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Liu G, Li W, Li S, Xu J, Wang X, Xu H, Liu D, Gao H. Culture-free detection of β-lactamase-Producing bacteria in urinary tract infections using a paper sensor. Biosens Bioelectron 2024; 257:116300. [PMID: 38657378 DOI: 10.1016/j.bios.2024.116300] [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: 02/04/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Developing simple, inexpensive, fast, sensitive, and specific probes for antibiotic-resistant bacteria is crucial for the management of urinary tract infections (UTIs). We here propose a paper-based sensor for the rapid detection of β-lactamase-producing bacteria in the urine samples of UTI patients. By conjugating a strongly electronegative group -N+(CH3)3 with the core structures of cephalosporin and carbapenem antibiotics, two visual probes were achieved to respectively target the extended-spectrum/AmpC β-lactamases (ESBL/AmpC) and carbapenemase, the two most prevalent factors causing antibiotic resistance. By integrating these probes into a portable paper sensor, we confirmed 10 and 8 cases out of 30 clinical urine samples as ESBL/AmpC- and carbapenemase-positive, respectively, demonstrating 100% clinical sensitivity and specificity. This paper sensor can be easily conducted on-site, without resorting to bacterial culture, providing a solution to the challenge of rapid detection of β-lactamase-producing bacteria, particularly in resource-limited settings.
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Affiliation(s)
- Guangming Liu
- Department of Urology, Tianjin First Center Hospital, Nankai University, Tianjin 300071, China
| | - Wenshuai Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, Frontiers Science Centers for Cell Responses and New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Siya Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, Frontiers Science Centers for Cell Responses and New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jia Xu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, Frontiers Science Centers for Cell Responses and New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xinsheng Wang
- Department of Urology, Tianjin First Center Hospital, Nankai University, Tianjin 300071, China
| | - Hua Xu
- Department of Intensive Care Unit, Key Laboratory for Critical Care Medicine of the Ministry of Health, Emergency Medicine Research Institute, Tianjin First Center Hospital, Nankai University, Tianjin 300071, China
| | - Dingbin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, Frontiers Science Centers for Cell Responses and New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Hongmei Gao
- Department of Intensive Care Unit, Key Laboratory for Critical Care Medicine of the Ministry of Health, Emergency Medicine Research Institute, Tianjin First Center Hospital, Nankai University, Tianjin 300071, China.
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2
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Seethalakshmi PS, Prabhakaran A, Kiran GS, Selvin J. Genomic insights into plasmid-mediated antimicrobial resistance in the bacterium Bhargavaea beijingensis strain PS04. Arch Microbiol 2023; 206:33. [PMID: 38133813 DOI: 10.1007/s00203-023-03746-y] [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: 09/16/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
The dissemination of antimicrobial-resistant bacteria through environment is a major health concern for public health. Pathogenic bacteria in natural environment can mediate the transfer of antimicrobial-resistant genes via horizontal gene transfer to naturally occurring bacteria in the soil. Bhargavaea beijingensis is a Gram-negative bacterium that is commonly found in soil and water. In recent years, there has been an emergence of antibiotic-resistant strains of environmental bacteria, which pose a significant threat to human health. One mechanism of antibiotic resistance in bacteria is through the acquisition of plasmids, which can carry genes that confer resistance to various antibiotics. In this study, a novel plasmid of repUS12 replicon type was identified in the strain PS04 of B. beijingensis, which carried the ermT and tet(L) genes, encoding resistance to macrolides, lincosamides, and tetracycline. The plasmid was found to be the first of its kind in B. beijingensis and was thought to have been acquired through horizontal gene transfer. The emergence of plasmid-mediated resistance in B. beijingensis highlights the need for continued surveillance and monitoring of antibiotic resistance in environmental bacteria.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India.
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3
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Shropshire WC, Amiji H, Bremer J, Selvaraj Anand S, Strope B, Sahasrabhojane P, Gohel M, Aitken S, Spitznogle S, Zhan X, Kim J, Greenberg DE, Shelburne SA. Genetic determinants underlying the progressive phenotype of β-lactam/β-lactamase inhibitor resistance in Escherichia coli. Microbiol Spectr 2023; 11:e0222123. [PMID: 37800937 PMCID: PMC10715226 DOI: 10.1128/spectrum.02221-23] [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: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE The increased feasibility of whole-genome sequencing has generated significant interest in using such molecular diagnostic approaches to characterize difficult-to-treat, antimicrobial-resistant (AMR) infections. Nevertheless, there are current limitations in the accurate prediction of AMR phenotypes based on existing AMR gene database approaches, which primarily correlate a phenotype with the presence/absence of a single AMR gene. Our study utilized a large cohort of cephalosporin-susceptible Escherichia coli bacteremia samples to determine how increasing the dosage of narrow-spectrum β-lactamase-encoding genes in conjunction with other diverse β-lactam/β-lactamase inhibitor (BL/BLI) genetic determinants contributes to progressively more severe BL/BLI phenotypes. We were able to characterize the complexity of the genetic mechanisms underlying progressive BL/BLI resistance including the critical role of β-lactamase encoding gene amplification. For the diverse array of AMR phenotypes with complex mechanisms involving multiple genomic factors, our study provides an example of how composite risk scores may improve understanding of AMR genotype/phenotype correlations.
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Affiliation(s)
- William C. Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hatim Amiji
- Frank H. Netter MD School of Medicine, Quinnipiac University, Hamden, Connecticut, USA
| | - Jordan Bremer
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Selvalakshmi Selvaraj Anand
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Benjamin Strope
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Pranoti Sahasrabhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marc Gohel
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel Aitken
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Spitznogle
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David E. Greenberg
- Department of Microbiology, UT Southwestern, Dallas, Texas, USA
- Department of Internal Medicine, UT Southwestern, Dallas, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, 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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4
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Davies TJ, Swann J, Sheppard AE, Pickford H, Lipworth S, AbuOun M, Ellington MJ, Fowler PW, Hopkins S, Hopkins KL, Crook DW, Peto TEA, Anjum MF, Walker AS, Stoesser N. Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli. Microb Genom 2023; 9:001151. [PMID: 38100178 PMCID: PMC10763500 DOI: 10.1099/mgen.0.001151] [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: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance and SRST2, run with the ResFinder database) and their outputs compared. For simulation tests where 3079 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for 3076 (99.9 %) simulations, ABRicate for 3054 (99.2 %), ARIBA for 2783 (90.4 %) and SRST2 for 2108 (68.5 %). For simulation tests where two closely related gene variants were inserted into random sequence constructs, KmerResistance identified the correct alleles in 35 338/46 318 (76.3 %) simulations, ABRicate identified them in 11 842/46 318 (25.6 %) simulations, ARIBA identified them in 1679/46 318 (3.6 %) simulations and SRST2 identified them in 2000/46 318 (4.3 %) simulations. In real data, across all methods, 1392/1818 (76 %) isolates had discrepant allele calls for at least 1 gene. In addition to highlighting areas for improvement in challenging scenarios, (e.g. identification of AMR genes at <10× coverage, identifying multiple closely related AMR genes present in the same sample), our evaluations identified some more systematic errors that could be readily soluble, such as repeated misclassification (i.e. naming) of genes as shorter variants of the same gene present within the reference resistance gene database. Such naming errors accounted for at least 2530/4321 (59 %) of the discrepancies seen in real data. Moreover, many of the remaining discrepancies were likely 'artefactual', with reporting of cut-off differences accounting for at least 1430/4321 (33 %) discrepants. Whilst we found that comparing outputs generated by running multiple algorithms on the same dataset could identify and resolve these algorithmic artefacts, the results of our evaluations emphasize the need for developing new and more robust genotyping algorithms to further improve accuracy and performance.
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Affiliation(s)
- Timothy J. Davies
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Hayleigh Pickford
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Samuel Lipworth
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Manal AbuOun
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J. Ellington
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | | | - Susan Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | - Katie L. Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy E. A. Peto
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Muna F. Anjum
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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5
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Shropshire WC, Endres BT, Borjan J, Aitken SL, Bachman WC, McElheny CL, Wu CT, Egge SL, Khan A, Miller WR, Bhatti MM, Saharasbhojane P, Kawai A, Shields RK, Shelburne SA, Doi Y. High-level ceftazidime/avibactam resistance in Escherichia coli conferred by the novel plasmid-mediated β-lactamase CMY-185 variant. J Antimicrob Chemother 2023; 78:2442-2450. [PMID: 37574665 PMCID: PMC10545501 DOI: 10.1093/jac/dkad249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023] Open
Abstract
OBJECTIVES To characterize a blaCMY variant associated with ceftazidime/avibactam resistance from a serially collected Escherichia coli isolate. METHODS A patient with an intra-abdominal infection due to recurrent E. coli was treated with ceftazidime/avibactam. On Day 48 of ceftazidime/avibactam therapy, E. coli with a ceftazidime/avibactam MIC of >256 mg/L was identified from abdominal drainage. Illumina and Oxford Nanopore Technologies WGS was performed on serial isolates to identify potential resistance mechanisms. Site-directed mutants of CMY β-lactamase were constructed to identify amino acid residues responsible for ceftazidime/avibactam resistance. RESULTS WGS revealed that all three isolates were E. coli ST410. The ceftazidime/avibactam-resistant strain uniquely acquired a novel CMY β-lactamase gene, herein called blaCMY-185, harboured on an IncI-γ/K1 conjugative plasmid. The CMY-185 enzyme possessed four amino acid substitutions relative to CMY-2, including A114E, Q120K, V211S and N346Y, and conferred high-level ceftazidime/avibactam resistance with an MIC of 32 mg/L. Single CMY-2 mutants did not confer reduced ceftazidime/avibactam susceptibility. However, double and triple mutants containing N346Y previously associated with ceftazidime/avibactam resistance in other AmpC enzymes, conferred ceftazidime/avibactam MICs ranging between 4 and 32 mg/L as well as reduced susceptibility to the newly developed cephalosporin, cefiderocol. Molecular modelling suggested that the N346Y substitution confers the reduction of avibactam inhibition due to steric hindrance between the side chain of Y346 and the sulphate group of avibactam. CONCLUSIONS We identified ceftazidime/avibactam resistance in E. coli associated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer ceftazidime/avibactam resistance.
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Affiliation(s)
- William C Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jovan Borjan
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samuel L Aitken
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William C Bachman
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chin-Ting Wu
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, TX, USA
| | - Stephanie L Egge
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
| | - Ayesha Khan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
| | - Micah M Bhatti
- Department of Laboratory Medicine, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pranoti Saharasbhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akito Kawai
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ryan K Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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6
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Shropshire WC, Strope B, Selvaraj Anand S, Bremer J, McDaneld P, Bhatti MM, Flores AR, Kalia A, Shelburne SA. Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistant Escherichia coli bloodstream infections. mSphere 2023; 8:e0018323. [PMID: 37427953 PMCID: PMC10449519 DOI: 10.1128/msphere.00183-23] [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: 04/10/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
Extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) is an urgent public health threat with sequence type clonal complex 131 (STc131), phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ec infections. To address the paucity of recent ESC-R-Ec molecular epidemiology data in the United States, we used whole-genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ec at a tertiary care cancer center in Houston, Texas, collected from 2016 to 2020. During the study time frame, there were 1,154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R-Ec. Using time series analyses, we identified a temporal dynamic of ESC-R-Ec distinct from ESC-susceptible E. coli (ESC-S-Ec), with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R-Ec strains revealed that while STc131 strains accounted for ~45% of total BSIs, the proportion of STc131 strains remained stable across the study time frame with infection peaks driven by genetically heterogeneous ESC-R-Ec clonal complexes. bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R-Ec), and amplification of bla CTX-M genes was widely detected in ESC-R-Ec strains, particularly in carbapenem non-susceptible, recurrent BSI strains. Bla CTX-M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R-Ec infections at a large tertiary care cancer center and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of worldwide ESC-R Enterobacterales infections, we sought to assess the current molecular epidemiology of ESC-R-Ec using a WGS analysis of many BSIs over a 5-year period. We identified fluctuating temporal dynamics of ESC-R-Ec infections, which have also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of STc131 over the study period and demonstrate a limited but genetically diverse group of ESC-R-Ec clonal complexes are detected during infection peaks. Additionally, we provide a widespread assessment of β-lactamase gene copy number in ESC-R-Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R-Ec strains. These data suggest that serious ESC-R-Ec infections are driven by a diverse array of strains in our cohort and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.
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Affiliation(s)
- William C. Shropshire
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin Strope
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Selvalakshmi Selvaraj Anand
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Jordan Bremer
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick McDaneld
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Micah M. Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Awdhesh Kalia
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Samuel 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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7
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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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8
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Monogue ML, Sanders JM, Pybus CA, Kim J, Zhan X, Clark AE, Greenberg DE. Ceftolozane/tazobactam heteroresistance in cystic fibrosis-related Pseudomonas aeruginosa infections. JAC Antimicrob Resist 2023; 5:dlad083. [PMID: 37441352 PMCID: PMC10333726 DOI: 10.1093/jacamr/dlad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Objectives Cystic fibrosis (CF) patients are often colonized with Pseudomonas aeruginosa. During treatment, P. aeruginosa can develop subpopulations exhibiting variable in vitro antimicrobial (ABX) susceptibility patterns. Heteroresistance (HR) may underlie reported discrepancies between in vitro susceptibility results and clinical responses to various ABXs. Here, we sought to examine the presence and nature of P. aeruginosa polyclonal HR (PHR) and monoclonal HR (MHR) to ceftolozane/tazobactam in isolates originating from CF pulmonary exacerbations. Methods This was a single-centre, non-controlled study. Two hundred and forty-six P. aeruginosa isolates from 26 adult CF patients were included. PHR was defined as the presence of different ceftolozane/tazobactam minimum inhibitory concentration (MIC) values among P. aeruginosa isolates originating from a single patient specimen. Population analysis profiles (PAPs) were performed to assess the presence of MHR, defined as ≥4-fold change in the ceftolozane/tazobactam MIC from a single P. aeruginosa colony. Results Sixteen of 26 patient specimens (62%) contained PHR P. aeruginosa populations. Of these 16 patients, 6 (23%) had specimens in which PHR P. aeruginosa isolates exhibited ceftolozane/tazobactam MICs with categorical differences (i.e. susceptible versus resistant) compared to results reported as part of routine care. One isolate, PSA 1311, demonstrated MHR. Canonical ceftolozane/tazobactam resistance genes were not found in the MHR isolates (MHR PSA 1311 or PHR PSA 6130). Conclusions Ceftolozane/tazobactam PHR exists among P. aeruginosa isolates in this work, and approximately a quarter of these populations contained isolates with ceftolozane/tazobactam susceptibiilty interpretations different from what was reported clinically, supporting concerns surrounding the utility of traditional susceptibility testing methodology in the setting of CF specimens. Genome sequencing of isolates with acquired MHR to ceftolozane/tazobactam revealed variants of unknown significance. Future work will be centred on determining the significance of these mutations to better understand these data in clinical context.
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Affiliation(s)
| | - James M Sanders
- Department of Pharmacy, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christine A Pybus
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaowei Zhan
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew E Clark
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David E Greenberg
- Department of Internal Medicine, Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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9
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McMahon S, Sahasrabhojane P, Kim J, Franklin S, Chang CC, Jenq RR, Hillhouse AE, Shelburne SA, Galloway-Peña J. Contribution of the Oral and Gastrointestinal Microbiomes to Bloodstream Infections in Leukemia Patients. Microbiol Spectr 2023; 11:e0041523. [PMID: 37022173 PMCID: PMC10269818 DOI: 10.1128/spectrum.00415-23] [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: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
Bloodstream infections (BSIs) pose a significant mortality risk for acute myeloid leukemia (AML) patients. It has been previously reported that intestinal domination (>30% relative abundance [RA] attributed to a single taxon) with the infecting taxa often precedes BSI in stem cell transplant patients. Using 16S rRNA amplicon sequencing, we analyzed oral and stool samples from 63 AML patients with BSIs to determine the correlation between the infectious agent and microbiome composition. Whole-genome sequencing and antimicrobial susceptibilities were performed on all BSI isolates. Species-level detection of the infectious agent and presence of antibiotic resistance determinants in the stool (blaCTX-M-15, blaCTX-M-14, cfrA, and vanA) were confirmed via digital droplet PCR (ddPCR). Individuals with Escherichia coli (stool P < 0.001), Pseudomonas aeruginosa (oral P = 0.004, stool P < 0.001), and viridans group streptococci (VGS) (oral P = 0.001) bacteremia had a significantly higher relative abundance of those respective genera than other BSI patients, which appeared to be site specific. Although 78% of patients showed presence of the infectious genera in the stool and/or saliva, only 7 exhibited microbiome domination. ddPCR confirmed species specificity of the 16S data and detected the antibiotic resistance determinants found in the BSI isolates within concurrent stools. Although gastrointestinal (GI) domination by an infecting organism was not present at the time of most BSIs in AML, the pathogens, along with AMR elements, were detectable in the majority of patients. Thus, rapid genetic assessment of oral and stool samples for the presence of potential pathogens and AMR determinants might inform personalized therapeutic approaches in immunocompromised patients with suspected infection. IMPORTANCE A major cause of mortality in hematologic malignancy patients is BSI. Previous studies have demonstrated that bacterial translocation from the GI microbiome is a major source of BSIs and is often preceded by increased levels of the infectious taxa in the GI (>30% abundance by 16S rRNA sequencing). In this study, we sought to better understand how domination and abundance levels of the oral and gut microbiome relate to bacteremia occurrence in acute myeloid leukemia patients. We conclude that analyses of both oral and stool samples can help identify BSI and antimicrobial resistance determinants, thus potentially improving the timing and tailoring of antibiotic treatment strategies for high-risk patients.
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Affiliation(s)
- Stephanie McMahon
- Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas, USA
| | - Pranoti Sahasrabhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, Houston, Texas, USA
| | - Jiwoong Kim
- Department of Bioinformatics and Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Samantha Franklin
- Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | - Andrew E. Hillhouse
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
- Texas A&M Institute for Genome Sciences & Society, Texas A&M University, College Station, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | - Jessica Galloway-Peña
- Interdisciplinary Genetics Program, Texas A&M University, College Station, Texas, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
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10
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Shropshire WC, Strope B, Anand SS, Bremer J, McDaneld P, Bhatti MM, Flores AR, Kalia A, Shelburne SA. Dynamic Periodicity of Extended-Spectrum Cephalosporin Resistant Bloodstream Escherichia coli Infections Driven by Non-CC131 Strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527510. [PMID: 36798241 PMCID: PMC9934547 DOI: 10.1101/2023.02.07.527510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Extended-spectrum cephalosporin resistant (ESC-R) Escherichia coli (ESC-R- Ec ) is an urgent public health threat with clonal complex (CC) 131, phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R- Ec infections. To address the paucity of recent ESC-R- Ec molecular epidemiology data in the United States (US), we used whole genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R- Ec at a tertiary care cancer center in Houston, Texas collected from 2016-2020. During the study timeframe, there were 1154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R. Using time series analyses, we identified a temporal dynamic of ESC-R E. coli BSIs ( Ec -BSIs), distinct from ESC-susceptible Ec -BSIs, with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R Ec -BSI strains revealed that while CC131 strains accounted for ∼45% of total infections, the proportion of CC131 strains remained stable across the time-period, and infection peaks were driven by genetically diverse, non-CC131 isolates. Bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R Ec -BSIs), and amplification of bla CTX-M genes was widely detected in ESC-R Ec -BSI strains, particularly in carbapenem non-susceptible strains and in strains causing recurrent BSIs. Bla CTX- M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R E. coli and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of ESC-R Enterobacterales infection, we sought to assess the current molecular epidemiology of ESC-R- Ec using a WGS based analysis of many BSIs over a several year period. We identified a clear temporal dynamic of ESC-R- Ec infections, which has also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of CC131 over the study period and demonstrate that non-CC131 strains drove the infection peaks. Additionally, we provide the first widespread assessment of β-lactamase gene copy number in ESC-R- Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R- Ec strains. These data suggest that even for a tertiary care center, serious ESC-R- Ec infections are driven by a diverse array of strains and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.
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11
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Shropshire WC, Endres BT, Borjan J, Aitken SL, Bachman WC, McElheny CL, Khan A, Bhatti MM, Saharasbhojane P, Kawai A, Shields RK, Shelburne SA, Doi Y. High-level ceftazidime-avibactam resistance in Escherichia coli conferred by the novel plasmid-mediated beta-lactamase CMY-185 variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527067. [PMID: 36778324 PMCID: PMC9915728 DOI: 10.1101/2023.02.03.527067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objectives To characterize a bla CMY variant associated with ceftazidime-avibactam (CZA) resistance from a serially collected Escherichia coli isolate. Methods A patient with an intra-abdominal infection due to recurrent E. coli was treated with CZA. On day 48 of CZA therapy, E. coli with a CZA MIC of >256 mg/L was identified from abdominal drainage. Illumina WGS was performed on all isolates to identify potential resistance mechanisms. Site-directed mutants of CMY β-lactamase were constructed to identify amino acid residues responsible for CZA resistance. Results WGS revealed that all three isolates were E. coli ST410. The CZA-resistant strain uniquely acquired a novel CMY β-lactamase gene, herein called bla CMY-185 , harbored on an IncIγ-type conjugative plasmid. The CMY-185 enzyme possessed four amino acid substitutions relative to CMY-2 including A114E, Q120K, V211S, and N346Y and conferred high-level CZA resistance with an MIC of 32 mg/L. Single CMY-2 mutants did not confer reduced CZA susceptibility. However, double and triple mutants containing N346Y previously associated with CZA resistance in other AmpC enzymes, conferred CZA MICs ranging between 4 and 32 mg/L as well as reduced susceptibility to the newly developed cephalosporin, cefiderocol. Molecular modelling suggested that the N346Y substitution confers the reduction of avibactam inhibition due to the steric hindrance between the side chain of Y346 and the sulfate group of avibactam. Conclusion We identified CZA resistance in E. coli associated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer CZA resistance.
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12
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Villodres AR, Benítez LG, Arroyo MJ, Méndez G, Mancera L, Domínguez AV, Jímenez JAL, Smani Y. Ultrasensitive and rapid identification of ESRI developer- and piperacillin/tazobactam-resistant Escherichia coli by the MALDIpiptaz test. Emerg Microbes Infect 2022; 11:2034-2044. [PMID: 35972021 PMCID: PMC9423838 DOI: 10.1080/22221751.2022.2113746] [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] [Indexed: 12/04/2022]
Abstract
Background The excessive use of piperacillin/tazobactam (P/T) has promoted the emergence of P/T-resistant Enterobacterales. We reported that in Escherichia coli, P/T contributes to the development of extended-spectrum resistance to β-lactam/β-lactamase inhibitor (BL/BLI) (ESRI) in isolates that are P/T susceptible but have low-level resistance to BL/BLI. Currently, the detection of P/T resistance relying on conventional methods is time-consuming. To overcome this issue, we developed a cost-effective test based on MALDI-MS technology, called MALDIpiptaz, which aims to detect P/T resistance and ESRI developers in E. coli. Methods We used automated Clover MS Data Analysis software to analyse the protein profile spectra obtained by MALDI-MS from a collection of 248 E. coli isolates (91 P/T-resistant, 81 ESRI developers and 76 P/T-susceptible). This software allowed to preprocess all the spectra to build different peak matrices that were analysed by machine learning algorithms. Results We demonstrated that MALDIpiptaz can efficiently and rapidly (15 min) discriminate between P/T-resistant, ESRI developer and P/T-susceptible isolates and allowed the correct classification between ESRI developers from their isogenic resistance to P/T. Conclusion The combination of excellent performance and cost-effectiveness are all desirable attributes, allowing the MALDIpiptaz test to be a useful tool for the rapid determination of P/T resistance in clinically relevant E. coli isolates.
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Affiliation(s)
- Angel Rodríguez Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Lydia Gálvez Benítez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Manuel J Arroyo
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016 Granada, Spain
| | - Gema Méndez
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016 Granada, Spain
| | - Luis Mancera
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016 Granada, Spain
| | - Andrea Vila Domínguez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - José Antonio Lepe Jímenez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Younes Smani
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Andalusian Center of Developmental Biology, CSIC, University of Pablo de Olavide, Seville, Spain
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13
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Cason C, D’Accolti M, Soffritti I, Mazzacane S, Comar M, Caselli E. Next-generation sequencing and PCR technologies in monitoring the hospital microbiome and its drug resistance. Front Microbiol 2022; 13:969863. [PMID: 35966671 PMCID: PMC9370071 DOI: 10.3389/fmicb.2022.969863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
The hospital environment significantly contributes to the onset of healthcare-associated infections (HAIs), which represent one of the most frequent complications occurring in healthcare facilities worldwide. Moreover, the increased antimicrobial resistance (AMR) characterizing HAI-associated microbes is one of the human health’s main concerns, requiring the characterization of the contaminating microbial population in the hospital environment. The monitoring of surface microbiota in hospitals is generally addressed by microbial cultural isolation. However, this has some important limitations mainly relating to the inability to define the whole drug-resistance profile of the contaminating microbiota and to the long time period required to obtain the results. Hence, there is an urgent need to implement environmental surveillance systems using more effective methods. Molecular approaches, including next-generation sequencing and PCR assays, may be useful and effective tools to monitor microbial contamination, especially the growing AMR of HAI-associated pathogens. Herein, we summarize the results of our recent studies using culture-based and molecular analyses in 12 hospitals for adults and children over a 5-year period, highlighting the advantages and disadvantages of the techniques used.
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Affiliation(s)
- Carolina Cason
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Maria D’Accolti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
| | - Irene Soffritti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
| | | | - Manola Comar
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Elisabetta Caselli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, Section of Microbiology and LTTA, University of Ferrara, Ferrara, Italy
- CIAS Research Centre, University of Ferrara, Ferrara, Italy
- *Correspondence: Elisabetta Caselli,
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14
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Lee JI, Kim SS, Kang DH. Development of DNA probes to detect Cronobacter sakazakii based on comparative genomics and its application in food samples. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Rebelo AR, Bortolaia V, Leekitcharoenphon P, Hansen DS, Nielsen HL, Ellermann-Eriksen S, Kemp M, Røder BL, Frimodt-Møller N, Søndergaard TS, Coia JE, Østergaard C, Westh H, Aarestrup FM. One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings. Front Microbiol 2022; 13:804627. [PMID: 35756053 PMCID: PMC9226621 DOI: 10.3389/fmicb.2022.804627] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings. We collected all bacterial isolates processed by all Danish Clinical Microbiology Laboratories in 1 day. We randomly selected 500 isolates without any preselection of species. We performed AST through standard broth microdilution (BMD) for 488 isolates (n = 6,487 phenotypic AST results) and compared results with in silico antibiograms obtained through WGS (Illumina NextSeq) followed by bioinformatics analyses using ResFinder 4.0 (n = 5,229 comparisons). A higher proportion of AMR was observed for Gram-negative bacteria (10.9%) than for Gram-positive bacteria (6.1%). Comparison of BMD with WGS data yielded a concordance of 91.7%, with discordant results mainly due to phenotypically susceptible isolates harboring genetic AMR determinants. These cases correspond to 6.2% of all isolate-antimicrobial combinations analyzed and to 6.8% of all phenotypically susceptible combinations. We detected fewer cases of phenotypically resistant isolates without any known genetic resistance mechanism, particularly 2.1% of all combinations analyzed, which corresponded to 26.4% of all detected phenotypic resistances. Most discordances were observed for specific combinations of species-antimicrobial: macrolides and tetracycline in streptococci, ciprofloxacin and β-lactams in combination with β-lactamase inhibitors in Enterobacterales, and most antimicrobials in Pseudomonas aeruginosa. WGS has the potential to be used for surveillance and routine clinical microbiology. However, in clinical microbiology settings and especially for certain species and antimicrobial agent combinations, further developments in AMR gene databases are needed to ensure higher concordance between in silico predictions and expected phenotypic AMR profiles.
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Affiliation(s)
- Ana Rita Rebelo
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Michael Kemp
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Bent Løwe Røder
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark
| | | | | | - John Eugenio Coia
- Department of Clinical Microbiology, Hospital of South West Jutland, Esbjerg, Denmark
| | - Claus Østergaard
- Department of Clinical Microbiology, Vejle Hospital, Vejle, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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16
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Miłobedzka A, Ferreira C, Vaz-Moreira I, Calderón-Franco D, Gorecki A, Purkrtova S, Dziewit L, Singleton CM, Nielsen PH, Weissbrodt DG, Manaia CM. Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127407. [PMID: 34629195 DOI: 10.1016/j.jhazmat.2021.127407] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 05/10/2023]
Abstract
Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.
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Affiliation(s)
- Aleksandra Miłobedzka
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; Institute of Evolutionary Biology, University of Warsaw, Warsaw, Poland.
| | - Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | | | - Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Caitlin M Singleton
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
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17
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The Relationship between Antibiotic Susceptibility and pH in the Case of Uropathogenic Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10121431. [PMID: 34943643 PMCID: PMC8697967 DOI: 10.3390/antibiotics10121431] [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: 09/30/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
Urinary tract infections (UTIs) are common bacterial infections caused mainly by enteric bacteria. Numerous virulence factors assist bacteria in the colonization of the bladder. Bacterial efflux pumps also contribute to bacterial communication and to biofilm formation. In this study, the phenotypic and genetic antibiotic resistance of clinical UTI pathogens such as Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis were determined by disk diffusion method and polymerase chain reaction (PCR). Following this, different classes of antibiotics were evaluated for their antibacterial activity at pH 5, 6, 7 and 8 by a microdilution method. Gentamicin (GEN) was the most potent antibacterial agent against E. coli strains. The effect of GEN on the relative expression of marR and sdiA genes was evaluated by quantitative PCR. The slightly acidic pH (pH 6) and GEN treatment induced the upregulation of marR antibiotic resistance and sdiA QS activator genes in both E. coli strains. Consequently, bacteria had become more susceptible to GEN. It can be concluded that antibiotic activity is pH dependent and so the artificial manipulation of urinary pH can contribute to a more effective therapy of multidrug resistant bacterial infections.
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18
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Nanayakkara AK, Boucher HW, Fowler VG, Jezek A, Outterson K, Greenberg DE. Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward. CA Cancer J Clin 2021; 71:488-504. [PMID: 34546590 DOI: 10.3322/caac.21697] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infection is the second leading cause of death in patients with cancer. Loss of efficacy in antibiotics due to antibiotic resistance in bacteria is an urgent threat against the continuing success of cancer therapy. In this review, the authors focus on recent updates on the impact of antibiotic resistance in the cancer setting, particularly on the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). This review highlights the health and financial impact of antibiotic resistance in patients with cancer. Furthermore, the authors recommend measures to control the emergence of antibiotic resistance, highlighting the risk factors associated with cancer care. A lack of data in the etiology of infections, specifically in oncology patients in United States, is identified as a concern, and the authors advocate for a centralized and specialized surveillance system for patients with cancer to predict and prevent the emergence of antibiotic resistance. Finding better ways to predict, prevent, and treat antibiotic-resistant infections will have a major positive impact on the care of those with cancer.
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Affiliation(s)
- Amila K Nanayakkara
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
| | - Helen W Boucher
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, Massachusetts
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Amanda Jezek
- Infectious Diseases Society of America, Arlington, Virginia
| | - Kevin Outterson
- CARB-X, Boston, Massachusetts
- Boston University School of Law, Boston, Massachusetts
| | - David E Greenberg
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
- Department of Microbiology, University of Texas Southwestern, Dallas, Texas
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19
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Wang Q, Vachon J, Prasad B, Pybus CA, Lapin N, Chopra R, Greenberg DE. Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion. NPJ Biofilms Microbiomes 2021; 7:68. [PMID: 34385452 PMCID: PMC8360946 DOI: 10.1038/s41522-021-00239-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Hundreds of thousands of human implant procedures require surgical revision each year due to infection. Infections are difficult to treat with conventional antibiotics due to the formation of biofilm on the implant surface. We have developed a noninvasive method to eliminate biofilm on metal implants using heat generated by intermittent alternating magnetic fields (iAMF). Here, we demonstrate that heat and antibiotics are synergistic in biofilm elimination. For Pseudomonas aeruginosa biofilm, bacterial burden was reduced >3 log with iAMF and ciprofloxacin after 24 h compared with either treatment alone (p < 0.0001). This effect was not limited by pathogen or antibiotic as similar biofilm reductions were seen with iAMF and either linezolid or ceftriaxone in Staphylococcus aureus. iAMF and antibiotic efficacy was seen across various iAMF settings, including different iAMF target temperatures, dose durations, and dosing intervals. Initial mechanistic studies revealed membrane disruption as one factor important for AMF enhanced antibacterial activity in the biofilm setting. This study demonstrates the potential of utilizing a noninvasive approach to reduce biofilm off of metallic implants.
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Affiliation(s)
- Qi Wang
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan Vachon
- Medical School, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bibin Prasad
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christine A Pybus
- Department of Internal Medicine, Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Norman Lapin
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rajiv Chopra
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
- Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - David E Greenberg
- Department of Internal Medicine, Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, USA.
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20
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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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21
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Hesp A, Veldman K, Brouwer MSM, Wagenaar JA, Mevius D, van Schaik G. Latent class analysis to assess whole-genome sequencing versus broth microdilution for monitoring antimicrobial resistance in livestock. Prev Vet Med 2021; 193:105406. [PMID: 34147959 DOI: 10.1016/j.prevetmed.2021.105406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) monitoring in animals is performed in commensal Escherichia coli, and other microorganisms relevant for human or veterinary health. Due to advances in the field and major reductions in cost, it is expected that whole-genome sequencing (WGS)-based antimicrobial susceptibility testing (AST) will (partly) replace culture-based AST. So far, no studies have been performed without using culture-based AST as the gold standard. Our aim was to use Bayesian latent class analysis to evaluate the accuracy of susceptibility testing of commensal E. coli by WGS-based AST versus culture-based AST as this test does not assume a gold standard. OpenBUGS was used to model two independent tests in three animal populations (N = 150, 50 bacterial isolates per population): veal calves, pigs, and broilers. This resulted in the first estimation of sensitivity and specificity of WGS-based AST versus culture-based AST to detect AMR without a gold standard. Both methods had high sensitivity (>0.92, lowest limit probability interval: 0.76) and specificity was generally high for both methods for all antimicrobial classes except for aminoglycosides and macrolides. We compared WGS results for different length and identity settings (%) of gene alignment and found few differences between the 60/90, 90/90 and 95/95 settings. We recommend to further investigate sensitivity and specificity of WGS-based AST by means of latent class analysis, especially for low-prevalent resistance.
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Affiliation(s)
- Ayla Hesp
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Kees Veldman
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Gerdien van Schaik
- Royal GD, Deventer, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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22
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Manishimwe R, Moncada PM, Bugarel M, Scott HM, Loneragan GH. Antibiotic resistance among Escherichia coli and Salmonella isolated from dairy cattle feces in Texas. PLoS One 2021; 16:e0242390. [PMID: 33961628 PMCID: PMC8104409 DOI: 10.1371/journal.pone.0242390] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/24/2021] [Indexed: 12/31/2022] Open
Abstract
In several developing countries, studies on antimicrobial resistance among bacteria from food animals are rare mostly because of under-resourced laboratories. The objective of this study was to develop and field-test a low cost protocol to estimate the isolate- and sample-level prevalence of resistance to critically important antibiotics among Escherichia coli and Salmonella isolated from dairy cattle feces. Using a predesigned protocol, fecal samples were collected to isolate non-type-specific E. coli and Salmonella using selective media without antibiotic supplements. Besides, samples were screened for E. coli and Salmonella isolates not susceptible to third-generation cephalosporins and quinolones using selective media supplemented with cefotaxime (1.0 μg/mL) and ciprofloxacine (0.5 μg/mL), respectively. All bacterial isolates were further tested for antibiotic susceptibility using disk diffusion. Bacterial isolates not susceptible to third-generation cephalosporins were tested for extended spectrum beta-lactamase (ESBL) phenotype using the combination disk test. Molecular methods were performed on selected bacterial isolates to identify and distinguish genetic determinants associated with the observed phenotypes. Among 85 non-type-specific E. coli isolated from MacConkey agar without antibiotics, the isolate-level prevalence of resistance to tetracycline was the highest (8.2%). Among 37 E. coli recovered from MacConkey agar with cefotaxime, 56.8% were resistant ceftriaxone. Among 22 E. coli isolates recovered from MacConkey agar with ciprofloxacin, 77.3% and 54.5% were resistant to nalidixic acid and ciprofloxacin, respectively. Sixteen Salmonella were isolated and only one demonstrated any resistance (i.e., single resistance to streptomycin). Among E. coli isolates not susceptible to ceftriaxone, an AmpC phenotype was more common than an ESBL phenotype (29 versus 10 isolates, respectively). Whole genome sequencing showed that phenotypic profiles of antibiotic resistance detected were generally substantiated by genotypic profiles. The tested protocol is suited to detecting and estimating prevalence of antimicrobial resistance in bacteria isolated from food animal feces in resource-limited laboratories in the developing world.
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Affiliation(s)
- Rosine Manishimwe
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Department of Veterinary Medicine, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Nyagatare, Rwanda
- * E-mail: ,
| | - Paola M. Moncada
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Marie Bugarel
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - H. Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Guy H. Loneragan
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, United States of America
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23
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Franklin AM, Brinkman NE, Jahne MA, Keely SP. Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments. J Microbiol Methods 2021; 184:106174. [PMID: 33774111 DOI: 10.1016/j.mimet.2021.106174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 12/26/2022]
Abstract
Antimicrobial resistance (AMR) in the environment is a growing global health concern, especially the dissemination of AMR into surface waters due to human and agricultural inputs. Within recent years, research has focused on trying to understand the impact of AMR in surface waters on human, agricultural and ecological health (One Health). While surface water quality assessments and surveillance of AMR have historically utilized culture-based methods, culturing bacteria has limitations due to difficulty in isolating environmental bacteria and the need for a priori information about the bacteria for selective isolation. The use of molecular techniques to analyze AMR at the genetic level has helped to overcome the difficulties with culture-based techniques since they do not require advance knowledge of the bacterial population and can analyze uncultivable environmental bacteria. The aim of this review is to provide an overview of common contemporary molecular methods available for analyzing AMR in surface waters, which include high throughput real-time polymerase chain reaction (HT-qPCR), metagenomics, and whole genome sequencing. This review will also feature how these methods may provide information on human and animal health risks. HT-qPCR works at the nanoliter scale, requires only a small amount of DNA, and can analyze numerous gene targets simultaneously, but may lack in analytical sensitivity and the ability to optimize individual assays compared to conventional qPCR. Metagenomics offers more detailed genomic information and taxonomic resolution than PCR by sequencing all the microbial genomes within a sample. Its open format allows for the discovery of new antibiotic resistance genes; however, the quantity of DNA necessary for this technique can be a limiting factor for surface water samples that typically have low numbers of bacteria per sample volume. Whole genome sequencing provides the complete genomic profile of a single environmental isolate and can identify all genetic elements that may confer AMR. However, a main disadvantage of this technique is that it only provides information about one bacterial isolate and is challenging to utilize for community analysis. While these contemporary techniques can quickly provide a vast array of information about AMR in surface waters, one technique does not fully characterize AMR nor its potential risks to human, animal, or ecological health. Rather, a combination of techniques (including both molecular- and culture-based) are necessary to fully understand AMR in surface waters from a One Health perspective.
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Affiliation(s)
- A M Franklin
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA.
| | - N E Brinkman
- Office of Research and Development, Center for Environmental Solutions and Emergency Response, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
| | - M A Jahne
- Office of Research and Development, Center for Environmental Solutions and Emergency Response, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
| | - S P Keely
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
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24
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Silveira MC, Rocha-de-Souza CM, de Oliveira Santos IC, Pontes LDS, Oliveira TRTE, Tavares-Teixeira CB, Cossatis NDA, Pereira NF, da Conceição-Neto OC, da Costa BS, Rodrigues DCS, Albano RM, da Silva FAB, Marques EA, Leão RS, Carvalho-Assef APD. Genetic Basis of Antimicrobial Resistant Gram-Negative Bacteria Isolated From Bloodstream in Brazil. Front Med (Lausanne) 2021; 8:635206. [PMID: 33791325 PMCID: PMC8005515 DOI: 10.3389/fmed.2021.635206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant microorganisms are a well-known global problem, and gram-negative bacilli are top-ranking. When these pathogens are associated with bloodstream infections (BSI), outcomes become even worse. Here we applied whole-genome sequencing to access information about clonal distribution, resistance mechanism diversity and other molecular aspects of gram-negative bacilli (GNB) isolated from bloodstream infections in Brazil. It was possible to highlight international high-risk clones circulating in the Brazilian territory, such as CC258 for Klebsiella pneumoniae, ST79 for Acinetobacter baumannii and ST233 for Pseudomonas aeruginosa. Important associations can be made such as a negative correlation between CRISPR-Cas and K. pneumoniae CC258, while the genes blaTEM, blaKPC and blaCTX−M are highly associated with this clone. Specific relationships between A. baumannii clones and blaOXA−51 variants were also observed. All P. aeruginosa ST233 isolates showed the genes blaVIM and blaOXA486. In addition, some trends could be identified, where a new P. aeruginosa MDR clone (ST3079), a novel A. baumannii clonal profile circulating in Brazil (ST848), and important resistance associations in the form of blaVIM−2 and blaIMP−56 being found together in one ST233 strain, stand out. Such findings may help to develop approaches to deal with BSI and even other nosocomial infections caused by these important GNB.
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Affiliation(s)
- Melise Chaves Silveira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | - Leilane da Silva Pontes
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | - Nataly de Almeida Cossatis
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | - Natacha Ferreira Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Bianca Santos da Costa
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Rodolpho Mattos Albano
- Departamento de Bioquímica, Instituto de Biologia Roberto de Alcântara Gome, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | | | - Elizabeth Andrade Marques
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | - Robson Souza Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
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25
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Feng Q, Frana T, Logue CM, McKean JD, Hurd SH, O'Connor AM, Dickson JS, Zhu S, Li G. Comparison of Antimicrobial Resistance Profiles in Salmonella spp. from Swine Upon Arrival and Postslaughter at the Abattoir. Microb Drug Resist 2021; 27:1144-1154. [PMID: 33539269 DOI: 10.1089/mdr.2020.0282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antimicrobial resistance (AMR) developed by Salmonella within animals used for food products is a major global issue. Monitoring AMR in animals destined for slaughter is, therefore, critical. Abattoirs may serve as potential candidate checkpoints for monitoring resistance patterns on farms. A complicating factor, however, is the impact of lairage on Salmonella detected in pigs at slaughter. This study sought to compare AMR patterns in Salmonella spp. in swine collected upon arrival (fecal samples) at the abattoir with those at postslaughter (cecal samples) and evaluate the feasibility of using slaughterhouse samples for surveillance of prevailing AMR Salmonella on farms. Eighty-four Salmonella isolates were recovered from a large, midwestern U.S. abattoir between September and November 2013. Isolates were tested for phenotypic AMR to 12 antimicrobials using the broth microdilution assay. Whole-genome sequencing identified the AMR genes harbored by the strains. Significant differences were observed in the isolate phenotypes and genotypes; however, no significant difference was observed in genotypic resistance patterns. Hence, the AMR profiles of Salmonella spp. postslaughter cannot be predicted from preslaughter samples. Further research considering the genetic diversity of isolates and statistical power of the genotypic analysis is warranted to improve the performance of WGS-inferred antimicrobial susceptibility.
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Affiliation(s)
- Qi Feng
- Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High-tech Research, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China.,Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Timothy Frana
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Catherine M Logue
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - James D McKean
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Scott H Hurd
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Annette M O'Connor
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA.,College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - James S Dickson
- Department of Animal Science, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Shanyuan Zhu
- Jiang Su Provincial Key Laboratory of Veterinary Bio-pharmaceutical High-tech Research, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China.,Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Ganwu Li
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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26
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Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
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Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
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27
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Shropshire WC, Aitken SL, Pifer R, Kim J, Bhatti MM, Li X, Kalia A, Galloway-Peña J, Sahasrabhojane P, Arias CA, Greenberg DE, Hanson BM, Shelburne SA. IS26-mediated amplification of blaOXA-1 and blaCTX-M-15 with concurrent outer membrane porin disruption associated with de novo carbapenem resistance in a recurrent bacteraemia cohort. J Antimicrob Chemother 2021; 76:385-395. [PMID: 33164081 PMCID: PMC7816169 DOI: 10.1093/jac/dkaa447] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/28/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Approximately half of clinical carbapenem-resistant Enterobacterales (CRE) isolates lack carbapenem-hydrolysing enzymes and develop carbapenem resistance through alternative mechanisms. OBJECTIVES To elucidate development of carbapenem resistance mechanisms from clonal, recurrent ESBL-positive Enterobacterales (ESBL-E) bacteraemia isolates in a vulnerable patient population. METHODS This study investigated a cohort of ESBL-E bacteraemia cases in Houston, TX, USA. Oxford Nanopore Technologies long-read and Illumina short-read sequencing data were used for comparative genomic analysis. Serial passaging experiments were performed on a set of clinical ST131 Escherichia coli isolates to recapitulate in vivo observations. Quantitative PCR (qPCR) and qRT-PCR were used to determine copy number and transcript levels of β-lactamase genes, respectively. RESULTS Non-carbapenemase-producing CRE (non-CP-CRE) clinical isolates emerged from an ESBL-E background through a concurrence of primarily IS26-mediated amplifications of blaOXA-1 and blaCTX-M-1 group genes coupled with porin inactivation. The discrete, modular translocatable units (TUs) that carried and amplified β-lactamase genes mobilized intracellularly from a chromosomal, IS26-bound transposon and inserted within porin genes, thereby increasing β-lactamase gene copy number and inactivating porins concurrently. The carbapenem resistance phenotype and TU-mediated β-lactamase gene amplification were recapitulated by passaging a clinical ESBL-E isolate in the presence of ertapenem. Clinical non-CP-CRE isolates had stable carbapenem resistance phenotypes in the absence of ertapenem exposure. CONCLUSIONS These data demonstrate IS26-mediated mechanisms underlying β-lactamase gene amplification with concurrent outer membrane porin disruption driving emergence of clinical non-CP-CRE. Furthermore, these amplifications were stable in the absence of antimicrobial pressure. Long-read sequencing can be utilized to identify unique mobile genetic element mechanisms that drive antimicrobial resistance.
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Affiliation(s)
- William C Shropshire
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Samuel L Aitken
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Division of Pharmacy, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Reed Pifer
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School at Houston, Houston, TX 77030, USA
| | - Jiwoong Kim
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah M Bhatti
- Department of Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiqi Li
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jessica Galloway-Peña
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Cesar A Arias
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX 77030, USA
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Ak. 9#131a2, Colombia
| | - David E Greenberg
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Internal Medicine, UT Southwestern, Dallas, TX 75390, USA
- Department of Microbiology, UT Southwestern, Dallas, TX 75390, USA
| | - Blake M Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Samuel A Shelburne
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
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Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers Retain Activity against Multidrug-Resistant Pseudomonas aeruginosa In Vitro and In Vivo. mBio 2021; 12:mBio.02411-20. [PMID: 33436433 PMCID: PMC7844538 DOI: 10.1128/mbio.02411-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Numerous Gram-negative bacteria are becoming increasingly resistant to multiple, if not all, classes of existing antibiotics. Multidrug-resistant Pseudomonas aeruginosa bacteria are a major cause of health care-associated infections in a variety of clinical settings, endangering patients who are immunocompromised or those who suffer from chronic infections, such as people with cystic fibrosis (CF). Most antimicrobials currently in the clinical pipeline are modifications of existing classes of antibiotics and are considered short-term solutions due to the emergence of resistance. Pseudomonas aeruginosa represents a major challenge for new antimicrobial drug discovery due to its versatile lifestyle, ability to develop resistance to most antibiotic classes, and capacity to form robust biofilms on surfaces and in certain hosts such as those living with cystic fibrosis (CF). A precision antibiotic approach to treating Pseudomonas could be achieved with an antisense method, specifically by using peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs). Here, we demonstrate that PPMOs targeting acpP (acyl carrier protein), lpxC (UDP-(3-O-acyl)-N-acetylglucosamine deacetylase), and rpsJ (30S ribosomal protein S10) inhibited the in vitro growth of several multidrug-resistant clinical P. aeruginosa isolates at levels equivalent to those that were effective against sensitive strains. Lead PPMOs reduced established pseudomonal biofilms alone or in combination with tobramycin or piperacillin-tazobactam. Lead PPMO dosing alone or combined with tobramycin in an acute pneumonia model reduced lung bacterial burden in treated mice at 24 h and reduced morbidity up to 5 days postinfection. PPMOs reduced bacterial burden of extensively drug-resistant P. aeruginosa in the same model and resulted in superior survival compared to conventional antibiotics. These data suggest that lead PPMOs alone or in combination with clinically relevant antibiotics represent a promising therapeutic approach for combating P. aeruginosa infections.
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Pollock J, Low AS, McHugh RE, Muwonge A, Stevens MP, Corbishley A, Gally DL. Alternatives to antibiotics in a One Health context and the role genomics can play in reducing antimicrobial use. Clin Microbiol Infect 2020; 26:1617-1621. [PMID: 32220638 DOI: 10.1016/j.cmi.2020.02.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND This review follows on from the International Conference on One Health Antimicrobial Resistance (ICOHAR 2019), where strategies to improve the fundamental understanding and management of antimicrobial resistance at the interface between humans, animals and the environment were discussed. OBJECTIVE This review identifies alternatives to antimicrobials in a One Health context, noting how advances in genomic technologies are assisting their development and enabling more targeted use of antimicrobials. SOURCES Key articles on the use of microbiota modulation, livestock breeding and gene editing, vaccination, antivirulence strategies and bacteriophage therapy are discussed. CONTENT Antimicrobials are central for disease control, but reducing their use is paramount as a result of the rise of transmissible antimicrobial resistance. This review discusses antimicrobial alternatives in the context of improved understanding of fundamental host-pathogen and microbiota interactions using genomic tools. IMPLICATIONS Host and microbial genomics and other novel technologies play an important role in devising disease control strategies for healthier animals and humans that in turn reduce our reliance on antimicrobials.
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Affiliation(s)
- J Pollock
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - A S Low
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - R E McHugh
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, Scotland, UK; Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - A Muwonge
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - M P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - A Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - D L Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK.
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Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap. BMJ Glob Health 2020; 5:e002244. [PMID: 33239336 PMCID: PMC7689591 DOI: 10.1136/bmjgh-2019-002244] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022] Open
Abstract
The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.
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Hujer AM, Long SW, Olsen RJ, Taracila MA, Rojas LJ, Musser JM, Bonomo RA. Predicting β-lactam resistance using whole genome sequencing in Klebsiella pneumoniae: the challenge of β-lactamase inhibitors. Diagn Microbiol Infect Dis 2020; 98:115149. [PMID: 32858260 DOI: 10.1016/j.diagmicrobio.2020.115149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/01/2020] [Accepted: 07/18/2020] [Indexed: 11/25/2022]
Abstract
Although multiple antimicrobial resistance (AMR) determinants can confer the same in vitro antimicrobial susceptibility testing (AST) phenotype, their differing effect on optimal therapeutic choices is uncertain. Using a large population-based collection of clinical strains spanning a 3.5-year period, we applied WGS to detect inhibitor resistant (IR), extended-spectrum β-lactamase (ESBL), and carbapenem resistant (CR) β-lactamase (bla) genes and compared the genotype to the AST phenotype in select isolates. All blaNDM-1 (9/9) and the majority of blaNDM-1/OXA-48 (3/4) containing isolates were resistant to CAZ/AVI as predicted by WGS. The combination of ATM and CAZ/AVI restored susceptibility by disk diffusion assay. Unexpectedly, clinical Kp isolates bearing blaKPC-8 (V240G) and blaKPC-14 (G242 and T243 deletion) did not test fully resistant to CAZ/AVI. Lastly, despite the complexity of the β-lactamase background, CAZ/AVI retained potency. Presumed phenotypes conferred by AMR determinants need to be tested if therapeutic decisions are being guided by their presence or absence.
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Affiliation(s)
- Andrea M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Department of Molecular Biology and Microbiology, Pharmacology, Biochemistry, and the Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH; CWRU-Cleveland VAMC, Center, for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH.
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Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in Escherichia coli. Antimicrob Agents Chemother 2020; 64:AAC.02026-19. [PMID: 32205351 PMCID: PMC7269502 DOI: 10.1128/aac.02026-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/11/2020] [Indexed: 12/27/2022] Open
Abstract
Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, and yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide a more reliable assessment of susceptibility than traditional methods, we predicted resistance from WGS for 976 Escherichia coli bloodstream infection isolates from Oxfordshire, United Kingdom, comparing against phenotypes from the BD Phoenix (calibrated against EUCAST guidelines). Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, and yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide a more reliable assessment of susceptibility than traditional methods, we predicted resistance from WGS for 976 Escherichia coli bloodstream infection isolates from Oxfordshire, United Kingdom, comparing against phenotypes from the BD Phoenix (calibrated against EUCAST guidelines). A total of 339/976 (35%) isolates were amoxicillin-clavulanate resistant. Predictions based solely on beta-lactamase presence/absence performed poorly (sensitivity, 23% [78/339]) but improved when genetic features associated with penicillinase hyperproduction (e.g., promoter mutations and copy number estimates) were considered (sensitivity, 82% [277/339]; P < 0.0001). Most discrepancies occurred in isolates with MICs within ±1 doubling dilution of the breakpoint. We investigated two potential causes: the phenotypic reference and the binary resistant/susceptible classification. We performed reference standard, replicated phenotyping in a random stratified subsample of 261/976 (27%) isolates using agar dilution, following both EUCAST and CLSI guidelines, which use different clavulanate concentrations. As well as disagreeing with each other, neither agar dilution phenotype aligned perfectly with genetic features. A random-effects model investigating associations between genetic features and MICs showed that some genetic features had small, variable and additive effects, resulting in variable resistance classification. Using model fixed-effects to predict MICs for the non-agar dilution isolates, predicted MICs were in essential agreement (±1 doubling dilution) with observed (BD Phoenix) MICs for 691/715 (97%) isolates. This suggests amoxicillin-clavulanate resistance in E. coli is quantitative, rather than qualitative, explaining the poorly reproducible binary (resistant/susceptible) phenotypes and suboptimal concordance between different phenotypic methods and with WGS-based predictions.
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Kim MH, Jeong H, Sim YM, Lee S, Yong D, Ryu CM, Choi JY. Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications. PLoS One 2020; 15:e0229416. [PMID: 32084241 PMCID: PMC7034955 DOI: 10.1371/journal.pone.0229416] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/05/2020] [Indexed: 12/28/2022] Open
Abstract
Acinetobacter baumannii is a highly potent nosocomial pathogen that is associated with increased in-hospital mortality. Here, we investigated the changes in molecular characteristics of carbapenem-resistant A. baumannii (CRAB) isolated from the blood samples of patients admitted to a tertiary hospital in South Korea from January 2009 to July 2015. Whole genome sequencing using the Illumina MiSeq platform and multi-locus sequence typing (MLST) were performed for 98 CRAB clinical isolates. In silico analyses for the prediction of antimicrobial resistance and virulence factor genes were performed. Plasmid sequences, including complete forms, were reconstructed from the sequence reads. Epidemiologic data were collected from the hospital database. MLST using the Oxford scheme revealed 10 sequence types of CRAB, of which ST191 was the dominant type (n = 59). Although blaOXA-23 was shared by most analysed strains, the compositions of antimicrobial resistance determinants differed among sequence types. ST447 and ST451/ST1809 with a few resistance genes were isolated during the later years of the study period. The number of virulence genes increased, while that of ST191 did not change significantly over the investigation period. Intriguingly MLST types, compositions of antimicrobial resistance genes, and virulence genes had no association with clinical outcomes of CRAB bacteraemia. In conclusion, active changes in or accumulations of antimicrobial resistance determinants and virulence genes in CRAB were not observed during the research period. Molecular characteristics of CRAB had no association with clinical outcomes of CRAB bacteraemia.
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Affiliation(s)
- Min Hyung Kim
- Department of Internal Medicine, Bundang Jesaeng Hospital, Seongam, Gyeonggi, South Korea
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- R&D Center, Medytox Inc., Suwon, Gyeonggi-do, South Korea
| | - Young Mi Sim
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
| | - Soohyun Lee
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of antimicrobial resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- * E-mail: (JYC); (CMR)
| | - Jun Yong Choi
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
- * E-mail: (JYC); (CMR)
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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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Whole-genome sequencing of Staphylococcus epidermidis bloodstream isolates from a prospective clinical trial reveals that complicated bacteraemia is caused by a limited number of closely related sequence types. Clin Microbiol Infect 2019; 26:646.e1-646.e8. [PMID: 31639470 DOI: 10.1016/j.cmi.2019.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVES The significance of isolating Staphylococus epidermidis from a blood culture is highly heterogeneous, ranging from contamination to an indication of a serious infection. Herein we sought to determine whether there is a relationship between S. epidermidis genotype and clinical severity of bacteraemia. METHODS S. epidermidis bacteraemias from a prospective, multicentre trial at 15 centres in the United States and one in Spain were classified as simple (including possible contamination), uncomplicated, and complicated. Whole-genome sequencing (WGS) was performed on 161 S. epidermidis isolates, and clinical outcomes were correlated with genotypic information. RESULTS A total of 49 S. epidermidis sequence types (STs) were identified. Although strains of all 49 STs were isolated from patients with either simple or uncomplicated infection, all strains causing complicated infections were derived from five STs: ST2, ST5, ST7, ST16, and ST32. ST2 and ST5 isolates were significantly more likely to cause uncomplicated and complicated bloodstream infections compared to simple bacteraemia (odds ratio 2.0, 95%CI 1.1-3.9, p 0.04). By multivariate regression analysis, having an ST2 or ST5 S. epidermidis bacteraemia was an independent predictor of complicated bloodstream infection (odds ratio 3.7, 95%CI 1.2-11.0, p 0.02). ST2/ST5 strains carried larger numbers of antimicrobial resistance determinants compared to non-ST2/ST5 isolates (6.34 ± 1.5 versus 4.4 ± 2.5, p < 0.001). CONCLUSION S. epidermidis bacteraemia was caused by a genetically heterogeneous group of organisms, but only a limited number of STs-particularly multidrug-resistant ST2 and ST5 strains-caused complicated infections.
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Bacterial cross-resistance to anti-infective compounds. Is it a real problem? Curr Opin Pharmacol 2019; 48:76-81. [DOI: 10.1016/j.coph.2019.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022]
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Hendriksen RS, Bortolaia V, Tate H, Tyson GH, Aarestrup FM, McDermott PF. Using Genomics to Track Global Antimicrobial Resistance. Front Public Health 2019; 7:242. [PMID: 31552211 PMCID: PMC6737581 DOI: 10.3389/fpubh.2019.00242] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022] Open
Abstract
The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology and microbial surveillance. The availability of bioinformatics tools and online accessible databases has been a prerequisite for this. We conducted a scientific literature review and here we present a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and provide future perspectives and recommendations. At least 47 freely accessible bioinformatics resources for detection of AMR determinants in DNA or amino acid sequence data have been developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder, and ResFinder. Bioinformatics resources differ for several parameters including type of accepted input data, presence/absence of software for search within a database of AMR determinants that can be specific to a tool or cloned from other resources, and for the search approach employed, which can be based on mapping or on alignment. As a consequence, each tool has strengths and limitations in sensitivity and specificity of detection of AMR determinants and in application, which for some of the tools have been highlighted in benchmarking exercises and scientific articles. The identified tools are either available at public genome data centers, from GitHub or can be run locally. NCBI and European Nucleotide Archive (ENA) provide possibilities for online submission of both sequencing and accompanying phenotypic antimicrobial susceptibility data, allowing for other researchers to further analyze data, and develop and test new tools. The advancement in whole genome sequencing and the application of online tools for real-time detection of AMR determinants are essential to identify control and prevention strategies to combat the increasing threat of AMR. Accessible tools and DNA sequence data are expanding, which will allow establishing global pathogen surveillance and AMR tracking based on genomics. There is however, a need for standardization of pipelines and databases as well as phenotypic predictions based on the data.
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Affiliation(s)
- Rene S. Hendriksen
- European Union Reference Laboratory for Antimicrobial Resistance, World Health Organisation, Collaborating Center for Antimicrobial Resistance and Genomics in Food borne Pathogens, FAO Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Valeria Bortolaia
- European Union Reference Laboratory for Antimicrobial Resistance, World Health Organisation, Collaborating Center for Antimicrobial Resistance and Genomics in Food borne Pathogens, FAO Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Heather Tate
- Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States
| | - Gregory H. Tyson
- Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States
| | - Frank M. Aarestrup
- European Union Reference Laboratory for Antimicrobial Resistance, World Health Organisation, Collaborating Center for Antimicrobial Resistance and Genomics in Food borne Pathogens, FAO Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Patrick F. McDermott
- Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Collineau L, Boerlin P, Carson CA, Chapman B, Fazil A, Hetman B, McEwen SA, Parmley EJ, Reid-Smith RJ, Taboada EN, Smith BA. Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. Front Microbiol 2019; 10:1107. [PMID: 31231317 PMCID: PMC6558386 DOI: 10.3389/fmicb.2019.01107] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/01/2019] [Indexed: 12/20/2022] Open
Abstract
Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food chain, and therefore support risk assessment activities. At this stage, it is unclear how WGS data can be integrated into quantitative microbial risk assessment (QMRA) models and whether their integration will impact final risk estimates or the assessment of risk mitigation measures. This review explores opportunities and challenges of integrating WGS data into QMRA models that follow the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR. We describe how WGS offers an opportunity to enhance the next-generation of foodborne AMR QMRA modeling. Instead of considering all hazard strains as equally likely to cause disease, WGS data can improve hazard identification by focusing on those strains of highest public health relevance. WGS results can be used to stratify hazards into strains with similar genetic profiles that are expected to behave similarly, e.g., in terms of growth, survival, virulence or response to antimicrobial treatment. The QMRA input distributions can be tailored to each strain accordingly, making it possible to capture the variability in the strains of interest while decreasing the uncertainty in the model. WGS also allows for a more meaningful approach to explore genetic similarity among bacterial populations found at successive stages of the food chain, improving the estimation of the probability and magnitude of exposure to AMR hazards at point of consumption. WGS therefore has the potential to substantially improve the utility of foodborne AMR QMRA models. However, some degree of uncertainty remains in relation to the thresholds of genetic similarity to be used, as well as the degree of correlation between genotypic and phenotypic profiles. The latter could be improved using a functional approach based on prediction of microbial behavior from a combination of 'omics' techniques (e.g., transcriptomics, proteomics and metabolomics). We strongly recommend that methodologies to incorporate WGS data in risk assessment be included in any future revision of the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.
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Affiliation(s)
- Lucie Collineau
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Brennan Chapman
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Benjamin Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Scott A. McEwen
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - E. Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Richard J. Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ben A. Smith
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
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Carbapenem versus Cefepime or Piperacillin-Tazobactam for Empiric Treatment of Bacteremia Due to Extended-Spectrum-β-Lactamase-Producing Escherichia coli in Patients with Hematologic Malignancy. Antimicrob Agents Chemother 2019; 63:AAC.01813-18. [PMID: 30509935 DOI: 10.1128/aac.01813-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022] Open
Abstract
Infections with extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli are common in patients with hematologic malignancy. The utility of cefepime and piperacillin-tazobactam as empiric therapy for ESBL-producing E. coli bacteremia in patients with hematologic malignancy is largely unknown. We conducted a single-center, retrospective cohort review of 103 adult inpatients with leukemia and/or hematopoietic stem cell transplant (HCT) recipients with monomicrobial ESBL-producing E. coli bacteremia. No association between increased 14-day mortality and empiric treatment with cefepime (8%) or piperacillin-tazobactam (0%) relative to that with carbapenems (19%) was observed (P = 0.19 and P = 0.04, respectively). This observation was consistent in multivariate Cox proportional hazards models adjusted for confounding and an inverse probability of treatment-weighted (IPTW) Cox proportional hazards model. Both fever and persistent bacteremia were more common in patients treated empirically with cefepime or piperacillin-tazobactam. Empiric treatment with cefepime or piperacillin-tazobactam did not result in increased mortality relative to that with treatment with carbapenems in patients with hematologic malignancy and ESBL-producing E. coli bacteremia, although most patients were changed to carbapenems early in treatment. However, due to prolonged fever and persistent bacteremia, their role may be limited in this patient population.
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Hawken SE, Snitkin ES. Genomic epidemiology of multidrug-resistant Gram-negative organisms. Ann N Y Acad Sci 2019; 1435:39-56. [PMID: 29604079 PMCID: PMC6167210 DOI: 10.1111/nyas.13672] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 12/12/2022]
Abstract
The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective strategies for controlling their proliferation. Recently, whole-genome sequencing has emerged as a disruptive technology that has transformed our understanding of the evolution and epidemiology of diverse rGNB species, and it has the potential to guide strategies for controlling the evolution and spread of resistance. Here, we review specific areas in which genomics has already made a significant impact, including outbreak investigations, regional epidemiology, clinical diagnostics, resistance evolution, and the study of epidemic lineages. While highlighting early successes, we also point to the next steps needed to translate this technology into strategies to improve public health and clinical medicine.
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Affiliation(s)
- Shawn E Hawken
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
- Division of Infectious Diseases/Department of Medicine, University of Michigan Medical School, Michigan, USA
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42
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Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates. Antimicrob Agents Chemother 2018; 63:AAC.01923-18. [PMID: 30373801 DOI: 10.1128/aac.01923-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/22/2018] [Indexed: 01/19/2023] Open
Abstract
Standard antimicrobial susceptibility testing (AST) approaches lead to delays in the selection of optimal antimicrobial therapy. Here, we sought to determine the accuracy of antimicrobial resistance (AMR) determinants identified by Nanopore whole-genome sequencing in predicting AST results. Using a cohort of 40 clinical isolates (21 carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae, 10 non-carbapenemase-producing carbapenem-resistant K. pneumoniae, and 9 carbapenem-susceptible K. pneumoniae isolates), three separate sequencing and analysis pipelines were performed, as follows: (i) a real-time Nanopore analysis approach identifying acquired AMR genes, (ii) an assembly-based Nanopore approach identifying acquired AMR genes and chromosomal mutations, and (iii) an approach using short-read correction of Nanopore assemblies. The short-read correction of Nanopore assemblies served as the reference standard to determine the accuracy of Nanopore sequencing results. With the real-time analysis approach, full annotation of acquired AMR genes occurred within 8 h from subcultured isolates. Assemblies sufficient for full resistance gene and single-nucleotide polymorphism annotation were available within 14 h from subcultured isolates. The overall agreement of genotypic results and anticipated AST results for the 40 K. pneumoniae isolates was 77% (range, 30% to 100%) and 92% (range, 80% to 100%) for the real-time approach and the assembly approach, respectively. Evaluating the patients contributing the 40 isolates, the real-time approach and assembly approach could shorten the median time to effective antibiotic therapy by 20 h and 26 h, respectively, compared to standard AST. Nanopore sequencing offers a rapid approach to both accurately identify resistance mechanisms and to predict AST results for K. pneumoniae isolates. Bioinformatics improvements enabling real-time alignment, coupled with rapid extraction and library preparation, will further enhance the accuracy and workflow of the Nanopore real-time approach.
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Extensive Gene Amplification as a Mechanism for Piperacillin-Tazobactam Resistance in Escherichia coli. mBio 2018; 9:mBio.00583-18. [PMID: 29691340 PMCID: PMC5915731 DOI: 10.1128/mbio.00583-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Although the TEM-1 β-lactamase (BlaTEM-1) hydrolyzes penicillins and narrow-spectrum cephalosporins, organisms expressing this enzyme are typically susceptible to β-lactam/β-lactamase inhibitor combinations such as piperacillin-tazobactam (TZP). However, our previous work led to the discovery of 28 clinical isolates of Escherichia coli resistant to TZP that contained only blaTEM-1 One of these isolates, E. coli 907355, was investigated further in this study. E. coli 907355 exhibited significantly higher β-lactamase activity and BlaTEM-1 protein levels when grown in the presence of subinhibitory concentrations of TZP. A corresponding TZP-dependent increase in blaTEM-1 copy number was also observed, with as many as 113 copies of the gene detected per cell. These results suggest that TZP treatment promotes an increase in blaTEM-1 gene dosage, allowing BlaTEM-1 to reach high enough levels to overcome inactivation by the available tazobactam in the culture. To better understand the nature of the blaTEM-1 copy number proliferation, whole-genome sequence (WGS) analysis was performed on E. coli 907355 in the absence and presence of TZP. The WGS data revealed that the blaTEM-1 gene is located in a 10-kb genomic resistance module (GRM) that contains multiple resistance genes and mobile genetic elements. The GRM was found to be tandemly repeated at least 5 times within a p1ESCUM/p1ECUMN-like plasmid when bacteria were grown in the presence of TZP.IMPORTANCE Understanding how bacteria acquire resistance to antibiotics is essential for treating infected patients effectively, as well as preventing the spread of resistant organisms. In this study, a clinical isolate of E. coli was identified that dedicated more than 15% of its genome toward tandem amplification of a ~10-kb resistance module, allowing it to escape antibiotic-mediated killing. Our research is significant in that it provides one possible explanation for clinical isolates that exhibit discordant behavior when tested for antibiotic resistance by different phenotypic methods. Our research also shows that GRM amplification is difficult to detect by short-read WGS technologies. Analysis of raw long-read sequence data was required to confirm GRM amplification as a mechanism of antibiotic resistance.
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Khan A, Miller WR, Arias CA. Mechanisms of antimicrobial resistance among hospital-associated pathogens. Expert Rev Anti Infect Ther 2018; 16:269-287. [PMID: 29617188 DOI: 10.1080/14787210.2018.1456919] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The introduction of antibiotics revolutionized medicine in the 20th-century permitting the treatment of once incurable infections. Widespread use of antibiotics, however, has led to the development of resistant organisms, particularly in the healthcare setting. Today, the clinician is often faced with pathogens carrying a cadre of resistance determinants that severely limit therapeutic options. The genetic plasticity of microbes allows them to adapt to stressors via genetic mutations, acquisition or sharing of genetic material and modulation of genetic expression leading to resistance to virtually any antimicrobial used in clinical practice. Areas covered: This is a comprehensive review that outlines major mechanisms of resistance in the most common hospital-associated pathogens including bacteria and fungi. Expert commentary: Understanding the genetic and biochemical mechanisms of such antimicrobial adaptation is crucial to tackling the rapid spread of resistance, can expose unconventional therapeutic targets to combat multidrug resistant pathogens and lead to more accurate prediction of antimicrobial susceptibility using rapid molecular diagnostics. Clinicians making treatment decisions based on the molecular basis of resistance may design therapeutic strategies that include de-escalation of broad spectrum antimicrobial usage, more focused therapies or combination therapies. These strategies are likely to improve patient outcomes and decrease the risk of resistance in hospital settings.
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Affiliation(s)
- Ayesha Khan
- a Department of Microbiology and Molecular Genetics , University of Texas McGovern Medical School , Houston , Texas , USA.,b Center for Antimicrobial Resistance and Microbial Genomics , University of Texas Health Science Center , Houston , TX , USA
| | - William R Miller
- b Center for Antimicrobial Resistance and Microbial Genomics , University of Texas Health Science Center , Houston , TX , USA.,c Department of Internal Medicine, Division of Infectious Diseases , McGovern Medical School
| | - Cesar A Arias
- a Department of Microbiology and Molecular Genetics , University of Texas McGovern Medical School , Houston , Texas , USA.,b Center for Antimicrobial Resistance and Microbial Genomics , University of Texas Health Science Center , Houston , TX , USA.,c Department of Internal Medicine, Division of Infectious Diseases , McGovern Medical School.,d Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics , Universidad El Bosque , Bogota , Colombia.,e School of Public Health , UTHealth Center for Infectious Diseases , Houston , TX , USA
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45
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Fleece ME, Pholwat S, Mathers AJ, Houpt ER. Molecular diagnosis of antimicrobial resistance in Escherichia coli. Expert Rev Mol Diagn 2018; 18:207-217. [PMID: 29431523 DOI: 10.1080/14737159.2018.1439381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Antimicrobial resistance is a growing global public health threat. The complexities of antimicrobial resistance in gram-negative bacteria such as Escherichia coli pose significant diagnostic and therapeutic challenges. Molecular diagnostics are emerging in this field. Areas covered: The authors review the clinical importance of pathogenic E. coli and discuss the mechanisms of resistance to common antibiotics used to treat these infections. We review the literature on antimicrobial susceptibility testing and discuss the current state of phenotypic as well as molecular methodologies. Clinical vignettes are presented to highlight how molecular diagnostics may be used for patient care. Expert commentary: The future use of molecular diagnostics for detection of antimicrobial resistance will be tailored to the context, whether hospital epidemiology, infection control, antibiotic stewardship, or clinical care. Further clinical research is needed to understand how to best apply molecular diagnostics to these settings.
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Affiliation(s)
- Molly E Fleece
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
| | - Suporn Pholwat
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
| | - Amy J Mathers
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
| | - Eric R Houpt
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
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Use of Next Generation Sequencing and Synergy Susceptibility Testing in Diagnosis and Treatment of Carbapenem-Resistant Klebsiella pneumoniae Blood Stream Infection. Case Rep Infect Dis 2018; 2018:3295605. [PMID: 29607230 PMCID: PMC5828565 DOI: 10.1155/2018/3295605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/11/2017] [Indexed: 02/05/2023] Open
Abstract
Early diagnosis and appropriate treatment for carbapenem-resistant Klebsiella pneumoniae (CR-Kp) infection is a big challenge for clinicians due to its high mortality. Every effort has been made to improve its clinical outcomes. However, treatment according to synergy susceptibility testing has never been reported in the literature. We reported a 29-year-old systemic lupus erythematosus female with CR-Kp blood stream infection. We highlighted the identification by next generation sequencing and treatment according to synergy susceptibility testing in the case.
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Lepage P, Blumental S. Specialty Grand Challenge In Pediatric Infectious Diseases. Front Pediatr 2017; 5:185. [PMID: 28894730 PMCID: PMC5581326 DOI: 10.3389/fped.2017.00185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 01/16/2023] Open
Affiliation(s)
- Philippe Lepage
- Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium.,Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sophie Blumental
- Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium.,Université Libre de Bruxelles (ULB), Brussels, Belgium
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