Current Issues in Clinical Microbiology, An Issue of the Clinics in Laboratory Medicine

1st Edition, Volume 40-4 - November 11, 2020
Editors: Nicole Pecora, Matthew Pettengill
Language: English
Hardback ISBN:
9 7 8 - 0 - 3 2 3 - 7 3 3 9 5 - 3
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 7 3 3 9 6 - 0

This issue of Clinics in Laboratory Medicine, guest edited by Drs. Nicole D. Pecora and Matthew Pettengill, will cover Current Issues in Clinical Microbiology. This issue is one of… Read more

Current Issues in Clinical Microbiology, An Issue of the Clinics in Laboratory Medicine

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This issue of Clinics in Laboratory Medicine, guest edited by Drs. Nicole D. Pecora and Matthew Pettengill, will cover Current Issues in Clinical Microbiology. This issue is one of four selected each year by our Editor-in-Chief, Dr. Milenko Jovan Tanasijevic. Topics discussed in this issue will include: Update in Diagnostics of Bloodstream Infections, Panels and Syndromic Testing in Clinical Microbiology, Lab Consolidation and Centralization, Update in Susceptibility Testing: Phenotypic and Genotypic Methods, Genomics in the Clinical Microbiology Laboratory, Automation in the Clinical Microbiology Laboratory, Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Strain?, Update on Biosafety and Emerging Infections for the Clinical Microbiology Lab, Update in Clinical Mycology, Point of Care Testing in Microbiology, Pediatric Diagnostic Microbiology, Antimicrobial Stewardship: What the Clinical Laboratory Needs to Know, Fellowship Training for the Future Clinical Microbiology Laboratory Director, Update in Diagnostics/Susceptibility of Mycobacterial Diseases, Role of the Clinical Microbiology Lab in One Health, Update in Infectious Disease Diagnosis in Surgical Pathology, and more.

Cover image
Title page
Table of Contents
Copyright
Contributors
Forthcoming Issues
Preface
Modern Blood Culture: Management Decisions and Method Options
Key points
Introduction
Selection of media and additive types for blood culture
Preventing contamination of blood cultures
Volume of blood collected for culture
Blood culture systems and alternative blood culturing methods
Incubation time
Processing positive blood cultures: staining methods and impact of Gram stain call time
Rapid identification from positive blood cultures: molecular testing
Rapid identification from positive blood cultures: mass spectrometry
Rapid, direct, phenotypic antimicrobial susceptibility testing options
Other direct enzyme-based targeted antimicrobial susceptibility testing methods
Stewardship/utilization
Panels and Syndromic Testing in Clinical Microbiology
Key points
Introduction
Detection of bloodstream pathogens
Meningitis/encephalitis syndromic panel
Detection of upper respiratory infection
Lower respiratory tract infection syndromic panel
Detection of gastrointestinal infections
Diagnostic and laboratory stewardship
Summary
Practical Aspects and Considerations When Planning a New Clinical Microbiology Laboratory
Key points
Preparation
Adjusting to an open floor plan
Biosafety
Specimen receiving
Specimen triage and STAT testing
Specimen setup: bacteriology and mycology
Virology and molecular microbiology
Mycology and mycobacteriology (sections with biosafety level-3 considerations)
Serology
Shared spaces
Teaching and telemedicine
General considerations
Update on Susceptibility Testing: Genotypic and Phenotypic Methods
Key points
Introduction
Antimicrobial resistance and interpretation
Phenotypic testing methods
Genotypic antimicrobial susceptibility testing
Clinical impact of antimicrobial susceptibility testing
Summary
Clinical Pathogen Genomics
Key points
Introduction
Whole-genome sequencing of cultured isolates
Clinical metagenomic next-generation sequencing of primary specimens
Clinical microbiology next-generation sequencing workflows
Advantages of in-house pathogen next-generation sequencing
Challenges of in-house pathogen next-generation sequencing: costs, infrastructure, validation, and reporting
Summary
Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus?
Key points
Introduction
Endemic versus highly pathogenic coronaviruses
Coronavirus genome
Molecular diagnosis of coronaviruses
Targeted coronavirus molecular detection
Are Clinical laboratories ready to identify a novel coronavirus?
Metagenomic next-generation sequencing for coronavirus diagnosis
Third-generation sequencing: a promising tool for rapid diagnosis
Discussion
Update on Biosafety and Emerging Infections for the Clinical Microbiology Laboratory
Key points
Introduction
Current practices
Best practices biosafety program
Current exposures and the risk of laboratory-acquired infections
Preparation for an emerging threat agent
Future vision
Summary
Point-of-Care Testing in Microbiology
Key points
Regulatory framework for point-of-care testing
Trends in point-of-care testing
Impact of point-of-care testing
Oversight and performance of point-of-care testing
Point-of-care testing in the Coronavirus Disease 2019 era
Summary
Update in Pediatric Diagnostic Microbiology
Key points
Introduction
Congenital cytomegalovirus infection
Congenital syphilis infection
Measles in children
Summary
Antimicrobial Stewardship: What the Clinical Laboratory Needs to Know
Key points
Introduction
Team roles
Technology and data
Antibiogram
Team action
Performance metrics and self-evaluation
Impact of antimicrobial stewardship programs
Future direction
Summary
Fellowship Training for the Future Clinical Microbiology Laboratory Director
Key points
Introduction
Overview of fellowship programs
Importance of defining the program mission and aims
Scope of training
Learner assessment
Program evaluation and continuous improvement
Role of the program director
Advice for current and future fellows
Future directions
Novel Assays/Applications for Patients Suspected of Mycobacterial Diseases
Key points
Introduction
Taxonomy
Nucleic acid amplification testing and its role of releasing tuberculosis suspects from airborne infection isolation
Microscopy
Non–sputum-based diagnosis of tuberculosis
Positive tuberculosis culture: ideal next steps?
Minimal inhibitory concentrations testing for M tuberculosis complex
Positive nontuberculous mycobacterial culture: ideal next steps?
Summary
Food Safety Genomics and Connections to One Health and the Clinical Microbiology Laboratory
Key points
Introduction
Impact of isolate diversity on whole genome sequencing cluster analysis?
Availability of data and materials’ section
Update in Infectious Disease Diagnosis in Anatomic Pathology
Key points
Introduction
Infection and the anatomic pathologist
Molecular testing of formalin-fixed paraffin-embedded tissues for pathogen detection
Targeted polymerase chain reaction
Broad-range bacterial 16S ribosomal RNA polymerase chain reaction and sequencing
Broad-range fungal 28S ribosomal RNA and internal transcribed spacers polymerase chain reaction and sequencing
Pitfalls
Summary
Blood Banking and Transfusion Medicine Challenges During the COVID-19 Pandemic
Key points
Introduction
Clinical manifestations of COVID-19
COVID-19 diagnosis
Management of COVID-19
Blood donation and blood products
Patient blood management during COVID-19 pandemic
Patient blood management strategies used in COVID-19 pandemic
Challenges of managing resumption of normal hospital surgical occupancy
Effect of COVID-19 pandemic on transfusion service and blood bank operations
Convalescent plasma
Blood safety during COVID-19
Risk of blood products contamination with COVID-19
Measuring the Serologic Response to Severe Acute Respiratory Syndrome Coronavirus 2: Methods and Meaning
Key points
Introduction
Viral antigens
Antibody kinetics
Test validation
Current clinical testing options
Implications for immunity
Summary

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Nicole Pecora

Matthew Pettengill