Microbiology: Barriers Against Infection

• Microbiology laboratory usage and opportunistic infections are crucial in healthcare.
• Early detection and prevention can improve patient outcomes.

Barriers Against Infections

• Barriers against infections are categorized as innate or adaptive.
• Innate defenses are inborn, require no prior stimulus, and are non-specific/non-immunologic.
• Adaptive defenses are acquired and specific/immunologic, and do require a prior stimulus.
• Non-immunologic host defenses are natural barriers or body defenses.
• Tears cleanse and contain antibacterial substances like lysozyme.
• Mucus prevents contact between organisms and cell surfaces.
• Ciliated epithelium moves pathogens in bronchial mucus and allows them to be swallowed or disposed of.
• Gastric acid is lethal to microorganisms without protective mechanisms.
• Defensins are antibacterial peptides produced by certain epithelial cells.
• Intestinal peristalsis propels microorganisms that cannot colonize the small or large bowel.
• Microbial flora is present on skin/mucosal membranes, occupying niches and regulating organisms.
• Intact skin serves as a barrier to microbial invasion.

Basics of Infections and Microorganisms

• Understanding the basics of infections requires looking at definition, classification of microorganisms, commensals vs pathogens, host-microbe interactions and stages of infection
• Infection is defined as inflammation plus a pathogen.
• Microorganisms can be classified into bacteria, fungi, viruses, and protists, as well as prions, viriods and algae.
• Bacteria is prokaryotic, viruses are acellular, and fungi & protists are eukaryotic
• Bacterial classification is based on phenotypic and genotypic characteristics, as well as ecology.
• Phenotypic characteristics include morphology, staining (Gram stain), growth requirements (O2), and biochemical tests.
• Genotypic classification relies on 16s ribosomal RNA genes for bacteria, and 18s for fungi.
• Gram-positive bacteria stain purple, while Gram-negative stain pink
• Gram-positive bacteria includes Staphylococci, Streptococci and Clostridium
• Gram-negative bacteria includes Neisseria and Coliforms

Bacterial Classification

• Gram-positive cocci include Staphylococci & Bacillus and Streptococci & Enterococci.
• Gram-positive bacilli includes Aerobic: Corynebacterium, Listeria spp and Anaerobic: Clostridium, Lactobacillus.
• Gram negative cocci includes Neissseria that is Aerobic: E.coli, Klebsiella, Proteus, Salmonella, Pseudomonas
• Gram negative bacilli-GUT includes Anaerobic: Bacteroides.
• Gram-negative spiral bacteria include Vibrios, Campylobacter, Helicobacter
• Bacteria that are not gram stainable and require special microcopy/stains/PCR are Spirochetes, Mycoplasma and Filamentous bacteria

Commensals vs Pathogens

• Commensals are normal human flora, co-habitat and are harmless, depending on host for survival.
• Commensals can become pathogenic when an opportunity arises.
• A breach in host defenses includes trauma, burns, exfoliative skin conditions, IV lines, foreign location such as Streptococcus viridians and immunosuppression.
• Normal flora is found in the nasopharynx, skin, upper/lower bowel, and vagina.

Host microbe environment Interaction Triangle

• Host microbe environment Interaction Triangle is affected by age, host defences, site and severity, Antimicrobial exposure and Concomitant diseases
• The environment can affect host microbe interactions via infection control practices, invasive procedure, hand hygiene etc..
• Commensal/Pathogen also affects host microbe environment and can affect infectivity and pathogenicity.
• Understanding how the host, microbe, and environment interact is key.
• Virulence factor includes adherence, Spread and evasion of host defences

Stages of Infection

• Stages of infection include encounter, enter, establish, damage, spread, and outcome, involving triangle interaction.

Microbiology Laboratory Usage

• Full blood count (FBC): White cell count and differential are considered to be use of diagnostic laboratory
• Acute phase reactants: C-Reactive Protein (C-RP)/ESR are also required
• Samples depend on site of infection such as Blood cultures, Wound swabs, Pus, Urine, IV-line.
• Sample may also include Nasopharyngeal swab, Tracheal aspirate and Tissue,Bone,Sputum or Stool
• Interventional radiology guided sampling is used if deep seated infection
• Other tests that can be run include Coagulation profile, Renal/Liver function tests and Molecular: Serology

Taking Samples

• When taking samples assess the need and send the right sample, at the right time, in the right laboratory container, with matching sample details
• Provide all clinical details, Contact details, and indicate high risk samples.
• It is advised to contact senior lab personnel if struggling to find results
• When taking samples be sure to include clinical diagnosis-reason for testing, place of patient and patient ID

Opportunistic Infections

• Opportunistic infections are caused by microbes that take advantage of opportunities in the host's environment.
• Occurrence is linked to weak immune systems, breached barriers and altered microbiome.

Risk Factors and Prevention

• 3 main factors increase opportunistic infection: Long life span, Advances in medical management, Incidence.
• Risk factors for opportunistic infections are burns/trauma, foreign bodies/invasive devices, co-morbidities, drugs & Immunosuppressive disorders
• These factors relate to Breach in barrier, Invasive procedures, Biofilm formation, Septic technique and Altered phagocytic functions
• You can suspect infection from Comorbid patients, Immunocompromised patients, long term high risk contact patients and those with invasive devices
• Multi-disciplinary team approach should prevent infection through reviews and checks

How To Suspect Opportunistic Infection

• You can suspect infection by looking for Unexplained temperatures (PUO), deteriorating health and non responding antibiotics
• Most reliable form of opportunistic detection is Repeat positive cultures from same site with PUO,
• A key detection is Positive routine surveillance cultures in immunocompromised patients

Prevention Measures

• Prevention of infection include strict infection control measures, reviewing and cleaning devices carefully
• Following all Antimicrobial policies and Educate staff to follow all local antimicrobial Stewardship
• You can use Hand hygiene/ ANTT, Isolation or Barrier nursing/Personnel and protective equipment

Case Study 1: IV Line Infection

• A patient is being treated for a severe chest infection that gets secondary infection at IV Line Site
• Likely pathogens are Staphylococcus aureus/epidermidis that contains exotoxins and can cause scaled skin, destroy RBC ,destroys leukocytes
• This bacteria is common in IV tubes and IV-line
• It can be treated by removing the IV line and sending line tip for testing

Staphylococcus Aures

• Staphylococcus aures virulence lies in Protein A Major Component, toxins and enzyme
• Laboratory can differentiate bacteria strains through use of testing such as agglutination

Case Study 2: Burns

• Patient is suffering oozing green pus leading to infection of wound
• Likely source are gram negative bacilli, resistant bacteria found in Moist environments and resistant to disinfectants
• These can be addressed through Virulence factor Lipo-polysaccharide LPS

Case Study 3: HIV

• Patient is HIV Positive, has a low fever with green sputum
• Test suggests the patient has Pneumocystis jirovecii - yeast, also called Pneumocystits carinii
• PJP and Pneumocystits carinii occurs when patients has CD4 count or 200 cell/mm3 in AIDs
• The patients may also have SOB
• PCR on Broncho can detect and it can be reversed with Cotrimoxazole high dose