Applied Microbiology in Intensive Care Medicine

Contents
Necrotizing Fasciitis: Pillars for Improved Patients’ Outcome
	1 Introduction
	2 Epidemiology
	3 Classification
	4 Risk Factors
	5 Pathophysiology
	6 Diagnosis
	7 Treatment
	8 Complications
	9 Prognosis
	10 Prevention
	11 Conclusion
	References
Hospital-Acquired Infections: Key for Prevention and Clinical Bundles
	1 Nosocomial or Hospital-Acquired Infections (HAIs)
	2 Epidemiology
	3 Risk Factors
		3.1 The Host Factors
		3.2 The Agent Factors
		3.3 The Environmental Factors
	4 Risk Factors for HAIs
	5 Surgical Site Infection Prevention Bundle
	6 Ventilator-Associated Pneumonia Prevention Bundle
		6.1 Head off the Bed
		6.2 Subglottic Suctioning of the Endotracheal Tube (ETT) and Cuff Pressure Measurement
		6.3 Oral Care
		6.4 SAT and SBT (Spontaneous Awakening and Spontaneous Breathing Trial)
		6.5 Stress Ulcer and Deep Venous Thrombosis Prophylaxis
	7 Catheter-Related Bloodstream Infection Prevention Bundle (CRBSI)
	8 Catheter-Associated Urinary Tract Infections (CAUTIs)
	9 Conclusion
	References
Antimicrobial Stewardship in ICU: A Success Story
	1 Introduction
	2 Definition of Antimicrobial Stewardship
	3 “The Evolution of Antibiotic Stewardship: A Historical Perspective”
	4 Milestones of Antimicrobial Stewardship
	5 Antimicrobial Stewardship in the Intensive Care Unit [12]
		5.1 The Goals of the Antimicrobial Stewardship Program
	6 Establishing a Stewardship Program: In the General Hospital Setting
	7 Key Elements of AMS in the ICU
	8 Key Strategies for Antimicrobial Stewardship in the ICU
	9 Barriers to Antibiotic Stewardship in ICU
	10 Barriers Specific to ICU in Antimicrobial Stewardship
	11 Overcoming Obstacles to Implement Antimicrobial Stewardship Interventions in the ICU
		11.1 Role of the Microbiology and Laboratory Antimicrobial Stewardship in ICUs
		11.2 Role of Antibiogram in Antimicrobial Stewardship in ICUs
		11.3 Reducing the Usage of High-Risk Medications
		11.4 Preauthorization and Formulary Restriction
		11.5 Role of Rapid Diagnostic Tools
		11.6 Role of Serum Biomarkers
		11.7 Role of Antibiotic Timeouts (ATO)
		11.8 Collaboration Between Infectious Diseases and ICU Physicians
		11.9 Collaboration Between Infection Prevention and Control and Antimicrobial Stewardship Program
		11.10 Computerized Decision Support System
		11.11 Infection Control
	12 Impact and Outcome of the Antimicrobial Stewardship in ICU
	13 Conclusion
	References
Perioperative Sepsis and Septic Shock: An Update
	1 Introduction
	2 Definition
	3 Epidemiology
	4 Risk Factors
	5 Pathophysiology
	6 Management
		6.1 Antimicrobial Administrations and Source Control
		6.2 Hemodynamic Monitoring and Resuscitation
		6.3 Vasopressors and Inotropes
		6.4 Perioperative Management
		6.5 Blood Transfusion
		6.6 Glycemic Control
		6.7 Vitamins and Steroids
	7 Organ Support Therapy
		7.1 Encephalopathy
		7.2 Lung Injury
		7.3 Hepatic Dysfunction
		7.4 Acute Kidney Injury
	8 Conclusion
	References
Urosepsis and Septic Shock: A Simple Infection Progressing to Complex One
	1 Introduction
	2 Epidemiology
	3 Risk Factors
	4 Classification of Urosepsis
	5 Microbiology
	6 Pathophysiology
		6.1 Pathophysiology of Sepsis
	7 Diagnosis
		7.1 Clinical Presentation
		7.2 Imaging Studies
	8 Management
		8.1 Source Control
	9 Conclusion
	References
Community-Acquired Pneumonia: Recent Advances
	1 Introduction
	2 Organism Responsible
	3 Predisposing Factors
	4 Pathogenesis
	5 Patterns of Involvement
	6 Presentation
	7 Differential Diagnosis
	8 Investigations
		8.1 Imaging
		8.2 Microbiology
		8.3 Other Investigations
	9 Patient Disposition
		9.1 Ambulatory Care
		9.2 Hospital Admission
		9.3 Intensive Care Unit (ICU) Admission
	10 Treatment
		10.1 Duration of Antibiotics
	11 Follow-Up
	12 Conclusions
	References
Septic Abdomen: An Update on Its Microbiology and Management
	1 Introduction
	2 Peritonitis: We Should Be Vigilant in the Initial Management
		2.1 Primary Peritonitis
		2.2 Secondary Peritonitis
			2.2.1 Epidemiology
			2.2.2 Pathophysiology of Secondary Peritonitis
			2.2.3 Inflammatory Cytokines
			2.2.4 Secondary Peritonitis and Intra-abdominal Hypertension
			2.2.5 Diagnosis
				Clinical Signs and Symptoms
			2.2.6 Management the Secondary Peritonitis
			2.2.7 The Outcome of Secondary Peritonitis
	3 Tertiary Peritonitis (TP)
		3.1 Risk Factors for Tertiary Peritonitis
		3.2 Microbiology of Tertiary Peritonitis
		3.3 Diagnosis
		3.4 Management
		3.5 Mortality and Outcome
	4 Navigating Acute Cholangitis: Unveiling Pathways to Diagnosis and Dynamic Management
		4.1 Introduction
		4.2 Pathophysiology
		4.3 Clinical Presentation
		4.4 Microbiology
		4.5 Management
		4.6 Pharmacological Therapy
		4.7 Biliary Drainage
	5 Acute Cholecystitis: From Pathophysiology to Precision Management
		5.1 Introduction
		5.2 Pathophysiology
		5.3 Diagnosis
		5.4 Microbiology
		5.5 Treatment
		5.6 Antibiotic Therapy
		5.7 Surgical Treatment
	6 Emerging Strategies in Pyogenic Liver Abscess: Unraveling Pathways from Diagnosis to Dynamic Management
		6.1 Introduction
		6.2 Microbiology
		6.3 Treatment
		6.4 Pharmacological Therapy
		6.5 Interventional Radiology
		6.6 Endoscopic Therapy
		6.7 Surgery
	7 Conclusion
	References
Descending Necrotizing Mediastinitis: A Life-Threatening Infection
	1 Introduction
	2 Clinical Presentation
	3 Risk Factors
	4 Microbiology
	5 Diagnosis (Fig. 1)
	6 Management
		6.1 Management of DNM Summarized in Fig. 2
	7 Complications and Prognosis
	8 Conclusion
	References
Acute Adult Supraglottitis: An Update
	1 Introduction
	2 Anatomy of the Larynx
	3 Embryology of the Larynx
	4 Physiology of the Larynx
	5 Pathophysiology
	6 Clinical Presentation
	7 History
	8 Examination
	9 Investigations
	10 Management of Supraglottitis
		10.1 Antimicrobial Therapy
		10.2 Therapy with Glucocorticosteroids
		10.3 Antipyretic Agents
		10.4 Adrenaline Nebulization
	11 Airway Management in Supraglottitis
		11.1 Indications for Securing Airway in AAS
		11.2 Airway Management Strategies
			11.2.1 Airway Management in Mild AAS
			11.2.2 Initial Stabilization
			11.2.3 Expertise and Skill
			11.2.4 Definitive Airway Management
		11.3 Complications of Airway Management
			11.3.1 Complication During Airway Manipulation
			11.3.2 Tube Dislodgment
	12 Morbidity and Mortality
	13 Conclusion
	References
Meningitis and Neurosurgical Treatment an Update
	1 Introduction
	2 Epidemiology
	3 Etiology
	4 CNS Infections and Their Neurosurgical Treatments
	5 Role of EVD in Treating Meningitis and Ventriculitis
	6 Intrathecal Drug
	7 Conclusion
	References
MRSA to VRE: Management and Prevention
	1 Introduction
	2 Advantages of Antibiotics
	3 Use and Abuse Leading to Antibiotic and Antimicrobial Resistance
		3.1 Abuse of Antibiotics
		3.2 Inappropriate Prescription
		3.3 Agricultural and Poultry Abuse
		3.4 The Newer Antibiotics
		3.5 Red File Barrier
	4 Antibiotic-Resistant Bacterial Infections
	5 Management of Antibiotic Resistance and Prevention
		5.1 Optimization of Antimicrobial Prevention
		5.2 Optimizing the Therapeutic Regimens
		5.3 Quicker and Improved Diagnosis
		5.4 Prevention of Transmission of Bacterial Infections
		5.5 National Initiative
		5.6 Fostering and Adopting the Antibiotic Stewardship Program
		5.7 International Efforts
	6 Conclusion
	References
Future of Applied Microbiology in Critical Care
	1 Introduction and Current Microbiologic Challenges in ICU
	2 Culture-Negative Sepsis
	3 Delay in Identification of Organism
	4 Delay in Identification of Antimicrobial Resistance
	5 Advances in Early Detection of Organisms and Detection of Resistance/Virulence Patterns [39–49]
	6 Bacteriology: Early Growth Identification
		6.1 MALDI-TOF MS
		6.2 Nucleic Acid Amplification Test (NAAT)
		6.3 Types of PCR
			6.3.1 Real-Time PCR
			6.3.2 Nested PCR
			6.3.3 Multiplex PCR
			6.3.4 Quantitative PCR
			6.3.5 Arbitrary Primed PCR
		6.4 Microarray Multiplex
		6.5 Gene Sequencing
		6.6 Bacterial AST
		6.7 MALDI-TOF
		6.8 rAST
	7 Multiplex Microarray
	8 Mycology
		8.1 I-MALDI-TOF
		8.2 II-T2Candida
		8.3 III-Serological Testing
		8.4 Galactomannan Antigen Detection
		8.5 NAAT
		8.6 Fungal AST
	9 Virology
		9.1 Viral AST
		9.2 Genotypic Antiviral Resistance Testing
		9.3 Phenotypic Drug Susceptibility Testing
		9.4 Plaque Reduction Assay
		9.5 Relevant Viral Resistance
		9.6 Mechanisms of CMV Resistance
	10 Mycobacterium
		10.1 Smear Microscopy
		10.2 MTB/Rif PCR
		10.3 Culture
		10.4 Classification
		10.5 Lipoarabinomannan (LAM) Point-of-Care (POC) Testing
		10.6 Culture Identification Methods
			10.6.1 DNA Probes
			10.6.2 MALDI-TOF MS
			10.6.3 High-Performance Liquid Chromatography (HPLC)
			10.6.4 Sequencing
		10.7 Mycobacterial AST
			10.7.1 Agar Proportion
			10.7.2 Broth Method
	11 Tropical Diseases
	12 Conclusions
	References
Importance of Infectious Disease Specialist and/or Clinical Microbiologist During Multidisciplinary Rounds in Intensive Care Unit
	1 Introduction
	2 MDT Rounds in ICU
	3 MDT Composition and Functions
	4 Significance of MDT Round and Patient Outcome
	5 Role of Infectious Disease Specialist in MDT
	6 Clinical Microbiologist Present During MDT Round; Time for Intensivist to Resurrect Lost Art
	7 Conclusion
	References
Obstetric Sepsis and Management
	1 Introduction
	2 Pathophysiology of Sepsis
	3 Relevant Physiological Changes of Pregnancy
	4 Etiology
	5 Risk Factors for Sepsis
	6 Clinical Presentations
	7 Identification and Assessment of Severity of Sepsis
		7.1 Sequential Organ Failure Assessment (SOFA)
		7.2 Quick SOFA (qSOFA)
		7.3 Modified SOFA
		7.4 Early warning System
	8 Management of Sepsis in Obstetric Patients
	9 Immediate Management: Care Bundles
	10 Investigations
		10.1 Lactate
		10.2 White Cell Count and C-Reactive Protein
		10.3 Procalcitonin
		10.4 Blood Cultures
	11 Isolating the Source of Infection
	12 Choice of Empiric Antibiotic Therapy
	13 Critical Care Considerations in Maternity Contexts
		13.1 General Resuscitation
		13.2 Oxygen
		13.3 Vasopressors
		13.4 Glycemic Control
		13.5 Steroids
		13.6 IV Immunoglobulins
	14 Obstetric Considerations and Delivery
	15 Isolation and Infection Control Considerations
	16 Future Directions in Maternal Sepsis
		16.1 Precision Medicine
		16.2 “Omics” Technologies in Sepsis
	17 Conclusions
	References
Infection and Sepsis Management in Trauma
	1 Introduction
	2 Definition of Sepsis and Polytrauma
	3 Epidemiology
	4 Immunological and Physiological Alterations in Polytrauma and Sepsis
	5 Infection Prevention, Diagnosis, and Management in Trauma
		5.1 Pre-Hospital Administration of Antibiotics
		5.2 Presumptive Antibiotics in the Emergency Department
	6 Intensive Care Management of Suspected or Proven Infection in Trauma Victims
		6.1 Evaluating for Infection in ICU Trauma Patients—Risk Factors
		6.2 Evaluating for Infection—Clinical Approach
		6.3 Evaluating for Infection—Biomarkers
	7 Management of Sepsis in Trauma—Special Considerations
	8 Future Directions
	9 Summary
	References
Intensivist’s Role in Epidemic and Pandemic
	1 Introduction
		1.1 COVID-19 and Utilization of Intensive Care Units
		1.2 Ebola Virus Disease (EVD) 2014 Pandemic
		1.3 Influenza A (H1N1) Pandemic 2009
		1.4 Severe Acute Respiratory Syndrome Associated with Coronavirus Pandemic 2003
		1.5 Polio Pandemic
	2 Intensivist and Intensive Care Planning During the Pandemic
	3 Critical Care/Intensive Care Therapy Preparation and Planning of Epidemic and Pandemic
		3.1 Supply Requirements During and for the Epidemic and Pandemic (Stuff)
		3.2 Staff
		3.3 Space: The Critical Care Without an Intensive Care Unit
	4 Conclusion
	References