance for all antibiotics (P < 0.05). Resistance gene identification-based approaches provided the highest degree of discrimination (AUCs, 0.88 to 0.99), with no statistically significant benefit being achieved by adding the patient epidemiologic predictors. In summary, sequence type or other lineage-based approaches could produce an excellent discrimination of antibiotic resistance and may be improved by incorporating readily available patient epidemiologic predictors but are less discriminatory than identification of the presence of known resistance loci.
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Babiker A, Mustapha MM, Pacey MP, Shutt KA, Ezeonwuka CD, Ohm SL, Cooper VS, Marsh JW, Doi Y, Harrison LH. Use of online tools for antimicrobial resistance prediction by whole-genome sequencing in methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). J Glob Antimicrob Resist 2019; 19:136-143. [PMID: 31005733 DOI: 10.1016/j.jgar.2019.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/31/2019] [Accepted: 04/06/2019] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES The antimicrobial resistance (AMR) crisis represents a serious threat to public health and has resulted in concentrated efforts to accelerate development of rapid molecular diagnostics for AMR. In combination with publicly available web-based AMR databases, whole-genome sequencing (WGS) offers the capacity for rapid detection of AMR genes. Here we studied the concordance between WGS-based resistance prediction and phenotypic susceptibility test results for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) clinical isolates using publicly available tools and databases. METHODS Clinical isolates prospectively collected at the University of Pittsburgh Medical Center between December 2016 and December 2017 underwent WGS. The AMR gene content was assessed from assembled genomes by BLASTn search of online databases. Concordance between the WGS-predicted resistance profile and phenotypic susceptibility as well as the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for each antibiotic/organism combination, using the phenotypic results as gold standard. RESULTS Phenotypic susceptibility testing and WGS results were available for 1242 isolate/antibiotic combinations. Overall concordance was 99.3%, with a sensitivity, specificity, PPV and NPV of 98.7% (95% CI 97.2-99.5%), 99.6% (95% CI 98.8-99.9%), 99.3% (95% CI 98.0-99.8%) and 99.2% (95% CI 98.3-99.7%), respectively. Additional identification of point mutations in housekeeping genes increased the concordance to 99.4%, sensitivity to 99.3% (95% CI 98.2-99.8%) and NPV to 99.4% (95% CI 98.4-99.8%). CONCLUSION WGS can be used as a reliable predicator of phenotypic resistance both for MRSA and VRE using readily available online tools.
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Affiliation(s)
- Ahmed Babiker
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Mustapha M Mustapha
- Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marissa P Pacey
- Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kathleen A Shutt
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chinelo D Ezeonwuka
- Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sara L Ohm
- Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jane W Marsh
- Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Microbial Genomic Epidemiology Laboratory, Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, USA
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