Advances and Trends in Clinical Microbiology-1판

This issue of Clinics in Laboratory Medicine, guest edited by James E. Kirby, will focus on Advances and Trends in 
Clinical Microbiology and take a look at the next 20 years. Topics include, but are not limited to, Rapid 
susceptibility testing methods; Synergy testing; Serology testing re-imagined; Total Laboratory Automation in Clinical 
Microbiology; MALDI-TOF; Superbugs of the Future, the Antimicrobial Laboratory Resistance Network, Partnerships between 
Public Health and the clinical microbiology laboratory; Next generation sequencing, from identification to 
susceptibility prediction; Distributed microbiology testing; Direct from Sample Identification; Biomarkers - predicting 
viral versus bacterial infection; PK/PD in the era of emerging multidrug-resistance; Training the next generation of 
clinical microbiologists; and Pictorial illustration of debate, developments, and controversy in clinical microbiology. 
 
Author Information  
Edited by James E. Kirby	




Contents

Preface: Our Pathogens Are Not Standing Still and Neither Can We
Rapid Susceptibility Testing Methods
When One Drug Is Not Enough: Context, Methodology, and Future Prospects in Antibacterial Synergy Tes
Clinical Microbiology in Underresourced Settings
Total Laboratory Automation: What Is Gained, What Is Lost, and Who Can Afford It?
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress
Next-Generation Sequencing in Clinical Microbiology: Are We There Yet?
Distributed Microbiology Testing: Bringing Infectious Disease Diagnostics to Point of Care
Direct-from-Specimen Pathogen Identification: Evolution of Syndromic Panels
Predicting Bacterial Versus Viral Infection, or None of the Above: Current and Future Prospects of B
What the Clinical Microbiologist Should Know About Pharmacokinetics/Pharmacodynamics in the Era of E
Mapping the Road to the Future: Training the Next Generation of Clinical Microbiologists, from Techn
We Cannot Do It Alone: The Intersection of Public Health, Public Policy, and Clinical Microbiology
Pictorial Illustration


What Is the Future of Clinical Microbiology?

CLINICS IN LABORATORY MEDICINE
FORTHCOMING ISSUES

December 2019

March 2020
RECENT ISSUES

June 2019

March 2019

Preface: Our Pathogens Are Not Standing Still and Neither Can We
REFERENCE

Rapid Susceptibility Testing Methods

Key points
INTRODUCTION
FROM REFERENCE TO COMMERCIAL METHODS: CURRENT STATE
WITH EMERGING ANTIMICROBIAL RESISTANCE, TIMELINESS BECOMES IMPORTANT
RAPID SUSCEPTIBILITY LANDSCAPE OVERVIEW
GENOTYPIC TESTING
THE GRAM-POSITIVE/NEGATIVE GENOTYPIC DIVIDE
CHALLENGES OF RAPID PHENOTYPIC ANTIMICROBIAL SUSCEPTIBILITY TESTING
MICROSCOPY-BASED RAPID PHENOTYPIC ANTIMICROBIAL SUSCEPTIBILITY TESTING
MICROSCOPY PLUS MICROFLUIDICS
ALTERNATIVE OPTICAL DETECTION METHODS
SPECTROMETRY-BASED DETECTION
SIGNAL AMPLIFICATION
DECISION SUPPORT MUST GO HAND IN HAND WITH RAPID ANTIMICROBIAL SUSCEPTIBILITY
SUMMARY
ACKNOWLEDGMENTS
REFERENCES


When One Drug Is Not Enough

Key points
INTRODUCTION
MECHANISMS OF COMBINATION ANTIBIOTIC ACTIVITY


Prevention of Resistance

Enhanced Activity
SYNERGY TESTING METHODS

Checkerboard Array

Diffusion-Based Methods

Time-Kill Assay

In Vitro Pharmacokinetic/Pharmacodynamic Models

Animal Models

SYNERGY TESTING IN THE CLINICAL MICROBIOLOGY LABORATORY
CLINICAL RELEVANCE OF IN VITRO SYNERGY TESTING RESULTS
THE FUTURE OF SYNERGY TESTING


Clinical Trials Incorporating In Vitro Synergy Data

Simpler Synergy Testing Methods


Maximizing the Usefulness of Synergy Data

SUMMARY
REFERENCES


Clinical Microbiology in Underresourced Settings

Key points
EXAMPLES OF PERSONNEL ISSUES
EXAMPLES OF SUPPLIES ISSUES
RISING TO THE CHALLENGE

Importance of Initial Assessment

Importance of Infrastructure

Utilization of Standard Operating Procedures and Other Written Materials

Working Within the Local, Regional, and National Health Care System

Being Patient

SUMMARY
REFERENCES


Total Laboratory Automation

Key points
AUTOMATED SYSTEMS: DEFINITIONS AND DIFFERENCES
WHY TOTAL AUTOMATION IN CLINICAL MICROBIOLOGY?
THE MICROBIOLOGY LABORATORY STAFF, WILL THEY ACCEPT AUTOMATION?
WHAT IS GAINED?


Quality: Automated Barcoding

Quality: Automated Plate Inoculation and Streaking

Efficiency: General

Efficiency: Decreased Incubation Time Required for the Detection of Organism Growth

Efficiency: 24/7 Automated Plate Inoculations and Incubation

Efficiency: Labor Savings

Efficiency: Work Flow

Measuring Efficiency

Accessibility of Culture Images

Safety
WHAT IS LOST?

Technical Knowledge and Skills

Pride and Ownership Associated with Conventional Workflow

Day Shift-Only Plate Reading

Automation Downtime
WHO CAN AFFORD AUTOMATION?

Return on Investment

Total Automation Occupies Less Space

Can You Afford Not to Automate?
THE FUTURE AND ADDITIONAL GAINS OF AUTOMATION IN MICROBIOLOGY
REFERENCES

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight

Key points
INTRODUCTION
ADVANCES IN ORGANISM IDENTIFICATION

Identification of Mycobacteria

Filamentous Fungi
ADVANCES IN ANTIMICROBIAL SUSCEPTIBILITY TESTING

Detection of Staphylococcal Methicillin Resistance

Detection of Reduced Vancomycin Susceptibility in Staphylococcus aureus

Growth-Based Susceptibility Testing of Bacteria

Stable Isotope Susceptibility Testing

Direct-on-Target Microdroplet Growth Assay

Growth-Based Susceptibility Testing of Fungi

Growth-Based Susceptibility Testing of Mycobacteria
ADVANCES IN ORGANISM IDENTIFICATION FROM CLINICAL SPECIMENS

Direct Organism Identification from Positive Blood Cultures

Short-Incubation Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Organism Identification Directly from Positive Blood Culture Broth

RAPID URINE MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME-OF-FLIGHT MASS SPECTROMETRY
SUMMARY
REFERENCES

Next-Generation Sequencing in Clinical Microbiology
Key points
INTRODUCTION

Whole-Genome Sequencing

Targeted Next-Generation Sequencing

Metagenomic Next-Generation Sequencing

Use of Next-Generation Sequencing for Clinical Care: Where Are We at Now?

What Does the Future Hold for Next-Generation Sequencing in Clinical Microbiology Laboratories
REFERENCES

Distributed Microbiology Testing

Key points
CONTEXT: POINT-OF-CARE TESTING, WHAT, WHERE, WHO, AND WHY?
POINT-OF-CARE TESTING IN THE NEAR FUTURE: STRENGTHS, WEAKNESSES, OPPORTUNITIES, AND THREATS
INFORMATICS AT THE POINT OF CARE
THE FAR FUTURE: THERANOS, BUT NOT SO STUPID
REFERENCES


Direct-from-Specimen Pathogen Identification

Key points
INTRODUCTION
RESPIRATORY TRACT SYNDROMIC PANELS


Upper Respiratory Tract Panels

Future target consideration

Surveillance potential for novel pathogens

Simple, rapid, and near point-of-care testing
GASTROINTESTINAL SYNDROMIC PANELS

Modular Panels

Comprehensive Panel

Existing Gaps

Targets of unclear or unestablished significance

Targets with clinical relevance but not universally included

Clostridioides difficile testing without clinical indication

Host response targeting

Demographic and region-specific testing

Detection of antimicrobial resistance

Gastrointestinal Panel Future Needs Summary
BLOODSTREAM SYNDROMIC PANELS

Future Directions and Considerations

Target wish list

Direct from whole blood testing

Antimicrobial susceptibility needs
CENTRAL NERVOUS SYSTEM SYNDROMIC PANELS

Existing Gaps

Acute versus chronic central nervous system infections

Shunt infections

Testing in cases of mosquito exposure

Syndromic testing paired with cytokine profiling

Antimicrobial susceptibility
SUMMARY
REFERENCES

Predicting Bacterial Versus Viral Infection, or None of the Above

Key points
INTRODUCTION
THE ROLE OF BIOMARKERS IN DIAGNOSIS AND MANAGEMENT OF INFECTIOUS DISEASES


The Role of Biomarkers for the Diagnosis and Management of Sepsis

C-reactive Protein

Pentraxin-3

Procalcitonin

Proadrenomedullin

Additional Biomarkers for Sepsis

The Role of Biomarkers for the Diagnosis and Management of Pneumonia

FUTURE DIRECTIONS FOR THE ROLE OF BIOMARKERS IN DIAGNOSIS OF INFECTIOUS DISEASES
SUMMARY
REFERENCES


What the Clinical Microbiologist Should Know About Pharmacokinetics/Pharmacodynamics in the Era of E

Key points
INTRODUCTION
LACTAMASE-MEDIATED RESISTANCE
PHARMACOLOGY OF ?LACTAMASE INHIBITION
EFFICACY OF LACTAM-LACTAMASE INHIBITOR COMBINATIONS
LIMITATIONS IN CURRENT PRACTICE WITH LACTAM-LACTAMASE INHIBITOR COMBINATIONS


Fixed Agent Pairings

Fixed Dose Ratio Pairings

Current Approaches to Susceptibility Testing

Conventional Pharmacokinetic/Pharmacodynamic Characterization of Combinations
ALTERNATIVE STRATEGIES FOR PAIRING AND ASSESSING LACTAM-LACTAMASE INHIBITOR