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Bryson AL, Bhalodi A, Liesman RM, Mathers AJ. Cefazolin as a predictor of urinary cephalosporin activity in indicated Enterobacterales. J Clin Microbiol 2024; 62:e0078821. [PMID: 38457194 PMCID: PMC11005412 DOI: 10.1128/jcm.00788-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Abstract
Traditionally, cephalothin susceptibility results were used to predict the susceptibility of additional cephalosporins; however, in 2013-2014, the Clinical and Laboratory Standards Institute (CLSI) revisited this practice and determined that cefazolin is a more accurate proxy than cephalothin for uncomplicated urinary tract infections (uUTIs). Therefore, a cefazolin surrogacy breakpoint was established to predict the susceptibility of seven oral cephalosporins for Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis in the context of uUTIs. Clinical microbiology laboratories face several operational challenges when implementing the cefazolin surrogacy breakpoint, which may lead to confusion for the best path forward. Here, we review the historical context and data behind the surrogacy breakpoints, review PK/PD profiles for oral cephalosporins, discuss challenges in deploying the breakpoint, and highlight the limited clinical outcome data in this space.
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Affiliation(s)
- Alexandra L. Bryson
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, Virginia, USA
| | - Amira Bhalodi
- Scientific and Medical Affairs Consulting, Newton, Pennsylvania, USA
| | - Rachael M. Liesman
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Amy J. Mathers
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health, Charlottesville, Virginia, USA
- Clinical Microbiology Laboratory, Department of Pathology, University of Virginia Health, Charlottesville, Virginia, USA
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2
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Tsubouchi T, Beltran CJ, Yagi M, Hamatani N, Takashina M, Shimizu S, Kanai T, Furutani KM. Beam delivery characteristics of the Hitachi carbon ion scanning system at Osaka Heavy Ion Medical Accelerator in Kansai (HIMAK). Med Phys 2024; 51:2239-2250. [PMID: 37877590 DOI: 10.1002/mp.16791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Using the pencil beam raster scanning method employed at most carbon beam treatment facilities, spots can be moved without interrupting the beam, allowing for the delivery of a dose between spots (move dose). This technique is also known as Dose-Driven-Continuous-Scanning (DDCS). To minimize its impact on HIMAK patient dosimetry, there's an upper limit to the move dose. Spots within a layer are grouped into sets, or "break points," allowing continuous irradiation. The beam is turned off when transitioning between sets or at the end of a treatment layer or spill. The control system beam-off is accomplished by turning off the RF Knockout (RFKO) extraction and after a brief delay the High Speed Steering Magnet (HSST) redirects the beam transport away from isocenter to a beam dump. PURPOSE The influence of the move dose and beam on/off control on the dose distribution and irradiation time was evaluated by measurements never before reported and modelled for Hitachi Carbon DDCS. METHOD We conducted fixed-point and scanning irradiation experiments at three different energies, both with and without breakpoints. For fixed-point irradiation, we utilized a 2D array detector and an oscilloscope to measure beam intensity over time. The oscilloscope data enabled us to confirm beam-off and beam-on timing due to breakpoints, as well as the relative timing of the RFKO signal, HSST signal, and dose monitor (DM) signals. From these measurements, we analyzed and modelled the temporal characteristics of the beam intensity. We also developed a model for the spot shape and amplitude at isocenter occurring after the beam-off signal which we called flap dose and its dependence on beam intensity. In the case of scanning irradiation, we measured move doses using the 2D array detector and compared these measurements with our model. RESULT We observed that the most dominant time variation of the beam intensity was at 1 kHz and its harmonic frequencies. Our findings revealed that the derived beam intensity cannot reach the preset beam intensity when each spot belongs to different breakpoints. The beam-off time due to breakpoints was approximately 100 ms, while the beam rise time and fall time (tdecay ) were remarkably fast, about 10 ms and 0.2 ms, respectively. Moreover, we measured the time lag (tdelay ) of approximately 0.2 ms between the RFKO and HSST signals. Since tdelay ≈ tdecay at HIMAK then the HSST is activated after the residual beam intensity, resulting in essentially zero flap dose at isocenter from the HSST. Our measurements of the move dose demonstrated excellent agreement with the modelled move dose. CONCLUSION We conducted the first move dose measurement for a Hitachi Carbon synchrotron, and our findings, considering beam on/off control details, indicate that Hitachi's carbon synchrotron provides a stable beam at HIMAK. Our work suggests that measuring both move dose and flap dose should be part of the commissioning process and possibly using our model in the Treatment Planning System (TPS) for new facilities with treatment delivery control systems with higher beam intensities and faster beam-off control.
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Affiliation(s)
- Toshiro Tsubouchi
- Department of Medical Physics, Osaka Heavy Ion Therapy Center, Osaka, Japan
| | - Chris J Beltran
- Department of Carbon Ion Radiotherapy, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Radiation Oncology, Division of Medical Physics, Mayo Clinic, Jacksonville, Florida, USA
| | - Masashi Yagi
- Department of Medical Physics, Osaka Heavy Ion Therapy Center, Osaka, Japan
- Department of Carbon Ion Radiotherapy, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Noriaki Hamatani
- Department of Medical Physics, Osaka Heavy Ion Therapy Center, Osaka, Japan
| | - Masaaki Takashina
- Department of Medical Physics, Osaka Heavy Ion Therapy Center, Osaka, Japan
| | - Shinichi Shimizu
- Department of Carbon Ion Radiotherapy, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tatsuaki Kanai
- Department of Carbon Ion Radiotherapy, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keith M Furutani
- Department of Carbon Ion Radiotherapy, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Radiation Oncology, Division of Medical Physics, Mayo Clinic, Jacksonville, Florida, USA
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Ravi V, Shamim U, Khan MA, Swaminathan A, Mishra P, Singh R, Bharali P, Chauhan NS, Pandey R. Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages. Front Med (Lausanne) 2024; 10:1294699. [PMID: 38288302 PMCID: PMC10823376 DOI: 10.3389/fmed.2023.1294699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Recombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants. Method Whole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points. Results Mutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis. Conclusion Together, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, for sustenance and adaptability, to maintain the epidemic spread of SARS-CoV-2 in the host population already high in immunity levels.
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Affiliation(s)
- Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Md Abuzar Khan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aparna Swaminathan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Rajender Singh
- CSIR-Central Drug Research Institute, (CSIR-CDRI), Lucknow, Lucknow, India
| | - Pankaj Bharali
- CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Russo C, Humphries R. Approaches to Testing Novel β-Lactam and β-Lactam Combination Agents in the Clinical Laboratory. Antibiotics (Basel) 2023; 12:1700. [PMID: 38136734 PMCID: PMC10740869 DOI: 10.3390/antibiotics12121700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The rapid emergence of multi-drug resistant Gram-negative pathogens has driven the introduction of novel β-lactam combination agents (BLCs) to the antibiotic market: ceftolozane-tazobactam, ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol, and sulbactam-durlobactam. These agents are equipped with innovative mechanisms that confer broad Gram-negative activity, notably against certain challenging carbapenemases. While their introduction offers a beacon of hope, clinical microbiology laboratories must navigate the complexities of susceptibility testing for these agents due to their diverse activity profiles against specific β-lactamases and the possibility of acquired resistance mechanisms in some bacterial isolates. This review explores the complexities of these novel antimicrobial agents detailing the intricacies of their application, providing guidance on the nuances of susceptibility testing, interpretation, and result reporting in clinical microbiology laboratories.
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Affiliation(s)
| | - Romney Humphries
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
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Patel JB, Alby K, Humphries R, Weinstein M, Lutgring JD, Naccache SN, Simner PJ. Updating breakpoints in the United States: a summary from the ASM Clinical Microbiology Open 2022. J Clin Microbiol 2023; 61:e0115422. [PMID: 37791777 PMCID: PMC10595059 DOI: 10.1128/jcm.01154-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Accurate antimicrobial susceptibility testing (AST) and reporting are essential for guiding appropriate therapy for patients and direction for public health prevention and control actions. A critical feature of AST reporting is the interpretation of AST results using clinical breakpoints for reporting as susceptible, susceptible-dose dependent, intermediate, or resistant. Breakpoints are subject to continuous adjustment and updating to best reflect current clinical data. These breakpoint changes can benefit patients and public health only if adopted in a timely manner. A recent survey identified that up to 70% of College of American Pathologists (CAP)-accredited U.S. laboratories and 45% of CAP-accredited laboratories outside the U.S. use various obsolete clinical breakpoints to interpret AST results to guide patient care. The reason for the ongoing use of obsolete breakpoints is multifactorial, including barriers encountered by laboratories, commercial AST device manufacturers, standards development organizations, and regulatory bodies alike. To begin to address this important patient safety issue, CAP implemented checklist requirements for CAP-accredited laboratories to ensure up-to-date clinical breakpoint use. Furthermore, the topic was discussed at the June 2022 American Society for Microbiology Clinical Microbiology Open (CMO) with various stakeholders to identify potential solutions. This minireview summarizes the breakpoint setting process in the U.S. and highlights solutions to close the gap between breakpoint revisions and implementation in clinical and public health laboratories. Solutions discussed include clarification of data requirements and minimum inhibitory concentration only reporting for regulatory clearance of AST devices, clinical data generation to close breakpoints gaps, advocacy, education, and greater dialogue between stakeholders.
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Affiliation(s)
- Jean B. Patel
- Beckman Coulter Microbiology, West Sacramento, California, USA
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Romney Humphries
- Division of Laboratory Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melvin Weinstein
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson University Hospital, New Brunswick, New Jersey, USA
| | - Joseph D. Lutgring
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Samia N. Naccache
- Department of Microbiology, LabCorp Seattle, Seattle, Washington, USA
| | - Patricia J. Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Maganga R, Sindiyo E, Musyoki VM, Shirima G, Mmbaga BT. Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania. Access Microbiol 2023; 5:acmi000540.v4. [PMID: 37601443 PMCID: PMC10436012 DOI: 10.1099/acmi.0.000540.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/13/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation. Gap statement There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries. Aim The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints. Methodology A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation. Results According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 -69.5 %), than those for ciprofloxacin (CIPRO) (18.6 -32.2 %), imipenem (IMI) (3.4 -35 %) and ceftazidime (CEF) (1.7 -45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT), IMI (3.4 % CB and 4.0 % COWT) and TET (67.8 % CB and 69.5 % COWT). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were significantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT, P<0.05). Conclusion AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI.
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Affiliation(s)
- Ruth Maganga
- University of Birmingham, Birmingham, B15 2TT, UK
- University of Glasgow, Glasgow, G12 8QQ, UK
- Kilimanjaro Christian Medical Center/Kilimanjaro Clinical Research Institute, PO Box 2236, Moshi, Tanzania
| | - Emmanuel Sindiyo
- The Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - Victor Moses Musyoki
- Department of Medical Microbiology, University of Nairobi, PO Box 19676-00202, Nairobi, Kenya
| | - Gabriel Shirima
- The Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Christian Medical Center/Kilimanjaro Clinical Research Institute, PO Box 2236, Moshi, Tanzania
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Manuel C, Maynard R, Abbott A, Adams K, Alby K, Sweeney A, Dien Bard J, Flores II, Rekasius V, Harrington A, Kidd TS, Mathers AJ, Tekle T, Simner PJ, Humphries RM. Evaluation of Piperacillin-Tazobactam Testing against Enterobacterales by the Phoenix, MicroScan, and Vitek2 Tests Using Updated Clinical and Laboratory Standards Institute Breakpoints. J Clin Microbiol 2023; 61:e0161722. [PMID: 36719243 PMCID: PMC9945575 DOI: 10.1128/jcm.01617-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/24/2022] [Indexed: 02/01/2023] Open
Abstract
In 2022, the Clinical and Laboratory Standards Institute (CLSI) updated piperacillin-tazobactam (TZP) breakpoints for Enterobacterales, based on substantial data suggesting that historical breakpoints did not predict treatment outcomes for TZP. The U.S. Food and Drug Administration (FDA) has not yet adopted these breakpoints, meaning commercial manufacturers of antimicrobial susceptibility testing devices cannot obtain FDA clearance for the revised breakpoints. We evaluated the Phoenix (BD, Sparks, MD), MicroScan (Beckman Coulter, Sacramento, CA), and Vitek2 (bioMérieux, Durham, NC) TZP MICs compared to reference broth microdilution for a collection of 284 Enterobacterales isolates. Phoenix (n = 167 isolates) demonstrated 84.4% categorical agreement (CA), with 4.2% very major errors (VMEs) and 1.8% major errors (MEs) by CLSI breakpoints. In contrast, CA was 85.0% with 4.3% VMEs and 0.8% MEs for the Phoenix with FDA breakpoints. MicroScan (n = 55 isolates) demonstrated 80.0% CA, 36.4% VMEs, and 4.8% MEs by CLSI breakpoints and 81.8% CA, 44.4% VMEs, and 0.0% MEs by FDA breakpoints. Vitek2 (n = 62 isolates) demonstrated 95.2% CA, 6.3% VMEs, and 0.0% MEs by CLSI and 96.8% CA, 0.0% VMEs, and 2.2% MEs by FDA breakpoints. Overall, the performance of the test systems was not substantially different using CLSI breakpoints off-label than using on-label FDA breakpoints. However, limitations were noted with higher-than-desired VME rates (all three systems) and lower-than-desired CA (MicroScan and Phoenix). Laboratories should consider adoption of the revised CLSI breakpoints with automated test systems but be aware that some performance challenges exist for testing TZP on automated systems, regardless of breakpoints applied.
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Affiliation(s)
- Carmila Manuel
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard Maynard
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - April Abbott
- Laboratory Medicine, Microbiology and Molecular Diagnostics, Deaconess Health System, Evansville, Indiana, USA
| | - Kara Adams
- Laboratory Medicine, Microbiology and Molecular Diagnostics, Deaconess Health System, Evansville, Indiana, USA
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Clinical Microbiology Laboratory, McLendon Clinical Laboratories, UNC Medical Center, Chapel Hill, North Carolina, USA
| | - Amy Sweeney
- Clinical Microbiology Laboratory, McLendon Clinical Laboratories, UNC Medical Center, Chapel Hill, North Carolina, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Irvin Ibarra Flores
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Violet Rekasius
- Department of Pathology and Laboratory Medicine, Loyola University, Chicago, Illinois, USA
| | - Amanda Harrington
- Department of Pathology and Laboratory Medicine, Loyola University, Chicago, Illinois, USA
| | - Tiffany S. Kidd
- Clinical Microbiology Laboratory, University of Virginia Medical Center, Charlottesville, Virginia, USA
| | - Amy J. Mathers
- Clinical Microbiology Laboratory, University of Virginia Medical Center, Charlottesville, Virginia, USA
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Tsigereda Tekle
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Patricia J. Simner
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, Baltimore, Maryland, USA
| | - Romney M. Humphries
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Xie G, Wang R, Zhang B, Sun L, Xiang W, Xu M, Zhu S, Guo L, Xu X, Yang W. Non-linear connections between maternal hemoglobin during the third trimester of pregnancy and birth weight outcomes in full-term newborns: Estimating the breakpoints. Front Nutr 2022; 9:1031781. [PMID: 36618680 PMCID: PMC9815559 DOI: 10.3389/fnut.2022.1031781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objective Anemia is still an unfinished global health problem, and adverse birth weight outcomes have everlasting influences on the health of later life. However, the non-linear connections and breakpoints of maternal hemoglobin with birth weight outcomes are still needed to be further elucidated. We aimed to reveal the non-linear connections between maternal hemoglobin during the third trimester of pregnancy and birth weight, low birth weight (LBW), macrosomia, small for gestational age (SGA), and large for gestational age (LGA) in full-term newborns and elucidate the breakpoints of the connections. Methods A total of 11,411 singletons, full-term, and live newborns, whose mothers conducted the examination of hemoglobin concentration before delivery, were included in this study. A generalized additive model was used to identify and visualize the non-linear connections between maternal hemoglobin and birth weight outcomes. Piecewise linear regression model was adopted to estimate the breakpoints of the connections and report the non-linear connections in detail. Results There were inverted "U"-shaped exposure-response connections between maternal hemoglobin concentration and birth weight and the risk of macrosomia. There was an increasing trend of the risk of LBW and a decreased trend of LGA with the increase in maternal hemoglobin concentration. The breakpoints of maternal hemoglobin for birth weight were 100 and 138 g/L, and those for SGA were 97 and 138 g/L. The breakpoints of maternal hemoglobin were 119 g/L for LBW, 105 g/L for macrosomia, and 106 g/L for LGA. When maternal hemoglobin concentration ranged from 100 to 138 g/L, maternal hemoglobin concentration increased per 1 g/L, and birth weight significantly decreased by 2.58 g (95% CI: -3.33, -1.83). When maternal hemoglobin concentration ranged from 97 to 138 g/L, maternal hemoglobin concentration increased per 1 g/L, and the risk of SGA significantly increased by 2% (95% CI: 1%, 3%). When maternal hemoglobin concentration was equal to or lower than 119 g/L, maternal hemoglobin concentration increased per 1 g/L, and the risk of LBW significantly increased by 3% (95% CI: 0%, 5%). When maternal hemoglobin concentration was higher than the breakpoints, the risks of macrosomia (OR = 0.99, 95% CI: 0.98, 0.99) and LGA (OR = 0.99, 95% CI: 0.98, 1.00) declined as the increase of maternal hemoglobin concentration. Conclusions There were non-linear connections between maternal hemoglobin and birth weight outcomes, and there are breakpoints in the connections. Cost-effective interventions targeting pregnant women in the prevention of abnormal maternal hemoglobin concentration should be taken to reduce the incidence of adverse birth weight outcomes.
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Affiliation(s)
- Guilan Xie
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Ruiqi Wang
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Boxing Zhang
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Landi Sun
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Wanwan Xiang
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Mengmeng Xu
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Sijing Zhu
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Leqian Guo
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xu Xu
- National Medical Center Office, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wenfang Yang
- Department of Obstetrics and Gynecology, Maternal and Child Health Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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9
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Nabal Díaz SG, Algara Robles O, García-Lechuz Moya JM. New definitions of susceptibility categories EUCAST 2019: clinic application. Rev Esp Quimioter 2022; 35 Suppl 3:84-88. [PMID: 36285865 PMCID: PMC9717465 DOI: 10.37201/req/s03.18.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
In January 2019, the European Committee for the Study of Antimicrobial Susceptibility (EUCAST) introduced some changes in the definitions of clinical categories for antibiotic susceptibility. The objective of these changes was to improve the credibility of category "I", optimizing and lengthening the survival and use of available antibiotics in the face of increasing antimicrobial resistance. This article aims to describe and explain these changes in the EUCAST criteria as well as make a short review about the factors on which the antibiotic susceptibility criteria depend.
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Affiliation(s)
| | | | - J M García-Lechuz Moya
- Juan M. García-Lechuz Moya, Clinical Microbiology Department. General University Hospital "Miguel Servet", Zaragoza. Spain.
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10
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Abstract
Cefiderocol, a siderophore catechol cephalosporin, recently introduced in the market has been developed to enhance the in vitro activity of extended spectrum cephalosporins and to avoid resistance mechanisms affecting cephalosporins and carbapenems. The in vitro study of cefiderocol in the laboratory requires iron depleted media when MIC values are determined by broth microdilution. Disk diffusion presents good correlation with MIC values. In surveillance studies and in clinical trials it has been demonstrated excellent activity against Gram-negatives, including carbapenemase producers and non-fermenters such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia. Few cefiderocol resistant isolates have been found in surveillance studies. Resistance mechanisms are not directly associated with porin deficiency and or efflux pumps. On the contrary, they are related with gene mutations affecting iron transporters, AmpC mutations in the omega loop and with certain beta-lactamases such us KPC-variants determining also ceftazidime-avibactam resistance, certain infrequent extended-spectrum betalactamases (PER, BEL) and metallo-beta-lactamases (certain NDM variants and SPM enzyme).
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Affiliation(s)
| | | | | | - R Cantón
- Rafael Cantón. Servicio de Microbiología. Hospital Universitario Ramón y Cajal. Carretera de Colmenar Km 91. 28034-Madrid. Spain.
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11
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Gupta V, Yu KC, Pogue JM, Watts JA, Clancy CJ. A Multicenter Comparison of Carbapenem-Nonsusceptible Enterobacterales and Pseudomonas aeruginosa Rates in the US (2016 to 2020): Facility-Reported Rates versus Rates Based on Updated Clinical Laboratory and Standards Institute Breakpoints. Microbiol Spectr 2022; 10:e0115822. [PMID: 35638777 PMCID: PMC9241696 DOI: 10.1128/spectrum.01158-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/06/2022] [Indexed: 12/04/2022] Open
Abstract
Adoption of revised antimicrobial susceptibility breakpoints is often slow, potentially leading to underreporting of antimicrobial resistance. We compared facility-reported rates of carbapenem nonsusceptibility (NS; intermediate or resistant) with NS rates based on current Clinical and Laboratory Standards Institute (CLSI) breakpoints for Enterobacterales or Pseudomonas aeruginosa isolates in ambulatory and inpatient adults in the BD Insights Research Database (US) from 2016 to 2020. Overall, 77.4% (937,926/1,211,845) and 90.6% (2,157,785/2,381,824) of nonduplicate Enterobacterales isolates with facility-reported susceptibility results had MIC data for ertapenem (ETP) and imipenem/meropenem/doripenem (IPM/MEM/DOR), respectively; 86.9% (255,844/294,426) of P. aeruginosa isolates had MIC data for IPM/MEM/DOR. Facility-reported susceptibility and susceptibility based on CLSI criteria resulted in comparable carbapenem susceptibility rates (99.3% versus 99.1% for ETP-susceptible Enterobacterales, 98.9% versus 98.4% for IPM/MEM/DOR-susceptible Enterobacterales, and 84.9% versus 83.3% for IPM/MEM/DOR-susceptible P. aeruginosa). However, compared with CLSI criteria, facilities underreported Enterobacterales- and IPM/MEM/DOR-NS isolates by 18.8% and 26.5%, respectively, and P. aeruginosa IPM/MEM/DOR-NS isolates by 9.8%. Underreporting was observed for both intermediate and resistant isolates. Our data suggest that delayed adoption of revised breakpoints has a small but potentially important impact on reported rates of antimicrobial resistance. Facilities should be aware of local epidemiology, evaluate potential underreporting of resistance, and assess the related clinical impact. IMPORTANCE Clinicians often base antimicrobial therapeutic decisions on laboratory determinations of pathogen susceptibility to an antibiotic based on MIC breakpoints. MIC breakpoints evolve over time based on new information; between 2010 and 2012 the CLSI lowered carbapenem breakpoints for Enterobacterales and Pseudomonas aeruginosa, and these were subsequently adopted by the US Food and Drug Administration. Carbapenems are important therapeutic options for these difficult-to-treat pathogens, so understanding resistance rates is critically important. However, laboratories can be slow to adopt updated breakpoints. We used MIC data to evaluate whether reports received by hospitals for carbapenem susceptibility were consistent with updated CLSI breakpoints. Although overall susceptibility rates were similar between hospital reports and susceptibility based on updated CLSI criteria, the percentages of carbapenem-resistant isolates were significantly underreported by hospital reports. Delayed adoption of MIC breakpoints may impact epidemiological understanding of resistance and contribute to the spread of resistant pathogens.
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Affiliation(s)
- Vikas Gupta
- Becton, Dickinson, and Company, Franklin Lakes, New Jersey, USA
| | - Kalvin C. Yu
- Becton, Dickinson, and Company, Franklin Lakes, New Jersey, USA
| | - Jason M. Pogue
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Janet A. Watts
- Becton, Dickinson, and Company, Franklin Lakes, New Jersey, USA
| | - Cornelius J. Clancy
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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12
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Pierce VM, Mathers AJ. Setting Antimicrobial Susceptibility Testing Breakpoints: A Primer for Pediatric Infectious Diseases Specialists on the Clinical and Laboratory Standards Institute Approach. J Pediatric Infect Dis Soc 2022; 11:73-80. [PMID: 34888640 DOI: 10.1093/jpids/piab106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/22/2021] [Indexed: 01/22/2023]
Abstract
Breakpoints are the values used by clinical microbiology laboratories to interpret the results of antimicrobial susceptibility testing (AST) and classify isolates as susceptible or resistant. Whether the breakpoints applied by laboratories accurately predict the likelihood of successful treatment with a particular antimicrobial is an issue of critical importance to quality clinical care. In the United States, the Food and Drug Administration (FDA) sets breakpoints, and globally, breakpoints are also set by 2 standards development organizations, the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST); individual laboratories may choose which breakpoints to implement. Many CLSI breakpoints are recognized by FDA, facilitating their incorporation into widely used commercial AST devices. The CLSI Subcommittee on AST's consensus approach to establishing (and as needed, revising) breakpoints involves integration of currently available microbiological, pharmacokinetic-pharmacodynamic, and clinical data. Here, an overview of the CLSI process for establishing breakpoints is provided.
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Affiliation(s)
- Virginia M Pierce
- Clinical Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Pediatric Infectious Disease Unit, MassGeneral Hospital for Children, Boston, Massachusetts, USA
| | - Amy J Mathers
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.,Clinical Microbiology Laboratory, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA
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13
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Simner PJ, Rauch CA, Martin IW, Sullivan KV, Rhoads D, Rolf R, She R, Souers RJ, Wojewoda C, Humphries RM. Raising the Bar: Improving Antimicrobial Resistance Detection by Clinical Laboratories by Ensuring Use of Current Breakpoints. Open Forum Infect Dis 2022; 9:ofac007. [PMID: 35146049 PMCID: PMC8826219 DOI: 10.1093/ofid/ofac007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background Antimicrobial resistance (AMR) is a pressing global challenge detected by antimicrobial susceptibility testing (AST) performed by clinical laboratories. AST results are interpreted using clinical breakpoints, which are updated to enable accurate detection of new and emerging AMR. Laboratories that do not apply up-to-date breakpoints impede global efforts to address the AMR crisis, but the extent of this practice is poorly understood. Methods A total of 1490 clinical laboratories participating in a College of American Pathologists proficiency testing survey for bacterial cultures were queried to determine use of obsolete breakpoints. Results Between 37.9% and 70.5% of US laboratories reported using obsolete breakpoints for the antimicrobials that were queried. In contrast, only 17.7%-43.7% of international laboratories reported using obsolete breakpoints (P < .001 for all comparisons). Use of current breakpoints varied by AST system, with more laboratories reporting use of current breakpoints in the US if the system had achieved US Food and Drug Administration clearance with current breakpoints. Among laboratories that indicated use of obsolete breakpoints, 55.9% had no plans to update to current standards. The most common reason cited was manufacturer-related issues (51.3%) and lack of internal resources to perform analytical validation studies to make the update (23.4%). Thirteen percent of laboratories indicated they were unaware of breakpoint changes or the need to update breakpoints. Conclusions These data demonstrate a significant gap in the ability to detect AMR in the US, and to a lesser extent internationally. Improved application of current breakpoints by clinical laboratories will require combined action from regulatory agencies, laboratory accreditation groups, and device manufacturers.
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Affiliation(s)
| | | | | | | | | | - Robin Rolf
- College of American Pathologists, Chicago, Illinois, USA
| | - Rosemary She
- University of Southern California, Los Angeles, California, USA
| | - Rhona J Souers
- College of American Pathologists, Chicago, Illinois, USA
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14
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Jones N, Shah P. Challenges in antimicrobial susceptibility testing interpretation: Fluoroquinolone susceptibility discordance. Am J Health Syst Pharm 2022; 79:829-830. [PMID: 35136918 DOI: 10.1093/ajhp/zxac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.
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Affiliation(s)
- Nathan Jones
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX, USA
| | - Punit Shah
- Department of Pharmacy, Houston Methodist Sugarland Hospital, Sugarland, TX, USA
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15
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Li Q, Chen Z, Xiong H, Li R, Yu C, Meng J, Shi P, Kong X. Novel Partial Exon 51 Deletion in the Duchenne Muscular Dystrophy Gene Identified via Whole Exome Sequencing and Long-Read Whole-Genome Sequencing. Front Genet 2021; 12:762987. [PMID: 34899847 PMCID: PMC8662377 DOI: 10.3389/fgene.2021.762987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD), one of the most common progressive and severely disabling neuromuscular diseases in children, can be largely attributed to the loss of function of the DMD gene on chromosome Xp21.2-p21.1. This paper describes the case of a 10-year-old boy diagnosed with DMD. Whole exome sequencing confirmed the hypothesized large partial exonic deletion of c.7310-11543_7359del (chrX:g.31792260_31803852del) spanning exon 51 and intron 50 in DMD. This large deletion was verified to be de novo by PCR, and the two breakpoints were further confirmed by Sanger sequencing and long-read whole-genome sequencing. Notably, this partial exonic deletion was the only complex variation in the deep intron regions or intron–exon junction regions in DMD. In addition, the case study demonstrates the clinical importance of using multiple molecular genetic testing methods for the diagnosis of rare diseases.
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Affiliation(s)
- Qianqian Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhanni Chen
- Genokon Institute of Medical Science and Laboratory, Xiamen, China
| | - Hui Xiong
- Genokon Institute of Medical Science and Laboratory, Xiamen, China
| | - Ranran Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Chenguang Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Cardio-X Center, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Meng
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Panlai Shi
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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16
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Conrads G, Klomp T, Deng D, Wenzler JS, Braun A, Abdelbary MMH. The Antimicrobial Susceptibility of Porphyromonas gingivalis: Genetic Repertoire, Global Phenotype, and Review of the Literature. Antibiotics (Basel) 2021; 10:1438. [PMID: 34943650 DOI: 10.3390/antibiotics10121438] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
The in vitro antimicrobial susceptibility of 29 strains of the major periodontal pathogen Porphyromonas gingivalis and three P. gulae (as an ancestor) to nine antibiotics (amoxicillin, amoxicillin/clavulanate, clindamycin, metronidazole, moxifloxacin, doxycycline, azithromycin, imipenem, and cefoxitin) was evaluated by E-testing of minimal inhibitory concentration (MIC) according to international standards. The results were compared with 16 international studies reporting MICs from 1993 until recently. In addition, 77 currently available P. gingivalis genomes were screened for antimicrobial resistance genes. E-testing revealed a 100% sensitivity of P. gingivalis and P. gulae to all antibiotics. This was independent of the isolation year (1970 until 2021) or region, including rural areas in Indonesia and Africa. Regarding studies worldwide (675 strains), several method varieties regarding medium, McFarland inoculation standards (0.5-2) and incubation time (48-168 h) were used for MIC-testing. Overall, no resistances have been reported for amoxicillin + clavulanate, cefoxitin, and imipenem. Few strains showed intermediate susceptibility or resistance to amoxicillin and metronidazole, with the latter needing both confirmation and attention. The only antibiotics which might fail in the treatment of P. gingivalis-associated mixed anaerobic infections are clindamycin, macrolides, and tetracyclines, corresponding to the resistance genes erm(B), erm(F), and tet(Q) detected in our study here, as well as fluoroquinolones. Periodical antibiotic susceptibility testing is necessary to determine the efficacy of antimicrobial agents and to optimize antibiotic stewardship.
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17
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Costa D, Granada I, Espinet B, Collado R, Ruiz-Xivillé N, Puiggros A, Uribe M, Arias A, Gómez C, Delgado J, Pereira A, Magnano L, Colomer D, López C, Beà S. Balanced and unbalanced translocations in a multicentric series of 2843 patients with chronic lymphocytic leukemia. Genes Chromosomes Cancer 2021; 61:37-43. [PMID: 34414624 DOI: 10.1002/gcc.22994] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 01/03/2023] Open
Abstract
Chromosomal translocations in chronic lymphocytic leukemia (CLL) are very rare, and therefore systematic analysis of large series of cases is needed to allow the identification of recurrent rearrangements, breakpoints involved, and target genes. The aims of the present study were to identify new translocations and their clinical impact and to establish their frequency in a large cohort of 2843 CLL patients. By conventional cytogenetics 250 translocations were identified in 215 (7.5%) patients, 186 (74%) were apparently balanced and 64 (26%) were unbalanced. All chromosomes were involved in translocations, except Y chromosome. The chromosomes more frequently translocated were in decreasing frequency chromosomes 14, 18, 13, 17, 1, 6, 2, 3, 8, and 11. Translocations were found in the karyotypes either as the unique chromosomal abnormality (27%), associated with another alteration (24%), or as a part of a complex karyotype (CK, 48%). A large proportion of rearranged breakpoints involved genes related to CLL such as IGH (14q32), RB1, MIR15A, MIR16-1 (13q14), BCL2 (18q21), IGL (22q11.2), TP53 (17p13), IRF4 (6p25-p23), ATM (11q22), and CDK6 (7q21). Overall, 76 novel CLL translocations were identified, including a recurrent t(8;11)(p21;q21-23). Whole-genome sequencing and/or copy-number microarray data of 24 cases with translocations confirmed all rearrangements, enabled refinement of 3 karyotypes and all breakpoints at gene level. The projected survival and time to first treatment significantly decreased linearly with the number of translocations. In summary, this study allowed to establish the frequency of translocations (7.5%) and to identify new translocations in a cohort of 2843 CLL patients.
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Affiliation(s)
- Dolors Costa
- Hematopathology Section, Department of Pathology, Hospital Clinic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Isabel Granada
- Hematological Laboratory Service, Germans Trias i Pujol University Hospital, Catalan Institute of Oncology, Josep Carreras Leukaemia Research Institute, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Rosa Collado
- Laboratorio de Citogenética y Biología Molecular, Servicio de Hematología, Consorcio Hospital General Universitario, Valencia, Spain
| | - Neus Ruiz-Xivillé
- Hematological Laboratory Service, Germans Trias i Pujol University Hospital, Catalan Institute of Oncology, Josep Carreras Leukaemia Research Institute, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Anna Puiggros
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Marisol Uribe
- Laboratorio de Citogenética y Biología Molecular, Servicio de Hematología, Consorcio Hospital General Universitario, Valencia, Spain
| | - Amparo Arias
- Hematopathology Section, Department of Pathology, Hospital Clinic, Barcelona, Spain
| | - Cándida Gómez
- Hematopathology Section, Department of Pathology, Hospital Clinic, Barcelona, Spain
| | - Julio Delgado
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - Arturo Pereira
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - Laura Magnano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematology Department, Hospital Clínic, Barcelona, Spain
| | - Dolors Colomer
- Hematopathology Section, Department of Pathology, Hospital Clinic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Sílvia Beà
- Hematopathology Section, Department of Pathology, Hospital Clinic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,University of Barcelona, Barcelona, Spain
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18
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Khan A, Arias CA, Abbott A, Dien Bard J, Bhatti MM, Humphries RM. Evaluation of the Vitek 2, Phoenix, and MicroScan for Antimicrobial Susceptibility Testing of Stenotrophomonas maltophilia. J Clin Microbiol 2021; 59:e0065421. [PMID: 34011524 DOI: 10.1128/JCM.00654-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Stenotrophomonas maltophilia causes high-mortality infections in immunocompromised hosts with limited therapeutic options. Many U.S. laboratories rely on commercial automated antimicrobial susceptibility tests (cASTs) and use CLSI breakpoints (BPs) for S. maltophilia. However, contemporary data on these systems are lacking. We assessed performance of Vitek 2, MicroScan WalkAway, and Phoenix relative to that of reference broth microdilution for trimethoprim-sulfamethoxazole (SXT), levofloxacin (LEV), minocycline (MIN), and ceftazidime (CAZ) with 109 S. maltophilia bloodstream isolates. Using CLSI breakpoints, categorical agreement (CA) was below 90% on all systems and drugs, with the exception of SXT by MicroScan (98.1%) and Phoenix (98.1%) and MIN by MicroScan (100%) and Phoenix (99.1%). For SXT, Vitek 2 yielded a 77.1% CA. LEV and CAZ CA ranged from 67% to 85%. Very major errors (VME) were >3% for SXT (MicroScan, Phoenix), LEV (MicroScan), and CAZ (all systems). Major errors (ME) were >3% for SXT (Vitek 2), LEV (Phoenix), and CAZ (MicroScan, Phoenix). Minor errors were >10% for CAZ and LEV on all systems. Data were analyzed with EUCAST pharmacokinetic/pharmacodynamic CAZ, LEV, ciprofloxacin (CIP), and tigecycline (TGC) breakpoints when possible. CA was <90% for all. VME were >3% for CAZ (all systems), LEV (MicroScan), and TGC (Vitek 2), and ME were >3% for LEV (MicroScan), CAZ (all systems), ciprofloxacin (Vitek 2 and MicroScan), and TGC (Vitek 2, Phoenix). Minor errors (MI) were >10% for all agents and systems, by EUCAST breakpoints with an intermediate category (LEV, CAZ, CIP). Laboratories should use caution with cASTs for S. maltophilia, as a high rate of errors may be observed.
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19
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Rodríguez CH, Nastro M, Vay C, Famiglietti A. In Vitro Activity of Minocycline Against Multidrug-Resistant Acinetobacter baumannii Isolates-Evaluation of Clinical Breakpoints and Review of Literature. Microb Drug Resist 2021; 27:1560-1563. [PMID: 33926231 DOI: 10.1089/mdr.2020.0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Therapeutic options for the treatment of infections by multidrug-resistant Acinetobacter baumannii strains are often limited. Minocycline (MIN) is an old antibiotic, with excellent activity against A. baumannii isolates, which can be administered orally. Currently, there is no single criterion regarding the breakpoints for MIN and A. baumannii. The activity of MIN was examined against a collection of A. baumannii isolates recovered from 15 hospitals of 6 countries of South America. A review of the literature was also performed. In our series and most of the studies, the percentages of MIN susceptible isolates exceeded 50%, regardless of the breakpoints utilized (4-2 or 1 μg/mL). However, a greater number of isolates not harboring Tet B were considered resistant with the breakpoints of 1 or 2 μg/mL, whereas isolates with tet(B) genes were still detected with minimum inhibitory concentration below all breakpoints considered. Tetracycline susceptibility may be used as a screening to discriminate the populations with and without acquired resistance mechanisms to MIN. In this study, MIN-resistant subpopulations were found in isolates harboring Tet B, with MIC ≤1 μg/mL, and their frequency increased after incubation with MIN. These subpopulations were not detected in isolates not harboring Tet B. The clinical correlation of these subpopulations should be evaluated in future studies.
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Affiliation(s)
- Carlos Hernán Rodríguez
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, INFIBIOC, UBA, Buenos Aires, Argentina
| | - Marcela Nastro
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, INFIBIOC, UBA, Buenos Aires, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, INFIBIOC, UBA, Buenos Aires, Argentina
| | - Angela Famiglietti
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, INFIBIOC, UBA, Buenos Aires, Argentina
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20
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Beredaki MI, Arendrup MC, Andes D, Mouton JW, Meletiadis J. The Role of New Posaconazole Formulations in the Treatment of Candida albicans Infections: Data from an In Vitro Pharmacokinetic-Pharmacodynamic Model. Antimicrob Agents Chemother 2021; 65:e01292-20. [PMID: 33468486 DOI: 10.1128/AAC.01292-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022] Open
Abstract
Posaconazole is more active than fluconazole against Candida albicans in vitro and is approved for the treatment of oropharyngeal candidiasis but not for that of invasive candidiasis (IC). Here, we explored the efficacy of posaconazole against C. albicans in an in vitro pharmacokinetic/pharmacodynamic (PK/PD) model of IC and determined the probability of pharmacodynamic target attainment for the oral solution and intravenous (i.v.)/tablet formulations. Three clinical C. albicans isolates (posaconazole MICs, 0.008 to 0.25 mg/liter) were studied in the in vitro PK/PD dilution model simulating steady-state posaconazole PK. The in vitro exposure-effect relationship, area under the 24-h free drug concentration curve (fAUC0-24)/MIC, was described and compared with in vivo outcome in animals with IC. PK/PD susceptibility breakpoints and trough levels required for optimal treatment were determined for EUCAST and CLSI 24-h/48-h (CLSI24h/CLSI48h) methods using the fAUC0-24/MIC associated with half-maximal activity (EI50) and Monte Carlo simulation analysis for oral solution (400 mg every 12 hours [q12h]) and i.v./tablet formulations (300 mg q24h). The in vitro mean (95% confidence interval [CI]) EI50 was 330 (183 to 597) fAUC0-24/MIC for CLSI24h and 169 (92 to 310) for EUCAST/CLSI48h methods, which are close to the near-stasis in vivo effect. The probability of target attainment for EI50 was estimated; for the wild-type isolates (MIC ≤ 0.06 mg/liter), it was low for the oral solution and higher than 95% for the i.v./tablet formulations for the EUCAST/CLSI48h methods but not for the CLSI 24-h method. Non-wild-type isolates with EUCAST/CLSI48h MICs of 0.125 and 0.25 mg/liter would require trough levels of >1.2 and >2.4 mg/liter, respectively. Posaconazole i.v./tablet formulations may have a role in the therapy of invasive infections by wild-type C. albicans isolates, provided that a steady state is reached quickly. A PK/PD susceptibility breakpoint at the epidemiological cutoff (ECV/ECOFF) of 0.06 mg/liter was determined.
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Guo J, Shi C, Chen X, Wang O, Liu P, Yang H, Xu X, Zhang W, Zhu H. stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads. Front Genet 2021; 12:636239. [PMID: 33815469 PMCID: PMC8012683 DOI: 10.3389/fgene.2021.636239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 11/13/2022] Open
Abstract
Co-barcoded reads originating from long DNA fragments (mean length >30 kbp) maintain both single base level accuracy and long-range genomic information. We propose a pipeline, stLFRsv, to detect structural variation using co-barcoded reads. stLFRsv identifies abnormal large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structural variants (SVs). Haplotype phasing by co-barcoded reads increases the signal to noise ratio, and barcode sharing profiles are used to filter out false positives. We integrate the short read SV caller smoove for smaller variants with stLFRsv. The integrated pipeline was evaluated on the well-characterized genome HG002/NA24385, and 74.5% precision and a 22.4% recall rate were obtained for deletions. stLFRsv revealed some large variants not included in the benchmark set that were verified by long reads or assembly. For the HG001/NA12878 genome, stLFRsv also achieved the best performance for both resource usage and the detection of large variants. Our work indicates that co-barcoded read technology has the potential to improve genome completeness.
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Affiliation(s)
- Junfu Guo
- BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Chang Shi
- BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xi Chen
- BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Ou Wang
- BGI-Shenzhen, Shenzhen, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
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22
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Kersh EN, Allen V, Ransom E, Schmerer M, Cyr S, Workowski K, Weinstock H, Patel J, Ferraro MJ. Rationale for a Neisseria gonorrhoeae Susceptible-only Interpretive Breakpoint for Azithromycin. Clin Infect Dis 2021; 70:798-804. [PMID: 30963175 DOI: 10.1093/cid/ciz292] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/04/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Azithromycin (AZI) is recommended with ceftriaxone (CRO) for treatment of uncomplicated gonococcal urethritis and cervicitis in the United States, and an AZI-susceptibility breakpoint is needed. Neither the Food and Drug Administration (FDA) nor the Clinical and Laboratory Standards Institute (CLSI) has set interpretive breakpoints for AZI susceptibility. As a result, AZI antimicrobial susceptibility testing (AST) cannot be interpreted using recognized standards. This has contributed to increasingly unavailable clinical laboratory AST, although gonorrhea is on the rise with >550 000 US gonorrhea cases reported to the Centers for Disease Control and Prevention in 2017, the highest number of cases since 1991. METHODS This article summarizes the rationale data reviewed by the CLSI in June 2018. RESULTS The CLSI decided to set a susceptible-only interpretive breakpoint at the minimum inhibitory concentration of ≤1 µg/mL. This is also the epidemiological cutoff value (ECV) (ie, the end of the wild-type susceptibility distribution). This breakpoint presumes that AZI (1-g single dose) is used in an approved regimen that includes an additional antimicrobial agent (ie, CRO 250 mg, intramuscular single dose). CONCLUSIONS Having a breakpoint can improve patient care and surveillance and allow future development and FDA regulatory approval of modernized AST to guide treatment. The breakpoint coincides with a European Committee on AST decision to remove previously established, differing AZI breakpoints and use the ECV as guidance for testing. The CLSI breakpoint is now the recognized standard that defines AZI susceptibility for gonococcal infections.
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Affiliation(s)
- Ellen N Kersh
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Eric Ransom
- Association of Public Health Laboratories, Silver Spring, Maryland
| | - Matthew Schmerer
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sancta Cyr
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kim Workowski
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia.,Emory University, Department of Medicine, Atlanta, Georgia
| | - Hillard Weinstock
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jean Patel
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mary Jane Ferraro
- Department of Medicine, Harvard Medical School, Boston.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston
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23
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Satlin MJ, Nicolau DP, Humphries RM, Kuti JL, Campeau SA, Lewis Ii JS, Weinstein MP, Jorgensen JH. Development of Daptomycin Susceptibility Breakpoints for Enterococcus faecium and Revision of the Breakpoints for Other Enterococcal Species by the Clinical and Laboratory Standards Institute. Clin Infect Dis 2021; 70:1240-1246. [PMID: 31504338 DOI: 10.1093/cid/ciz845] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/22/2019] [Indexed: 12/16/2022] Open
Abstract
Daptomycin is one of the few treatment options for infections caused by enterococci that are resistant to ampicillin and vancomycin, such as vancomycin-resistant Enterococcus faecium. The emergence and clinical significance of daptomycin-resistant enterococci and evolving microbiologic, pharmacokinetic-pharmacodynamic, and clinical data indicated that the pre-2019 Clinical and Laboratory Standards Institute (CLSI) susceptible-only breakpoint of ≤4 μg/mL for daptomycin and enterococci was no longer appropriate. After analyzing data that are outlined in this article, the CLSI Subcommittee on Antimicrobial Susceptibility Testing established new breakpoints for daptomycin and enterococci. For E. faecium, a susceptible dose-dependent (SDD) breakpoint of ≤4 μg/mL was established based on an increased dosage of 8-12 mg/kg/day (≥8 μg/mL-resistant). CLSI suggests infectious diseases consultation to guide daptomycin use for the SDD category. For Enterococcus faecalis and other enterococcal species, revised breakpoints of ≤2 μg/mL-susceptible, 4 μg/mL-intermediate, and ≥8 μg/mL-resistant were established based on a standard dosage of 6 mg/kg/day.
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Affiliation(s)
- Michael J Satlin
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York
| | - David P Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Connecticut
| | | | - Joseph L Kuti
- Center for Anti-Infective Research and Development, Hartford Hospital, Connecticut
| | | | - James S Lewis Ii
- Department of Pharmacy, Oregon Health and Science University, Portland
| | - Melvin P Weinstein
- Departments of Medicine and Pathology and Laboratory Medicine Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - James H Jorgensen
- Department of Pathology, University of Texas Health Sciences Center at San Antonio
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24
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Rafalskiy VV, Kriukova NO, Korenev DS. [Resistance of pathogens of community-acquired urinary tract infections: lessons from Russian multicenter microbiological studies. Part II]. Urologiia 2020:116-120. [PMID: 33185358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The choice of antimicrobials for the treatment of urinary tract infections (UTIs) is determined by many factors, however, at present, population antibiotic resistance of uropathogens is used as one of the most important criteria. At the same time, there are cases when the clinical efficacy of an antimicrobial drug does not correlate with in vitro activity, in particular, such discordance was found for fosfomycin trometamol. Comparison of data from microbiological studies of UTI pathogens performed at different times is of great practical and scientific interest. At the same time, such comparisons have limitations, such as the use of different criteria for interpreting the sensitivity of microorganisms, the peculiarities of the formation of the studied patient population, and collection of strains in different geographical areas. Therefore, for all the seeming simplicity and clarity of the data on the sensitivity of uropathogens, their use to substantiate rational antimicrobial therapy is associated with numerous nuances that can significantly distort their objective assessment. In this connection, it is important to conduct not only microbiological, but also clinical studies to obtain data on the comparative effectiveness of the antimicrobials used.
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Affiliation(s)
- V V Rafalskiy
- Medical Institute Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - N O Kriukova
- Medical Institute Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - D S Korenev
- Medical Institute Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
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25
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Rafalskiy VV, Kriukova NO, Korenev DS. [Resistance of pathogens of community-acquired urinary tract infections: lessons from russian multicenter microbiological studies]. Urologiia 2020:124-130. [PMID: 32897026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The review describes large-scale microbiological studies performed in Russia over the past 20 years to study urinary tract infections (UTIs). The article analyzes data on the structure of UTI pathogens, as well as on the antibiotic resistance of the main uropathogens, compares the data with similar foreign studies. From 1999 year, 7 large multicenter microbiological studies were carried out in Russia to obtain the data of the antimicrobial resistance of uropathogens caused community-acquired UTIs. An analysis of the data allows described trends in antimicrobial resistance - high level of resistance of uropathogens to aminopenicillins, co-trimoxazole, fluoroquinolones, an increase antimicrobial resistance to amoxicillin / clavulanate, and third generation cephalosporins. In review discussed a critical assessment of various approaches to the use of data on the sensitivity of uropathogens to antimicrobial drugs when antimicrobial therapy is provided. The necessity of comparing not only microbiological data obtained from different sources, but also clinical data, characteristics of pharmacodynamics and pharmacokinetics of antimicrobial drugs is discussed. The review discusses the difficulties associated with the clinical interpretation of data on the sensitivity of microorganisms, primarily in the limited objective information describing the correlation of in vitro data with the clinical efficacy of therapy. The publication substantiates the need for a wider conduct of not only microbiological, but also clinical studies to obtain data on the comparative efficacy of the used antimicrobial drugs.
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Affiliation(s)
- V V Rafalskiy
- Medical Institute Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - N O Kriukova
- Medical Institute Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - D S Korenev
- Medical Institute Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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26
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Fissel JA, Yarbrough ML, Tekle T, Burnham CA, Simner PJ. Reporting Considerations for Cefepime-Susceptible and -Susceptible-Dose Dependent Results for Carbapenemase-Producing Enterobacterales. J Clin Microbiol 2020; 58:e01271-20. [PMID: 32641398 DOI: 10.1128/JCM.01271-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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27
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Furo IDO, Kretschmer R, O'Brien PC, Pereira JC, Garnero ADV, Gunski RJ, O'Connor RE, Griffin DK, Gomes AJB, Ferguson-Smith MA, de Oliveira EHC. Chromosomal Evolution in the Phylogenetic Context: A Remarkable Karyotype Reorganization in Neotropical Parrot Myiopsitta monachus (Psittacidae). Front Genet 2020; 11:721. [PMID: 32754200 PMCID: PMC7366516 DOI: 10.3389/fgene.2020.00721] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Myiopsitta monachus is a small Neotropical parrot (Psittaciformes: Arini Tribe) from subtropical and temperate regions of South America. It has a diploid chromosome number 2n = 48, different from other members of the Arini Tribe that have usually 70 chromosomes. The species has the lowest 2n within the Arini Tribe. In this study, we combined comparative chromosome painting with probes generated from chromosomes of Gallus gallus and Leucopternis albicollis, and FISH with bacterial artificial chromosomes (BACs) selected from the genome library of G. gallus with the aim to shed light on the dynamics of genome reorganization in M. monachus in the phylogenetic context. The homology maps showed a great number of fissions in macrochromosomes, and many fusions between microchromosomes and fragments of macrochromosomes. Our phylogenetic analysis by Maximum Parsimony agree with molecular data, placing M. monachus in a basal position within the Arini Tribe, together with Amazona aestiva (short tailed species). In M. monachus many chromosome rearrangements were found to represent autopomorphic characters, indicating that after this species split as an independent branch, an intensive karyotype reorganization took place. In addition, our results show that M. monachus probes generated by flow cytometry provide novel cytogenetic tools for the detection of avian chromosome rearrangements, since this species presents breakpoints that have not been described in other species.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Cultura de Tecidos e Citogenética, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Brazil.,Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Rafael Kretschmer
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Patricia Caroline O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Jorge C Pereira
- Animal and Veterinary Research Centre (CEVAV), University of Tràs-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | | | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, Brazil
| | | | | | | | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Edivaldo Herculano Correa de Oliveira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Cultura de Tecidos e Citogenética, Seção de Meio Ambiente, Instituto Evandro Chagas, Ananindeua, Brazil.,Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
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28
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Pang H, Yu X, Kim YM, Wang X, Jinkins JK, Yin J, Li S, Gu H. Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1. Front Genet 2020; 11:577. [PMID: 32655619 PMCID: PMC7325322 DOI: 10.3389/fgene.2020.00577] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023] Open
Abstract
The subchromosomal region 1q21.1 is one of the hotspots in the human genome for deletions and reciprocal duplications, owing to the existence of hundreds of segmental duplications. Recurrent deletions and duplications in this region are thought to be causative in patients with variable clinical manifestations. Based on the genomic locations, deletions and duplications at the 1q21.1 locus have been associated with distinguishable syndromes: chromosome 1q21.1 deletion syndrome, chromosome 1q21.1 duplication syndrome, and thrombocytopenia-absent radius (TAR) syndrome, which is partially due to deletions at the proximal 1q21.1 region. We report here diverse, recurrent deletions and duplications at the 1q21.1 locus in 36 patients from a cohort of 5,200 individuals. Among the 36 patients, 18 patients carry 1q21.1 deletions, nine individuals have reciprocal duplications at 1q21.1, two patients share an identical short deletion, and the remaining seven possess variable sizes of duplications at the proximal 1q21.1 region. Furthermore, we provide cytogenetic characterization and detailed clinical features for each patient. Notably, duplications at the proximal 1q21.1 region have not been associated with a defined disorder in publications. However, recurrent duplications at the proximal 1q21.1 region among the seven patients strongly suggested that the variants are likely pathogenic. The common phenotypical features of those disorders are also summarized to facilitate clinical diagnoses and genetic counseling.
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Affiliation(s)
- Hui Pang
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Xiaowei Yu
- The First Affiliated Hospital of Jilin University, Changchun, China
| | - Young Mi Kim
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Xianfu Wang
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Jeremy K Jinkins
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Jianing Yin
- The First Affiliated Hospital of Jilin University, Changchun, China
| | - Shibo Li
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Hongcang Gu
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
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29
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Prada JM, Davis EL, Touloupou P, Stolk WA, Kontoroupis P, Smith ME, Sharma S, Michael E, de Vlas SJ, Hollingsworth TD. Elimination or Resurgence: Modelling Lymphatic Filariasis After Reaching the 1% Microfilaremia Prevalence Threshold. J Infect Dis 2020; 221:S503-S509. [PMID: 31853554 PMCID: PMC7289550 DOI: 10.1093/infdis/jiz647] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The low prevalence levels associated with lymphatic filariasis elimination pose a challenge for effective disease surveillance. As more countries achieve the World Health Organization criteria for halting mass treatment and move on to surveillance, there is increasing reliance on the utility of transmission assessment surveys (TAS) to measure success. However, the long-term disease outcomes after passing TAS are largely untested. Using 3 well-established mathematical models, we show that low-level prevalence can be maintained for a long period after halting mass treatment and that true elimination (0% prevalence) is usually slow to achieve. The risk of resurgence after achieving current targets is low and is hard to predict using just current prevalence. Although resurgence is often quick (<5 years), it can still occur outside of the currently recommended postintervention surveillance period of 4-6 years. Our results highlight the need for ongoing and enhanced postintervention monitoring, beyond the scope of TAS, to ensure sustained success.
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Affiliation(s)
- Joaquin M Prada
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Emma L Davis
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, Mathematics Institute and School of Life Sciences, University of Warwick, Coventry, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Headington, Oxford, UK
| | | | - Wilma A Stolk
- Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Periklis Kontoroupis
- Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Morgan E Smith
- Department of Biological Sciences, University of Notre Dame, South Bend, Indiana, USA
| | - Swarnali Sharma
- Department of Biological Sciences, University of Notre Dame, South Bend, Indiana, USA
| | - Edwin Michael
- Department of Biological Sciences, University of Notre Dame, South Bend, Indiana, USA
| | - Sake J de Vlas
- Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - T Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Headington, Oxford, UK
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30
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Beredaki MI, Georgiou PC, Siopi M, Kanioura L, Andes D, Arendrup MC, Mouton JW, Meletiadis J. Toward Harmonization of Voriconazole CLSI and EUCAST Breakpoints for Candida albicans Using a Validated In Vitro Pharmacokinetic/Pharmacodynamic Model. Antimicrob Agents Chemother 2020; 64:e00170-20. [PMID: 32229492 DOI: 10.1128/AAC.00170-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/26/2020] [Indexed: 12/29/2022] Open
Abstract
CLSI and EUCAST susceptibility breakpoints for voriconazole and Candida albicans differ by one dilution (≤0.125 and ≤0.06 mg/liter, respectively) whereas the epidemiological cutoff values for EUCAST (ECOFF) and CLSI (ECV) are the same (0.03 mg/liter). We therefore determined the pharmacokinetic/pharmacodynamic (PK/PD) breakpoints of voriconazole against C. albicans for both methodologies with an in vitro PK/PD model, which was validated using existing animal PK/PD data. Four clinical wild-type and non-wild-type C. albicans isolates (voriconazole MICs, 0.008 to 0.125 mg/liter) were tested in an in vitro PK/PD model. For validation purposes, mouse PK were simulated and in vitro PD were compared with in vivo outcomes. Human PK were simulated, and the exposure-effect relationship area under the concentration-time curve for the free, unbound fraction of a drug from 0 to 24 h (fAUC0-24)/MIC was described for EUCAST and CLSI 24/48-h methods. PK/PD breakpoints were determined using the fAUC0-24/MIC associated with half-maximal activity (EI50) and Monte Carlo simulation analysis. The in vitro 24-h PD EI50 values of voriconazole against C. albicans were 2.5 to 5 (1.5 to 17) fAUC/MIC. However, the 72-h PD were higher at 133 (51 to 347) fAUC/MIC for EUCAST and 94 (35 to 252) fAUC/MIC for CLSI. The mean (95% confidence interval) probability of target attainment (PTA) was 100% (95 to 100%), 97% (72 to 100%), 83% (35 to 99%), and 49% (8 to 91%) for EUCAST and 100% (97 to 100%), 99% (85 to 100%), 91% (52 to 100%), and 68% (17 to 96%) for CLSI for MICs of 0.03, 0.06, 0.125, and 0.25 mg/liter, respectively. Significantly, >95% PTA values were found for EUCAST/CLSI MICs of ≤0.03 mg/liter. For MICs of 0.06 to 0.125 mg/liter, trough levels 1 to 4 mg/liter would be required to attain the PK/PD target. A PK/PD breakpoint of C. albicans voriconazole at the ECOFF/ECV of 0.03 mg/liter was determined for both the EUCAST and CLSI methods, indicating the need for breakpoint harmonization for the reference methodologies.
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Abstract
Although not as ubiquitous as antibacterial susceptibility testing, antifungal susceptibility testing (AFST) is a tool of increasing importance in clinical microbiology laboratories. The goal of AFST is to reliably produce MIC values that may be used to guide patient therapy, inform epidemiological studies, and track rates of antifungal drug resistance. There are three methods that have been standardized by standards development organizations: broth dilution, disk diffusion, and azole agar screening for Aspergillus Other commonly used methods include gradient diffusion and the use of rapid automated instruments. Novel methodologies for susceptibility testing are in development. It is important for laboratories to consider not only the method of testing but also the interpretation (or lack thereof) of in vitro data.
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32
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Pogue JM, Jones RN, Bradley JS, Andes DR, Bhavnani SM, Drusano GL, Dudley MN, Flamm RK, Rodvold KA, Ambrose PG. Polymyxin Susceptibility Testing and Interpretive Breakpoints: Recommendations from the United States Committee on Antimicrobial Susceptibility Testing (USCAST). Antimicrob Agents Chemother 2020; 64:e01495-19. [PMID: 31767718 DOI: 10.1128/AAC.01495-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The polymyxins are important agents for carbapenem-resistant Gram-negative bacilli. The United States Committee on Antimicrobial Susceptibility Testing breakpoint recommendations for colistin and polymyxin B are that isolates of Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae are considered susceptible at MIC values of ≤2 mg/liter. These recommendations are contingent upon dosing and testing strategies that are described in this commentary. Importantly, these recommendations are not applicable to lower respiratory tract infections, for which we recommend no breakpoints. Furthermore, there is no breakpoint recommendation for polymyxin B for lower urinary tract infections.
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Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
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Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
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Nielsen LE, Forrester JB, Girotto JE, Dassner AM, Humphries R. One Size Fits All? Application of Susceptible-Dose-Dependent Breakpoints to Pediatric Patients and Laboratory Reporting. J Clin Microbiol 2019; 58:e01446-19. [PMID: 31666359 DOI: 10.1128/JCM.01446-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Clinical and Laboratory Standards Institute antimicrobial and antifungal standards define a susceptible-dose-dependent (SDD) category for certain organisms and drug combinations. Reporting MICs within the SDD category suggests that treatment success is likely with increased drug exposure. These breakpoints are based on pharmacokinetic, pharmacodynamic, and clinical outcome data from adults and not pediatric patients. This commentary aims to discuss the implications of reporting SDD interpretations for pediatric patients and recommends laboratory reporting comments.
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Ling C, Dai Y, Fang L, Yao F, Liu Z, Qiu Z, Cui L, Xia F, Zhao C, Zhang S, Wang K, Zhang X. Exonic rearrangements in DMD in Chinese Han individuals affected with Duchenne and Becker muscular dystrophies. Hum Mutat 2019; 41:668-677. [PMID: 31705731 PMCID: PMC7028077 DOI: 10.1002/humu.23953] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 01/12/2023]
Abstract
Exonic deletions and duplications within DMD are the main pathogenic variants in Duchenne and Becker muscular dystrophies (DMD/BMD). However, few studies have profiled the flanking sequences of breakpoints and the potential mechanism underlying the breakpoints in different fragile regions of DMD. In this study, 896 Chinese male probands afflicted with DMD/BMD were selected from unrelated families and analyzed using multiplex ligation‐dependent probe amplification of the DMD gene, in which we identified exon deletions in 784 subjects and duplications in 112 subjects. Deletions occurred most frequently in the genomic region encompassing exons 45–55, accounting for 73% of all deletion patterns. Furthermore, to unravel the potential mechanism that induced breaks, DMD gene capture and sequencing were performed to identify the breakpoints in 37 subjects with deletions encompassing exons 45–55 of DMD; we found that DMD instability did not arise from a single cause; instead, long‐sequence motifs, nonconsensus microhomologies, low‐copy repeats, and microindels were embedded around the breakpoints, which may predispose DMD to instability. In summary, this study highlights the heterogeneous characteristics of the flanking sequences around the breakpoints and helps us to understand the mechanism underlying DMD gene instability.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Fang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fengxia Yao
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhe Liu
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhengqing Qiu
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chen Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kai Wang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xue Zhang
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, McKusick-Zhang Center for GeneticMedicine, School of Basic Medicine Peking, Union Medical College, Beijing, China
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McAuliffe GN, Smith M, Cooper G, Forster RF, Roberts SA. Variability in Azithromycin Susceptibility Results for Neisseria gonorrhoeae Obtained Using Gradient MIC Strip and Agar Dilution Techniques. J Clin Microbiol 2019; 57:e01353-19. [PMID: 31578264 DOI: 10.1128/JCM.01353-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/29/2019] [Indexed: 12/29/2022] Open
Abstract
Azithromycin is a component of empirical treatment regimens for Neisseria gonorrhoeae infections, but antimicrobial susceptibility testing for this agent is technically challenging. We compared the intertest variability, MIC values, and CLSI/EUCAST categorization of clinical and reference isolates of N. gonorrhoeae treated with azithromycin by testing 107 clinical isolates and nine reference isolates by agar dilution and in duplicates using MIC test strips (Liofilchem, Italy) and Etests (bioMérieux, France). Replicate isolate agreement within 1 log2 between duplicate tests was 87% for MIC test strips and 100% for Etests (P < 0.001). Essential agreement with the agar dilution method was higher for Etests (91%) than for MIC test strips (44%, P < 0.001). The geometric mean MIC was highest for MIC test strips (0.8 mg/liter) and significantly higher than both Etest (0.47 mg/liter, P < 0.001) and agar dilution (0.26 mg/liter, P < 0.001) methods. Etest MICs were higher than those obtained with agar dilution (P < 0.001). Agar dilution, MIC test strip, and Etest methods categorized 96%, 85%, and 95% (P = 0.003) of clinical isolates, respectively, as susceptible/wild type according to CLSI/EUCAST criteria. Our results illustrate the difficulties underlying azithromycin susceptibility testing for N. gonorrhoeae and demonstrate that results can vary using different methods. This variability could influence antimicrobial resistance reporting between laboratories involved in N. gonorrhoeae surveillance programs.
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Bertold M, Manuela B, Inge D, Sebastien L, Lorène MJ, Charly G, Miguel PE, Hamada A, Han A, Matteo C. Detecting the onset of autumn leaf senescence in deciduous forest trees of the temperate zone. New Phytol 2019; 224:166-176. [PMID: 31209882 PMCID: PMC6713559 DOI: 10.1111/nph.15991] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/31/2019] [Indexed: 05/26/2023]
Abstract
Information on the onset of leaf senescence in temperate deciduous trees and comparisons on its assessment methods are limited, hampering our understanding of autumn dynamics. We compare five field proxies, five remote sensing proxies and two data analysis approaches to assess leaf senescence onset at one main beech stand, two stands of oak and birch, and three ancillary stands of the same species in Belgium during 2017 and 2018. Across species and sites, onset of leaf senescence was not significantly different for the field proxies based on Chl leaf content and canopy coloration, except for an advanced canopy coloration during the extremely dry and warm 2018. Two remote sensing indices provided results fully consistent with the field data. A significant lag emerged between leaf senescence onset and leaf fall, and when a threshold of 50% change in the seasonal variable under study (e.g. Chl content) was used to derive the leaf senescence onset. Our results provide unprecedented information on the quality and applicability of different proxies to assess leaf senescence onset in temperate deciduous trees. In addition, a sound base is offered to select the most suited methods for the different disciplines that need this type of data.
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Affiliation(s)
- Mariën Bertold
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
| | - Balzarolo Manuela
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Dox Inge
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
| | - Leys Sebastien
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
| | - Marchand J. Lorène
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
- UMR 6553 ECOBIO (Ecosystèmes, Biodiversité, Evolution), Université de Rennes 1, CNRS, Av du Général Leclerc, 35042 Rennes, France
| | - Geron Charly
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
- Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Portillo-Estrada Miguel
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
| | - AbdElgawad Hamada
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Asard Han
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
| | - Campioli Matteo
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2160 Wilrijk, Belgium
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Khan A, Rivas LM, Spencer M, Martinez R, Lam M, Rojas P, Porte L, Silva F, Braun S, Valdivieso F, Mv Lhauser M, Lafourcade M, Miller WR, García P, Arias CA, Munita JM. A Multicenter Study To Evaluate Ceftaroline Breakpoints: Performance in an Area with High Prevalence of Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Lineage. J Clin Microbiol 2019; 57:e00798-19. [PMID: 31315958 PMCID: PMC6711923 DOI: 10.1128/jcm.00798-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/04/2019] [Indexed: 12/12/2022] Open
Abstract
Ceftaroline (CPT) is a broad-spectrum agent with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). The sequence type 5 (ST5) Chilean-Cordobés clone, associated with CPT nonsusceptibility, is dominant in Chile, a region with high rates of MRSA infections. Here, we assessed the in vitro activity of CPT against a collection of MRSA isolates collected between 1999 and 2018 from nine hospitals (n = 320) and community settings (n = 41) in Santiago, Chile, and evaluated performance across testing methodologies. We found that our hospital-associated isolates exhibited higher CPT MIC distributions (MIC50 and MIC90 of 2 mg/liter) than the community isolates (MIC50 and MIC90 of 0.5 mg/liter), a finding that was consistent across time and independent of the culture source. High proportions (64%) of isolates were CPT nonsusceptible despite the absence of CPT use in Chile. Across methodologies, the Etest underestimated the MIC relative to the gold standard broth microdilution (BMD) test (MIC50 and MIC90 of 1 and 1.5 mg/liter, respectively). There was low (∼51%) categorical agreement (CA) between Etest and BMD results across CLSI and EUCAST breakpoints. The recent revision of CLSI guidelines abolished "very major error" (VME) from the previous guidelines (81%), which perform similarly to the EUCAST guidelines. The level of concordance between CLSI and EUCAST for BMD testing and Etest was >95%. Disk diffusion performed poorly relative to BMD under CLSI (CA, 55%) and EUCAST (CA, 36%) guidelines. Comparison of EUCAST to CLSI for disk diffusion (with EUCAST used as the reference) showed low agreement (CA, 25%; VME, 70%). In summary, CPT-nonsusceptible MRSA are dominant in clinical settings in Chile. Our results provide data to support the reevaluation of CPT breakpoints and to improve agreement across methodologies and agencies.
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Affiliation(s)
- Ayesha Khan
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
- MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Lina M Rivas
- Genomics and Resistant Microbes Group, Facultad de Medicina-Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
| | - Maria Spencer
- Genomics and Resistant Microbes Group, Facultad de Medicina-Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
| | - Rodrigo Martinez
- Genomics and Resistant Microbes Group, Facultad de Medicina-Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
| | - Marusella Lam
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Lorena Porte
- Genomics and Resistant Microbes Group, Facultad de Medicina-Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
| | | | | | | | | | | | - William R Miller
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
| | - Patricia García
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cesar A Arias
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
- Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, Texas, USA
| | - Jose M Munita
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
- Genomics and Resistant Microbes Group, Facultad de Medicina-Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Millennium Science Initiative, Santiago, Chile
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Humphries RM, Abbott AN, Hindler JA. Understanding and Addressing CLSI Breakpoint Revisions: a Primer for Clinical Laboratories. J Clin Microbiol 2019; 57:e00203-19. [PMID: 30971460 DOI: 10.1128/JCM.00203-19] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Clinical and Laboratory Standards Institute (CLSI) has revised several breakpoints since 2010 for bacteria that grow aerobically. In 2019, these revisions include changes to the ciprofloxacin and levofloxacin breakpoints for the Enterobacteriaceae and Pseudomonas aeruginosa, daptomycin breakpoints for Enterococcus spp., and ceftaroline breakpoints for Staphylococcus aureus Implementation of the revisions is a challenge for all laboratories, as not all systems have FDA clearance for the revised (current) breakpoints, compounded by the need for laboratories to perform validation studies and to make updates to laboratory information system/electronic medical record builds in the setting of limited information technology infrastructure. This minireview describes the breakpoint revisions in the M100 supplement since 2010 and strategies for the laboratory on how to best adopt these in clinical testing.
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Abstract
Pedogenic thresholds describe where soil properties or processes change in an abrupt/nonlinear fashion in response to small changes in environmental forcing. Contrastingly, soil process domains refer to the space between thresholds where soil properties are either unchanged, or change gradually, across a broad range of environmental forcing. Here, we test quantitatively for the presence of thresholds in patterns of soil properties across a climatic gradient on soils developed from ~20 ky old basaltic substrate on the Island of Hawai'i. From multiple soil properties, we quantitatively identified a threshold at ~750 mm/y of water balance (precipitation minus potential evapotranspiration), delineating the upper water balance boundary of soil fertility in these soils. From the threshold in the ratio of exchangeable Ca to total Ca we identified the lower water balance boundary of soil fertility in these soils at -1000 mm/y, however this threshold was qualitatively described as it lies near the limit of the climate gradient data where the statistical approach can not be applied. These two results represent the first time that pedogenic thresholds have been identified using statistically rigorous methods and the limitations of said methods, respectively. Comparing the 20 ky soils to soils that developed on basaltic substrates of 1.2 ky, 7.5 ky, 150 ky, and 4100 ky in a time-climate matrix, we found that our quantitative analysis supports previous qualitatively identified thresholds in the soils developed from older substrates. We also identified the 20 ky as the transition from kinetic to supply limitation for plant nutrients in soil in this system.
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Affiliation(s)
- Jesse Bloom Bateman
- Department of Earth System Science, Stanford University, Stanford, CA 94305.,Institute of the Environment and Sustainability, University of California, Los Angeles, CA
| | - Oliver A Chadwick
- Department of Geography, University of California, Santa Barbara, CA
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Das S, Li J, Riccobene T, Carrothers TJ, Newell P, Melnick D, Critchley IA, Stone GG, Nichols WW. Dose Selection and Validation for Ceftazidime-Avibactam in Adults with Complicated Intra-abdominal Infections, Complicated Urinary Tract Infections, and Nosocomial Pneumonia. Antimicrob Agents Chemother 2019; 63:e02187-18. [PMID: 30670413 DOI: 10.1128/AAC.02187-18] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Avibactam is a non-β-lactam β-lactamase inhibitor that has been approved in combination with ceftazidime for the treatment of complicated intra-abdominal infections, complicated urinary tract infections, and nosocomial pneumonia, including ventilator-associated pneumonia. In Europe, ceftazidime-avibactam is also approved for the treatment of Gram-negative infections with limited treatment options. Selection and validation of the ceftazidime-avibactam dosage regimen was guided by an iterative process of population pharmacokinetic (PK) modelling, whereby population PK models for ceftazidime and avibactam were developed using PK data from clinical trials and updated periodically. These models were used in probability of target attainment (PTA) simulations using joint pharmacodynamic (PD) targets for ceftazidime and avibactam derived from preclinical data. Joint PTA was calculated based on the simultaneous achievement of the individual PK/PD targets (50% free time above the ceftazidime-avibactam MIC for ceftazidime and free time above a critical avibactam threshold concentration of 1 mg/liter for avibactam). The joint PTA analyses supported a ceftazidime-avibactam dosage regimen of 2,000 + 500 mg every 8 h by 2-h intravenous infusion for patients with creatinine clearance (CLCR) >50 ml/min across all approved indications and modified dosage regimens for patients with CLCR ≤50 ml/min. Subgroup simulations for individual phase 3 patients showed that the dosage regimen was robust, with high target attainment (>95%) against MICs ≤8 mg/liter achieved regardless of older age, obesity, augmented renal clearance, or severity of infection. This review summarizes how the approved ceftazidime-avibactam dosage regimens were developed and validated using PK/PD targets, population PK modeling, and PTA analyses.
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McKinnell JA, Bhaurla S, Marquez-Sung P, Pucci A, Baron M, Kamali T, Bugante J, Schwartz B, Balter S, Terashita D, Butler-Wu S, Gunzenhauser J, Hindler J, Humphries RM. Public Health Efforts Can Impact Adoption of Current Susceptibility Breakpoints, but Closer Attention from Regulatory Bodies Is Needed. J Clin Microbiol 2019; 57:e01488-18. [PMID: 30567751 PMCID: PMC6425187 DOI: 10.1128/jcm.01488-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Microbiological testing, including interpretation of antimicrobial susceptibility testing results using current breakpoints, is crucial for clinical care and infection control. Continued use of obsolete Enterobacteriaceae carbapenem breakpoints is common in clinical laboratories. The purposes of this study were (i) to determine why laboratories failed to update breakpoints and (ii) to provide support for breakpoint updates. The Los Angeles County Department of Public Health conducted a 1-year outreach program for 41 hospitals in Los Angeles County that had reported, in a prior survey of California laboratories, using obsolete Enterobacteriaceae carbapenem breakpoints. In-person interviews with hospital stakeholders and customized expert guidance and resources were provided to aid laboratories in updating breakpoints, including support from technical representatives from antimicrobial susceptibility testing device manufacturers. Forty-one hospitals were targeted, 7 of which had updated breakpoints since the prior survey. Of the 34 remaining hospitals, 27 (79%) assumed that their instruments applied current breakpoints, 17 (50%) were uncertain how to change breakpoints, and 10 (29%) lacked resources to perform a validation study for off-label use of the breakpoints on their systems. Only 7 hospitals (21%) were familiar with the FDA/CDC Antibiotic Resistance Isolate Bank. All hospitals launched a breakpoint update process; 16 (47%) successfully updated breakpoints, 12 (35%) received isolates from the CDC in order to validate breakpoints on their systems, and 6 (18%) were planning to update within 1 year. The public health intervention was moderately successful in identifying and overcoming barriers to updating Enterobacteriaceae carbapenem breakpoints in Los Angeles hospitals. However, the majority of targeted hospitals continued to use obsolete breakpoints despite 1 year of effort. These findings have important implications for the quality of patient care and patient safety. Other public health jurisdictions may want to utilize similar resources to bridge the patient safety gap, while manufacturers, the FDA, and others determine how best to address this growing public health issue.
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Affiliation(s)
- James A McKinnell
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
- Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Disease, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - S Bhaurla
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - P Marquez-Sung
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - A Pucci
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - M Baron
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - T Kamali
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - J Bugante
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - B Schwartz
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - S Balter
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - D Terashita
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - S Butler-Wu
- University of Southern California, Los Angeles, California, USA
| | - J Gunzenhauser
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - J Hindler
- Acute Communicable Disease Control Unit, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - R M Humphries
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
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Humphries RM, Hindler JA, Shaffer K, Campeau SA. Evaluation of Ciprofloxacin and Levofloxacin Disk Diffusion and Etest Using the 2019 Enterobacteriaceae CLSI Breakpoints. J Clin Microbiol 2019; 57:e01797-18. [PMID: 30567744 DOI: 10.1128/JCM.01797-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
In 2019, the Clinical and Laboratory Standards Institute (CLSI) published revisions to the Enterobacteriaceae ciprofloxacin and levofloxacin breakpoints. We evaluated the performance of disk diffusion and Etest compared to that of reference broth microdilution by use of the revised breakpoints. Fifty-eight Enterobacteriaceae isolates with ciprofloxacin MICs of 0.5 μg/ml or 1.0 μg/ml on initial testing were specifically selected for evaluation. These MICs are susceptible by the 2018 breakpoints and not susceptible by the 2019 breakpoints. For ciprofloxacin disk diffusion, the categorical agreement (CA) was 46.6%, with 0 very major errors (VME), 4 major errors (ME) (21.1%), and 27 minor errors (mE) (46.6%) using the 2019 CLSI disk breakpoints. For levofloxacin, the CA was 72.4%, with 0 VME, 0 ME, and 16 mE (27.6%) using the 2019 CLSI disk breakpoints. Using an error rate-bound evaluation method, levofloxacin but not ciprofloxacin disk diffusion yielded an acceptable minor error rate of <40% for isolates with an MIC plus or minus 1 doubling dilution of the intermediate breakpoint. For Etest compared to the reference broth microdilution, the essential agreement was 100% for both ciprofloxacin and levofloxacin and the CA was 81.0% and 65.5%, respectively. No VME or ME were observed by Etest, and 11 minor errors for ciprofloxacin (19.0%) and 20 (34.5%) for levofloxacin were observed. By the error rate-bound method, the minor error rate for ciprofloxacin was acceptable, but minor error rates for levofloxacin remained outside the acceptance range (i.e., 42.6% for isolates with an MIC within 1 dilution of the breakpoint). In general, the disk diffusion and Etest methods performed well with this challenging collection of isolates, although laboratories must be aware of minor errors, particularly for isolates with results near the breakpoint.
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Kidd JM, Abdelraouf K, Asempa TE, Humphries RM, Nicolau DP. Pharmacodynamics of Daptomycin against Enterococcus faecium and Enterococcus faecalis in the Murine Thigh Infection Model. Antimicrob Agents Chemother 2018; 62:e00506-18. [PMID: 30012755 DOI: 10.1128/AAC.00506-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/09/2018] [Indexed: 01/16/2023] Open
Abstract
The Clinical and Laboratory Standards Institute (CLSI) daptomycin MIC susceptibility breakpoint for the treatment of enterococcal infections is ≤4 μg/ml. However, patients receiving daptomycin for the treatment of infections caused by enterococci with MICs of ≤4 μg/ml may experience treatment failures. We assessed the pharmacodynamics of daptomycin against enterococci in a neutropenic murine thigh infection model and determined the exposures necessary for bacteriostasis and a 1-log10-CFU reduction of Enterococcus faecalis and Enterococcus faecium We further characterized daptomycin efficacy at clinically achievable exposures. Six E. faecium and 6 E. faecalis isolates (daptomycin MICs, 0.5 to 32 μg/ml) were studied. Daptomycin was administered at various doses over 24 h to achieve area under the free drug concentration-time curve-to-MIC ratios (fAUC0-24/MIC) ranging from 1 to 148. Daptomycin regimens that simulate mean human exposures following doses of 6, 8, and 10 mg/kg of body weight/day were also studied. Efficacy was assessed by the differences in the number of log10 CFU per thigh at 24 h. The Hill equation was used to estimate the fAUC0-24/MIC required to achieve bacteriostasis and a 1-log10-CFU reduction. For E. faecium, a 1-log10-CFU reduction required an fAUC0-24/MIC of 12.9 (R2 = 0.71). For E. faecalis, a 1-log10-CFU reduction was not achieved, while the fAUC0-24/MIC required for stasis was 7.2 (R2 = 0.8). With a human-simulated regimen of 6 mg/kg/day, a 1-log10-CFU reduction was observed in 3/3 E. faecium isolates with MICs of <4 μg/ml and 0/3 E. faecium isolates with MICs of ≥4 μg/ml; however, a 1-log10-CFU reduction was not achieved for any of the 6 E. faecalis isolates. These results, alongside clinical data, prompt a reevaluation of the current breakpoint.
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Humphries RM, Ferraro MJ, Hindler JA. Impact of 21st Century Cures Act on Breakpoints and Commercial Antimicrobial Susceptibility Test Systems: Progress and Pitfalls. J Clin Microbiol 2018; 56:e00139-18. [PMID: 29436415 PMCID: PMC5925699 DOI: 10.1128/jcm.00139-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance is the most pressing medical challenge of the past decade. At the front line are clinical laboratories, which are responsible for accurately reporting antimicrobial susceptibility test (AST) results to clinicians and public health authorities. The ability of the laboratory to detect resistance has been hampered by several factors. In 2016, the 21st Century Cures Act was signed into law, marking an important step toward resolving many regulatory dilemmas that hampered development and updates to commercial AST systems (cASTs). We describe the pathway and history of U.S. regulation of cASTs and outline both the rewards and unmet needs possible from the 21st Century Cures Act.
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Affiliation(s)
| | - Mary Jane Ferraro
- Departments of Medicine and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Janet A Hindler
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, USA
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Darton TC, Tuyen HT, The HC, Newton PN, Dance DAB, Phetsouvanh R, Davong V, Campbell JI, Hoang NVM, Thwaites GE, Parry CM, Thanh DP, Baker S. Azithromycin Resistance in Shigella spp. in Southeast Asia. Antimicrob Agents Chemother 2018; 62:e01748-17. [PMID: 29378707 DOI: 10.1128/AAC.01748-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/02/2017] [Indexed: 11/20/2022] Open
Abstract
Infection by Shigella spp. is a common cause of dysentery in Southeast Asia. Antimicrobials are thought to be beneficial for treatment; however, antimicrobial resistance in Shigella spp. is becoming widespread. We aimed to assess the frequency and mechanisms associated with decreased susceptibility to azithromycin in Southeast Asian Shigella isolates and use these data to assess appropriate susceptibility breakpoints. Shigella isolates recovered in Vietnam and Laos were screened for susceptibility to azithromycin (15 μg) by disc diffusion and MIC. Phenotypic resistance was confirmed by PCR amplification of macrolide resistance loci. We compared the genetic relationships and plasmid contents of azithromycin-resistant Shigella sonnei isolates using whole-genome sequences. From 475 available Shigella spp. isolated in Vietnam and Laos between 1994 and 2012, 6/181 S. flexneri isolates (3.3%, MIC ≥ 16 g/liter) and 16/294 S. sonnei isolates (5.4%, MIC ≥ 32 g/liter) were phenotypically resistant to azithromycin. PCR amplification confirmed a resistance mechanism in 22/475 (4.6%) isolates (mphA in 19 isolates and ermB in 3 isolates). The susceptibility data demonstrated the acceptability of the S. flexneri (MIC ≥ 16 g/liter, zone diameter ≤ 15 mm) and S. sonnei (MIC ≥ 32 g/liter, zone diameter ≤ 11 mm) breakpoints with a <3% discrepancy. Phylogenetic analysis demonstrated that decreased susceptibility has arisen sporadically in Vietnamese S. sonnei isolates on at least seven occasions between 2000 and 2009 but failed to become established. While the proposed susceptibility breakpoints may allow better recognition of resistant isolates, additional studies are required to assess the impact on the clinical outcome. The potential emergence of azithromycin resistance highlights the need for alternative options for management of Shigella infections in countries where Shigella is endemic.
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Huse HK, Miller SA, Chandrasekaran S, Hindler JA, Lawhon SD, Bemis DA, Westblade LF, Humphries RM. Evaluation of Oxacillin and Cefoxitin Disk Diffusion and MIC Breakpoints Established by the Clinical and Laboratory Standards Institute for Detection of mecA-Mediated Oxacillin Resistance in Staphylococcus schleiferi. J Clin Microbiol 2018; 56:e01653-17. [PMID: 29187565 PMCID: PMC5786728 DOI: 10.1128/jcm.01653-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 01/30/2023] Open
Abstract
Staphylococcus schleiferi is a beta-hemolytic, coagulase-variable colonizer of small animals that can cause opportunistic infections in humans. In veterinary isolates, the rate of mecA-mediated oxacillin resistance is significant, with reported resistance rates of >39%. The goal of this study was to evaluate oxacillin and cefoxitin disk diffusion (DD) and MIC breakpoints for detection of mecA-mediated oxacillin resistance in 52 human and 38 veterinary isolates of S. schleiferi Isolates were tested on multiple brands of commercial media and according to Clinical and Laboratory Standards Institute (CLSI) methods. Zone diameters and MIC values were interpreted using CLSI breakpoints (CLSI, Performance Standards for Antimicrobial Susceptibility Testing. M100-S27, 2017) for Staphylococcus aureus/Staphylococcus lugdunensis, coagulase-negative staphylococci (CoNS), and Staphylococcus pseudintermedius Results were compared to those of mecA PCR. Twenty-nine of 90 (32%) isolates were mecA positive. Oxacillin inhibition zone sizes and MICs interpreted by S. pseudintermedius breakpoints reliably differentiated mecA-positive and mecA-negative isolates, with a categorical agreement (CA) of 100% and no very major errors (VMEs) or major errors (MEs) for all media. For cefoxitin DD results interpreted using S. aureus/S. lugdunensis and CoNS breakpoints, CA values were 85% and 75%, respectively, and there were 72% and 64% VMEs, respectively, and 0 MEs. For cefoxitin MICs interpreted using S. aureus/S. lugdunensis breakpoints, CA was 81%, and there were 60% VMEs and no MEs. Our data demonstrate that oxacillin DD or MIC testing methods using the current S. pseudintermedius breakpoints reliably identify mecA-mediated oxacillin resistance in S. schleiferi, while cefoxitin DD and MIC testing methods perform poorly.
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Affiliation(s)
- H K Huse
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - S A Miller
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - S Chandrasekaran
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - J A Hindler
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - S D Lawhon
- Texas A&M University College of Veterinary Medicine, College Station, Texas, USA
| | - D A Bemis
- University of Tennessee College of Veterinary Medicine, Knoxville, Tennessee, USA
| | | | - R M Humphries
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
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Crowley B, Ruffner M, McDonald McGinn DM, Sullivan KE. Variable immune deficiency related to deletion size in chromosome 22q11.2 deletion syndrome. Am J Med Genet A 2018; 176:2082-2086. [PMID: 29341423 DOI: 10.1002/ajmg.a.38597] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/15/2017] [Accepted: 12/12/2017] [Indexed: 12/13/2022]
Abstract
The clinical features of 22q11.2 deletion syndrome include virtually every organ of the body. This review will focus on the immune system and the differences related to deletion breakpoints. A hypoplastic thymus was one of the first features described in this syndrome and low T cell counts, as a consequence of thymic hypoplasia, are the most commonly described immunologic feature. These are most prominently seen in early childhood and can be associated with increased persistence of viruses. Later in life, evidence of T cell exhaustion may be seen and secondary deficiencies of antibody function have been described. The relationship of the immunodeficiency to the deletion breakpoints has been understudied due to the infrequent analysis of people carrying smaller deletions. This manuscript will review the immune deficiency in 22q11.2 deletion syndrome and describe differences in the T cell counts related to the deletion breakpoints. Distal, non-TBX1 inclusive deletions, were found to be associated with better T cell counts. Another new finding is the relative preservation of T cell counts in those patients with a 22q11.2 duplication.
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Affiliation(s)
- Blaine Crowley
- The Division of Clinical Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Melanie Ruffner
- The Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Donna M McDonald McGinn
- The Division of Clinical Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kathleen E Sullivan
- The Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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Toutain PL, Bousquet-Mélou A, Damborg P, Ferran AA, Mevius D, Pelligand L, Veldman KT, Lees P. En Route towards European Clinical Breakpoints for Veterinary Antimicrobial Susceptibility Testing: A Position Paper Explaining the VetCAST Approach. Front Microbiol 2017; 8:2344. [PMID: 29326661 PMCID: PMC5736858 DOI: 10.3389/fmicb.2017.02344] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/15/2017] [Indexed: 01/05/2023] Open
Abstract
VetCAST is the EUCAST sub-committee for Veterinary Antimicrobial Susceptibility Testing. Its remit is to define clinical breakpoints (CBPs) for antimicrobial drugs (AMDs) used in veterinary medicine in Europe. This position paper outlines the procedures and reviews scientific options to solve challenges for the determination of specific CBPs for animal species, drug substances and disease conditions. VetCAST will adopt EUCAST approaches: the initial step will be data assessment; then procedures for decisions on the CBP; and finally the release of recommendations for CBP implementation. The principal challenges anticipated by VetCAST are those associated with the differing modalities of AMD administration, including mass medication, specific long-acting product formulations or local administration. Specific challenges comprise mastitis treatment in dairy cattle, the range of species and within species breed considerations and several other variable factors not relevant to human medicine. Each CBP will be based on consideration of: (i) an epidemiological cut-off value (ECOFF) - the highest MIC that defines the upper end of the wild-type MIC distribution; (ii) a PK/PD breakpoint obtained from pre-clinical pharmacokinetic data [this PK/PD break-point is the highest possible MIC for which a given percentage of animals in the target population achieves a critical value for the selected PK/PD index (fAUC/MIC or fT > MIC)] and (iii) when possible, a clinical cut-off, that is the relationship between MIC and clinical cure. For the latter, VetCAST acknowledges the paucity of such data in veterinary medicine. When a CBP cannot be established, VetCAST will recommend use of ECOFF as surrogate. For decision steps, VetCAST will follow EUCAST procedures involving transparency, consensus and independence. VetCAST will ensure freely available dissemination of information, concerning standards, guidelines, ECOFF, PK/PD breakpoints, CBPs and other relevant information for AST implementation. Finally, after establishing a CBP, VetCAST will promulgate expert comments and/or recommendations associated with CBPs to facilitate their sound implementation in a clinical setting.
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Affiliation(s)
- Pierre-Louis Toutain
- UMR 1331 Toxalim, INRA, ENVT, Toulouse, France
- The Royal Veterinary College, University of London, London, United Kingdom
| | | | - Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Ludovic Pelligand
- The Royal Veterinary College, University of London, London, United Kingdom
| | - Kees T. Veldman
- National Reference Laboratory on Antimicrobial Resistance in Animals, Lelystad, Netherlands
| | - Peter Lees
- The Royal Veterinary College, University of London, London, United Kingdom
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Drew RS, Rice B, Rüütel K, Delpech V, Attawell KA, Hales DK, Velasco C, Amato‐Gauci AJ, Pharris A, Tavoschi L, Noori T. HIV continuum of care in Europe and Central Asia. HIV Med 2017; 18:490-499. [PMID: 28117527 PMCID: PMC5516161 DOI: 10.1111/hiv.12480] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVES The European Centre for Disease Prevention and Control (ECDC) supports countries to monitor progress in their response to the HIV epidemic. In line with these monitoring responsibilities, we assess how, and to what extent, the continuum of care is being measured across countries. METHODS The ECDC sent out questionnaires to 55 countries in Europe and Central Asia in 2014. Nominated country representatives were questioned on how they defined and measured six elements of the continuum. We present our results using three previously described frameworks [breakpoints; Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 targets; diagnosis and treatment quadrant]. RESULTS Forty countries provided data for at least one element of the continuum. Countries reported most frequently on the number of people diagnosed with HIV infection (37; 93%), and on the number in receipt of antiretroviral therapy (ART) (35; 88%). There was little consensus across countries in their approach to defining linkage to, and retention in, care. The most common breakpoint (>19% reduction between two adjacent elements) related to the estimated number of people living with HIV who were diagnosed (18 of 23; 78%). CONCLUSIONS We present continuum data from multiple countries that provide both a snapshot of care provision and a baseline against which changes over time in care provision across Europe and Central Asia may be measured. To better inform HIV testing and treatment programmes, standard data collection approaches and definitions across the HIV continuum of care are needed. If countries wish to ensure an unbroken HIV continuum of care, people living with HIV need to be diagnosed promptly, and ART needs to be offered to all those diagnosed.
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Affiliation(s)
- RS Drew
- Independent ConsultantStowmarketUK
| | - B Rice
- HIV Measurement and Surveillance Methodology ConsortiumLondon School of Hygiene and Tropical MedicineLondonUK
| | - K Rüütel
- Infectious Diseases and Drug Monitoring DepartmentNational Institute for Health DevelopmentTallinnEstonia
| | - V Delpech
- HIV and STI DepartmentCentre for Infectious Disease Surveillance and ControlPublic Health EnglandLondonUK
| | | | - DK Hales
- Independent ConsultantNew YorkNYUSA
| | - C Velasco
- ISGlobalBarcelona Centre for International Health Research (CRESIB)Hospital Clinic – University of BarcelonaBarcelonaSpain
| | - AJ Amato‐Gauci
- Programme on HIV, STI and Viral HepatitisEuropean Centre for Disease Prevention and ControlStockholmSweden
| | - A Pharris
- Programme on HIV, STI and Viral HepatitisEuropean Centre for Disease Prevention and ControlStockholmSweden
| | - L Tavoschi
- Programme on HIV, STI and Viral HepatitisEuropean Centre for Disease Prevention and ControlStockholmSweden
| | - T Noori
- Programme on HIV, STI and Viral HepatitisEuropean Centre for Disease Prevention and ControlStockholmSweden
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