Lecture 3- SCI 8007SEF Medical Microbiology %26 Virology-Introduction to Medical Microbiology I_2024

VITEK MS is used for the identification of microorganisms using mass spectrometry.

Group A – S. pyogenes, Group B – S. agalactiae, Group C – S. dysgalactiae subsp equisimilis, Group D – S. gallolyticus or Enterococcus, Group G – S. dysgalactiae subsp equisimilis.

1. Number of peaks in the reference spectrum matching the test spectrum. 2. Number of peaks in the test spectrum matching the reference spectrum. 3. Peak height symmetry of the matching peaks.

Protein A is a surface protein that can bind the Fc region of immunoglobulin G (IgG) antibody.

B. anthracis and B. cereus are clinically important species; others are contaminants.

They are large Gram-positive straight edged rods, but clinical specimen isolates can be Gram variable or appear Gram-negative.

The capsule or slime layer helps bacteria resist phagocytosis and enhances their virulence.

Intermediately to highly resistant to vancomycin (e.g. 16 – 256 μg/mL) but sensitive to teicoplanin, and it is plasmid-borne.

Almost 25%.

No, Corynebacterium do not form spores.

Proximity to other patients who are colonized with VRE, especially those with diarrhea and high VRE counts, increases the risk.

VRE cases in Hong Kong are currently under control.

Partial acid-fast.

The target slides need to be thoroughly washed after use.

Coagulase helps bacteria evade the immune response by promoting blood clotting.

Most are facultative anaerobes; some are fastidious and require CO2.

CNS is an opportunistic pathogen that can cause problems in immunocompromised patients, particularly through biofilm formation in catheterized patients and prosthetic valve endocarditis.

They grow best at 37 °C on Blood Agar (BA) and Chocolate agar.

CNS lacks many virulence factors that are present in Staphylococcus aureus.

PYR: negative.

VRE is resistant to vancomycin, making infections difficult to treat and increasing the risk of complications.

Otitis media, sinusitis, and meningitis

Spore forming Bacillus and Non-spore forming rods.

Pharyngitis, sore throat, tonsillitis, scarlet fever, wound infections, and necrotizing fasciitis.

Vancomycin-resistant Enterococcus

MRSA stands for Methicillin-Resistant Staphylococcus aureus, a strain of Staphylococcus aureus that has developed resistance to methicillin and other antibiotics.

Can cause cellulitis.

Gram positive short rods.

To screen all ICU patients for MRSA at admission to prevent ICU spread of MRSA.

bioMérieux and BBL.

Transfer a large, single colony of microorganism to the tube; more than one colony may be needed if the microorganism is small.

Adding formic acid improves the disruption of the cells and is especially recommended for Gram-positive bacteria and yeasts.

Most Enterococcus species are vancomycin sensitive, but vancomycin-resistant Enterococcus (VRE) emerges.

Gram-positive cocci in 'grape-like' clusters.

Staphylococcus aureus.

No matching hint.

Bacillus, Corynebacterium, and Lactobacillus.

Coagulase converts fibrinogen to fibrin, leading to clot formation, which helps the bacteria resist phagocytosis.

Mycobacterium.

The overuse and misuse of antibiotics are the primary factors contributing to the development of drug-resistant Staphylococcus aureus.

The three values are multiplied together, normalized to 1000, and then the base 10 logarithm is taken.

They are normal flora of the intestinal tract and are associated with bacteraemia, endocarditis, wound and soft tissue infections, as well as nosocomial urinary tract infections.

Bacillus cereus is associated with gastrointestinal infections, local infections, and systemic infections.

Corynebacterium are pleomorphic Gram positive rods that can appear in V-shaped or Chinese character formations.

Colony and Gram stain morphology may resemble S. agalactiae (GBS).

E. faecium is resistant to penicillin and ampicillin.

Bacillus anthracis

Gram positive cocci in tetrads.

Bamboo plants

It enlarges the area of haemolysis formed by the β-haemolysin from S. aureus.

The matrix with crystallized sample is fired with a laser beam, causing the matrix to absorb laser energy, convert it to heat, and trigger vaporization and desorption of the sample.

Bacillus species are catalase-positive.

Better growth in CO2 or anaerobic conditions.

White to golden yellow convex colonies, mostly β-haemolytic.

It is primarily used for the identification of biomolecules, including proteins and microorganisms.

It is useful for initial classification.

Disposable, single use only slides (MBT Biotarget 96) and reusable, ground steel target plates with hydrophobic target rings.

The target plate will become unusable if dropped or bent.

In most body sites covered with skin or lined with mucous membranes.

In 1986 in France and the UK.

CA-MRSA (Community-associated MRSA) strains are isolated from individuals in the community without recent healthcare exposure, affecting younger and healthier individuals.

PYR, bile esculin, and 6.5% NaCl.

Add 300 μL of water to each microcentrifuge tube.

Gram-positive diplococci or in short chains.

GBS is associated with stillbirth and life-threatening neonatal infections such as meningitis, septicemia, and pneumonia.

They usually form large whitish-greyish, spreading colonies with irregular edges.

A score value greater than 2.00 indicates that an organism can be reported to the genus and species level.

Skin flora.

Small, grey colonies that may be mucoid, dry, or umbilicated.

The widespread use of avoparcin.

S. bovis

Big β-haemolytic large colony.

GBS is sensitive to penicillin.

Streptococcus group C and G.

Streptococcus pneumoniae is typically found in pairs.

The first case of VRE in Hong Kong was an imported case in 1997.

Specimen types, clinical information, and clinical significance.

They are aimed to evade elimination by host defense mechanisms.

Microaerophilic (reduced oxygen tension) or anaerobic conditions.

HA-MRSA (Hospital-associated MRSA) circulates and is transmitted to individuals in healthcare facilities, with risk factors including long-term hospitalization, surgery, and ICU stays.

High-level resistance to both vancomycin and teicoplanin (e.g. >256 μg/mL), and it is plasmid-borne.

A genomic region inserted into the Staphylococcal genome that contains the mecA gene and other genes.

It is compared to reference strains in a database for closely matched bacterial identity.

Gram positive cocci in clusters.

28.5%.

α-hemolytic.

CAMP test: positive.

Prosthetic valve endocarditis occurs in patients with artificial devices and poor blood circulation, where CNS can be a causative agent.

Obligate aerobe.

Bruker MALDI-TOF can identify closely related species like Bacillus anthracis and Bacillus cereus, but Bacillus anthracis is not included in the MALDI Biotyper database.

Streptolysin S (stable in oxygen) and Streptolysin O (labile in oxygen).

Mild diarrhea, fever, and chills

α or γ-hemolytic

VRE prevalence in Canada varies by region and healthcare facility, with increasing reports in recent years.

Severely ill patients, those receiving multiple and prolonged courses of antimicrobial therapy, and organ transplant recipients.

Yes, they may be clinically significant or contaminants.

Flora of skin, mouth, gut, and vagina.

Gram-positive cocci in chains, with S. pneumoniae appearing as diplococci.

Usually Group D antigen positive.

Lactobacillus and Listeria.

Grouped as Group B.

Christie, Atkins, Munch-Petersen.

The TAT for MRSA PCR is 24 hours, while MRSA culture takes 3 days.

CAMP factor.

High-level resistance to vancomycin and usually teicoplanin (e.g. >256 μg/mL), and it is chromosome-borne.

Bacillus cereus is resistant to penicillin.

Large (>0.5 mm), grey, translucent colony with a wide zone of β-haemolysis.

MRSA was first isolated in the United States in 1968.

All pregnant women should be screened for GBS at 35 to 37 weeks gestation.

C. urealyticum is associated with urinary tract infections.

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

Mycobacterium tuberculosis is the Gram positive organism known for causing tuberculosis.

Sporadic cases of VRE colonization or infections have been reported in renal, medicine, and orthopaedics departments.

Penicillin and cefotaxime

Patient specimens.

Desorbed microbial cell components, mainly intracellular proteins.

Molar tooth colony.

Exotoxins and M protein.

Spores may not be visible in direct smears but appear in colony smears.

Bacillus cereus is involved in food poisoning, specifically known as 'fried rice syndrome'.

Most are facultative anaerobes, while some are obligate aerobes.

Haemolytic reactions are best observed with transmitted light shining from behind the agar plate.

CNS can lead to biofilm formation, which complicates treatment and increases the risk of infections.

MRSA is a strain of Staphylococcus aureus that is resistant to methicillin and other commonly used antibiotics.

No matching hint.

The ccr (cassette chromosome recombinase) gene is responsible for the attachment of the SCC mec cassette to the staphylococcal chromosome.

ICU-acquired MRSA infections decreased after the implementation of MRSA PCR screening.

Arrow-shaped haemolysis.

Erysipelothrix produces hydrogen sulfide, forming a black precipitate in triple sugar iron (TSI) agar.

Vancomycin-Resistant Enterococcus

Gram positive cocci include Staphylococcus, Micrococcus, Streptococcus, and Enterococcus. Gram positive rods/bacilli include Bacillus, Corynebacterium, Lactobacillus, Mycobacterium tuberculosis, and Actinomyces.

Streptococcus pneumoniae

Enterococcus can be identified through culture on selective media, testing for bile esculin hydrolysis, and checking for growth in high salt concentrations.

VITEK MS was developed by bioMérieux.

Classified according to Lancefield grouping based on carbohydrate antigens on the cell wall.

Endocarditis, septic arthritis, peritonitis, pericarditis, osteomyelitis, and soft tissue infections

Yes, S. pyogenes is sensitive to bacitracin.

The identification scheme typically involves assessing hemolysis patterns on blood agar, catalase test results, and further biochemical tests to differentiate species.

Risk factors include exposure to VRE and being a susceptible host.

To screen for Streptococcus pyogenes.

The two forms of coagulase are bound coagulase, which is on the cell wall and detected by slide tests or commercial tests like Staphaurex, and free coagulase, which is secreted into the extracellular environment and detected by tube tests.

Proteins

Large translucent to opaque, flat, grey-white colony.

Corynebacterium.

Drug resistance in S. aureus limits treatment options, making infections harder to treat and increasing the risk of complications.

E. faecalis is sensitive to penicillin and ampicillin.

CA-MRSA was first reported in the 1990s in Australia, New Zealand, and America.

α or γ - haemolytic

CA-MRSA strains carry the PVL gene (Panton-Valentine leucocidin), which codes for a cytotoxin.

Tiny, small grey, smooth, or dull colony

A small zone of intact erythrocytes immediately adjacent to the bacterial colony, with a zone of complete red-cell hemolysis surrounding it.

Most clinical isolates are β-hemolytic.

C. diphtheriae causes diphtheria, produces diphtheria toxin, and forms a pseudomembrane in the throat.

Facultative anaerobe.

Negative

Ions are accelerated by an electric field of known strength.

Optochin sensitivity and positive bile solubility.

The toxin produced by Bacillus cereus is resistant to heat and not easily destroyed by cooking.

The volumes of 70% FA and ACN must be equal to achieve a final ACN concentration of 50%.

No matching hint.

Slide and tube coagulase positive.

It represents the probability of isolate identification based on a composite score of matching peaks between reference and test spectra.

Facultative anaerobes, Gram-positive cocci in chains, small grey-white colonies, α or γ-haemolytic, rare β-haemolytic.

E. faecalis and E. faecium.

Alteration of peptidoglycan synthesis pathway.

Each species has a different protein composition.

It increased from less than 1% to approximately 15%.

May confuse with S. aureus in identification.

It alters penicillin binding protein 2 (PBP2) production, encoding a new PBP2a, resulting in a loss of target affinity.

Bacillus cereus is beta-hemolytic.

It likely originated in coagulase-negative staphylococcal species.

Erysipelothrix is α-haemolytic and forms small colonies.

Allow the formic acid to evaporate before adding the matrix solution to avoid spilling of the samples into neighboring spots.

Yes, van A and van B are transmittable.

Meningitis in neonates, pregnant women, and immunocompromised patients.

No, Lactobacillus does not form spores.

Dairy products, e.g., cheese and ice cream.

They are usually opportunistic pathogens, with S. lugdunensis and S. saprophyticus being notable examples.

Psychrotrophic, able to grow as low as 0°C.

Lactobacillus is catalase negative.

Positive for urease and sucrose fermentation; negative for nitrate reductase and xylose fermentation.

Pharyngitis, skin and soft tissue infections, toxic shock-like syndrome, bacteraemia, arthritis, osteomyelitis, respiratory infections, abscesses, endocarditis, and meningitis.

Erysipelothrix is resistant to vancomycin, unlike most Gram-positive bacteria which are sensitive.

They have very similar patterns in MALDI-TOF mass spectrometry.

Branched Gram positive rods.

Rheumatic heart disease and acute glomerulonephritis.

May be positive for bound coagulase, but negative for free coagulase.

Narrow zone of β-haemolytic; some strains are γ-haemolytic.

Actinomycosis, which involves abscesses of the jaw and sinus tracts to the skin surface.

Coagulase, optochin, bacitracin, PYR, and/or Lancefield tests.

Drug resistance is a significant concern in bacterial infections.

Erysipelothrix is a Gram positive curved-shaped rod.

Group A Streptococcus which contains Group A antigen.

To help in the extraction process by vortexing thoroughly after adding 900 μL of ethanol.

GBS can cause postpartum infections such as bacteremia and endometritis in pregnant women.

Growth is enhanced with CO2

Gastrointestinal anthrax, Cutaneous anthrax, Inhalational anthrax

Staphylococcus and Micrococcus are typically found in clusters.

Sample molecules are ionized and transferred into a gas phase, generating generally singly charged ions from analytes.

Most clinical specimens, either as a colonizer or a pathogen.

The Biotyper provides matching hints with further taxonomical information or cautionary details to prevent misinterpretation.

Resistant

Extraction must be performed.

Pipette 1 μL of supernatant onto a steel target, avoiding the pellet at the bottom, and air dry.

Vancomycin is the drug of choice for MRSA.

Hyaluronidase and lipase.

Grouping and PYR test.

Actinomyces.

They contain a capsule composed of hyaluronic acid to prevent phagocytosis.

Screening tests to group into genera, such as catalase and oxidase tests.

Broth based enrichment with NaCl salt.

Up to 30% of healthy women may colonize with GBS in the genital tract.

Smear a thin film of biological material directly onto a clean MALDI target using a pipette tip or wooden toothpick.

Intermediately resistant to vancomycin (e.g. 8 – 16 μg/mL) but sensitive to teicoplanin, and it is chromosome-borne.

Catalase positive (S. agalactiae is negative).

The matrix is used to prepare the sample for analysis by mixing or coating it, which entraps and co-crystallizes the sample when dried.

Increased consumption of vancomycin.

GeneXpert and BD MAX.

A score value between 1.70 and 2.00 allows for reporting to the genus level only.

Urinary tract infection in young women.

Centrifuge for 2 minutes to remove excess ethanol.

May be positive for bound coagulase, but negative for free coagulase.

C. jeikeium can cause opportunistic infections.

Small variant colonies (SVC) can occur.

Any score should be correlated with gram stain and culture characteristics, clinical context, and biochemical features.

MRSA was originally localized in hospital environments.

Bacteraemia and endocarditis

Sensitive

Follow up by VITEK; other sites report Streptococcus dysgalactiae.

Positive for ornithine decarboxylase and PYR.

Catalase positive.

The patient will be isolated in a single room, and all healthcare workers will comply strictly with contact precautions.

Gram positive cocci can be found in clusters (e.g., Staphylococcus, Micrococcus), chains (e.g., Streptococcus, Enterococcus), or pairs (e.g., Streptococcus pneumoniae).

Centrifuge at maximum speed (13,000 to 15,000 rpm) for 2 minutes.

MALDI-TOF uses time of flight measurements to determine an ion's mass-to-charge ratio.

It is part of animal flora and can occupationally cause human disease.

The common practice of storing boiled rice at room temperature for subsequent preparation of fried rice has been implicated in Bacillus cereus outbreaks.

Lactobacillus forms tiny, α-hemolytic grey colonies.

Erysipelothrix is found in soil, water, and the digestive tract of many animals.

Bruker MALDI-TOF and Biomerieux MALDI-TOF.

Positive

Yellow pigment colony.

It is relatively less virulent than S. pyogenes.

Food poisoning and Toxic Shock Syndrome.

mec A gene and SCC mec.

Corynebacterium are catalase positive.

Motility positive (S. agalactiae is non-motile).

Lactobacillus are long and filamentous rods in chains.

Erysipelothrix is catalase-negative.

40 - 60%.

Catalase positive and oxidase positive.

Streptococcus and Enterococcus are typically found in chains.

Coagulase negative.

No, they are usually non-pathogenic.

Susceptible to Bacitracin (0.04U).

VRE can persistently colonize the GI tract for 3 months to 2 years.

Lactobacillus helps maintain the acidic environment needed for healthy vaginal flora.

Antibiotic resistance in VRE leads to limited treatment options and the potential transfer of resistance to other organisms.

A colony size of a pin head or poppy seed is generally enough.

A score value less than 1.7 indicates that no organism identification is possible.

Allow the samples to dry at room temperature.

Add 50 μL of 70% FA and vortex thoroughly, letting it stand for approximately 5 minutes.

In 1999, MRSA accounted for 50% of S. aureus isolates from patients in ICUs.

Inhalational anthrax, which may result in respiratory distress and death

Lactobacillus is found in the oral cavity, gastrointestinal tract, and female genital tract.

Impetigo.

VRSA was reported in Japan in 1996.

By the early 1990s, MRSA accounted for 20-25% of Staphylococcus aureus isolates from hospitalized patients in the US.

Optochin - resistant

Resistant to novobiocin.

11-35% of carriers can develop infections, which are associated with increased mortality, longer hospital stays, ICU admissions, surgical procedures, and higher costs.

Involves dermis, red, hot, swelling, and painful.

Heavier ions of the same charge reach lower speeds, while ions with higher charge will increase in velocity.

Usually contaminants from skin, mucosa, oropharynx, or environments.

Resistant to nitrofurantoin.

Streptococcus pyogenes is bacitracin sensitive.

Ions are accelerated through a vacuum by an applied electrical field and are separated based on their mass-to-charge ratio (m/z) before detection.

PYR positive.

Erysipelothrix causes erysipeloid, which is characterized by erythematous edema.

Responsible for gingivitis and dental caries

Overlay with 1 μL of matrix and allow to dry at room temperature.

Lactobacillus is considered a probiotic because it is a good bacteria.

To screen for S. agalactiae.

Ions with the same charge have the same kinetic energy after acceleration.

Associated with endocarditis, bacteraemia, and meningitis; accounts for 50% to 60% of cases of subacute bacterial endocarditis (SBE)

The mass-to-charge ratio determines the arrival time of ions at the detector.

Vitek 2 GPI and API Staph.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF).

Active surveillance may be required during a VRE outbreak.

Seldom fatal, causes wound infection known as 'Malignant pustule'

Skin infections and skin lesions.

It may cross-react with group A antiserum.

No, it is non-motile

VRE can survive in the environment for prolonged periods, ranging from 7 days to 4 months.

No, it cannot be identified by MALDI-TOF

Catalase positive.

Erysipelothrix is an occupational disease commonly found in butchers and fishermen.

Penicillin

Species canis and dysgalactiae have very similar patterns, making distinction difficult.

No matching hint.

In immunocompromised patients.