Bacteriology

Total Laboratory Automation (TLA) in Clinical Microbiology

Total laboratory automation (TLA) is a system that automates culture-based testing in the clinical microbiology laboratory.

API and RAPID ID For Microbial Identification

BioMérieux's API identification products are test kits for the identification of Gram-positive bacteria, Gram-negative bacteria, and yeast.

ESKAPE Pathogens

ESKAPE is the acronym for six nosocomial pathogens that can ‘escape’ commonly used antibiotics and can develop into MDR.

Killed or Live Vaccine, Which One to Choose?

Live, attenuated vaccines and inactivated vaccines are two basic types of vaccines used to protect susceptible individuals from infectious diseases.

Relapsing Fever: Etiology, Pathogenesis, Lab Diagnosis

Relapsing fever is a bacterial infection characterized by recurrent episodes of fever and nonspecific symptoms following exposure to insect vector-carrying Borrelia species.

Infective dose (ID) and Lethal Dose (LD)

Infective dose is defined as a minimum number of microorganisms required for an infection to proceed.

Treponema pallidum: Properties, Pathogenesis, and Disease

Treponema pallidum is the causative agent of syphilis, an infectious venereal disease in humans. Primary, secondary, tertiary latent stages.

How do Probiotics work?

Probiotic microorganisms displace pathogens and enhance the development and stability of the microbial balance in the large intestine.

Scrub typhus: Overview, Pathogenesis and Lab Diagnosis

Scrub typhus also known as bush typhus, is an emerging infectious disease caused by a bacteria called Orientia tsutsugamushi

Archaea: Characteristics, Similarities, Differences with Bacteria

Archaea is a group of phylogenetically related prokaryotes distinct from Bacteria and known for tolerance to physiochemical extremes.

Spirochetes: Morphology, Classification, Disease

Spirochetes are long, thin, flexible, spirally coiled helical bacilli. Spirochetes cause syphilis, Lyme disease, relapsing fever, leptospirosis, yaws.

Normal Flora of the Skin-Skin Microbiome

Human skin is home to billions of diverse bacteria, archaea, fungi, and viruses with bacteria making up the vast majority

Bacillus cereus: Morphology, Disease, Biochemical Tests

Bacillus is a gram-positive rods. It produces two enterotoxins, emetic (vomiting) and diarrheal – causing two types of illness.

Moraxella catarrhalis: Properties, Lab Diagnosis

Moraxella catarrhalis is a small gram-negative diplococci that resembles Neisseria and causes otitis media in children.

ESBL and Classification of β-lactamases

ESBL are a group of enzymes produced by both Gram-negative and Gram-positive bacteria which can hydrolyze all β- lactam agents except

Borrelia burgdorferi (Lyme disease): Clinical Features, Diagnosis

Lyme disease or Lyme borreliosis is a vector-borne zoonotic disease caused by Borrelia burgdorferi.

Enterococcus faecalis: Properties, Pathogenesis, Lab Diagnosis

Enterococcus is gram-positive cocci in chains and is catalase negative. It causes infections of Urinary tract and biliary tract.

Serratia marcescens: Properties, Pathogenesis, Diagnosis

Enteric gram-negative rod, produces red-pigmented colonies. It causes hospital-acquired pneumonia, UTI and sepsis.

Phenotypic Methods for the Detection of Carbapenemases

Phenotypic assays to detect carbapenemase-producing organisms are either growth-based assays (MHT or CIM) or hydrolysis methods.

Demonstration of Treponema pallidum Using Dark-Field Microscopy

Dark field microscopy is the most specific and sensitive technique to diagnose syphilis when an active chancre or condyloma lata is present.

Critical (Panic) Values in Microbiology

Presence of bacteria in sterile body fluids, isolation of Mycobacterium tuberculosis or any other bio-terrorism agents should be reported immediately.

Rejection Criteria for Microbiological Specimens

Clerical errors, inappropriate containers/conditions, inappropriate or inadequate specimens, delay in transit lead to sample rejection.

Bordetella pertussis: Properties, Pathogenesis, Lab Diagnosis

Agent of whooping cough (pertussis), Bordetella pertussis is a small gram-negative coccobacilli.

Bacterial Quorum Sensing

Quorum sensing (QS) is a bacterial cell-cell signaling mechanism that helps them to adjust gene expressions based on requirements.

WHO AWaRe Classification of Antibiotics

AWaRe classifies antibiotics into three stewardship groups: Access, Watch and Reserve to emphasize their optimal use.

Bacteroides fragilis: Properties, Pathogenesis, Lab Diagnosis

Bacteroides fragilis is a gram-negative, pleomorphic anaerobe responsible for variety of anaerobic infections including peritonitis.

Actinomyces: Properties, Disease, Lab Diagnosis

Actinomyces is a heterogeneous group of gram-positive, pleomorphic bacilli responsible for the disease actinomycosis.

Carba NP Test (CNPt): Principle, Procedure, Results

Carba NP test (CNPt) is a biochemical test for rapid detection of carbapenemase production on Gram-negative bacilli.

Francisella tularensis: Properties, Pathogenesis, Lab Diagnosis

Francisella tularensis is a gram-negative coccobacillus and is the etiologic agent of tularemia. It is transmitted to humans from rodents and rabbits.

Burkholderia pseudomallei: Properties, Lab Diagnosis

Burkholderia pseudomallei is a water- and soil-borne gram-negative bacterium. Causative agent of melioidosis, it is regarded as a potential bioterror agent.

Leptospira interrogans: Pathogenesis, Lab Diagnosis

Leptospira interrogans is a tightly coiled fine spirochete responsible for the disease leptospirosis (weil's disease).

Neisseria meningitidis: Properties, Pathogenesis, Lab Diagnosis

Meningococci are capsulated gram-negative diplococci. Commensal of nasopharyx they may cause meningitis in susceptible persons.

Macrolides: Mode of Action, Mechanism of Resistance

Macrolides (erythromycin, azithromycin, clarithromycin) inhibit bacterial protein synthesis by binding with the 50S subunit of the ribosome.

Nocardia: Properties, Pathogenesis, Lab Diagnosis

Nocardia species are gram-positive, variably acid-fast, filamentous, and strictly aerobic organisms belonging to the actinomycetes group.

Legionella pneumophila: Properties, Pathogenesis, Lab Diagnosis

Legionella is a gram-negative pleomorphic rod, responsible for a serious type of pneumonia called Legionnaires' disease.

Laboratory Diagnosis of Mycobacterium tuberculosis Infection

Ziehl-Neelsen staining, culture in Lowenstein-Jensen medium and GeneXpert MTB/RIF assay are useful methods for the diagnosis of tuberculosis.

Fluorescence Microscope: Principle, Types, Applications

Fluorescence microscopy is widely used in diagnostic microbiology (diagnosis of tuberculosis, trichomoniasis) and in microbial ecology.

Corynebacterium diphtheriae: Pathogenesis, Lab Diagnosis

Gram positive club shaped (chinese letter form) bacteria responsible for diphtheria.

Clostridium perfringens: Properties, Diseases, Diagnosis

Commensal in the large intestine of humans and is responsible for the disease, gas gangrene.

Clostridium tetani: Properties, Pathogenesis, Lab Diagnosis

Gram positive, obligate anaerobe, looks like drum-stick shaped and causes tetanus.

Clostridium botulinum: Properties, Pathogenesis, Lab Diagnosis

Gram positive, anaerobic rod which produces powerful neurotoxin "botulinum toxin".

Yersinia pestis: Properties, Disease, Lab Diagnosis

Yersinia pestis is a short gram-negative rod, responsible for deadly zoonotic disease, plague.

Dark-field Microscopy: Principle and Uses

Dark-field microscopy is used for the observation of living, unstained cells. The specimen is brightly illuminated while the background is dark.

Bacillus anthracis: Properties, Pathogenesis, Lab Diagnosis

A potential biological weapon which causes important zoonotic disease called anthrax.

Streptococcus agalactiae (GBS): Properties, Pathogenesis, Lab Diagnosis

Streptococcus agalactiae (GBS), is a beta-hemolytic, CAMP test positive, gram-positive cocci. It can cause severe infection in newborns.

Listeria monocytogenes: Properties, Pathogenesis, Lab Diagnosis

Listeria monocytogenes is a facultative intracellular Gram-positive coccobacilli responsible for listeriosis, one of the serious food-borne infections.

Listeria monocytogenes Virulence Factors

Internalin, listeriolysin O, phospholipases, etc are major virulence factors of Listeria monocytogenes.

Toxins of Clostridium perfringens and their roles

Alpha (α) toxin, Beta (β) toxin, Epsilon (ε) toxin, and Iota (ι) toxin are the major toxins of Clostridium perfringens.

pH Requirements of Microorganism

Most microorganisms grow best around neutral pH values (6.5 - 7.0), but some thrive in extreme pH conditions (pH10).

Beta-Lactam Antibiotics: Mechanism of Action, Resistance

Penicillins, cephalosporins, monobactams, and carbapenems are major beta-lactam antibiotics; active against both gram-positive and negative bacteria.

Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC)

MIC test determines the antimicrobial activity of a test agent against a specific bacteria. It is done via E-test, tube/agar dilution method.

GasPak Anaerobic System: Principle, Application

Simple to use, best for laboratories with less sample load and the most commonly used method for anaerobiosis.

Helicobacter pylori Virulence Factors: Roles in Pathogenesis

Major virulence factors of H. pylori are flagella, urease enzyme, adhesins, VacA, CagA, OpiA, and DupA.

Neisseria gonorrhoeae (gonococcus) Virulence Factors

Pili, outer membrane proteins, IgA1 protease and lipo-oligosaccharide (LOS) are important virulence factors of Neisseria gonorrhoeae.

Hydrogen Sulfide (H₂S) Production Test

Bacterial species capable of producing H₂S release sulfide which combines with iron present in the medium forming black precipitate.

Bacterial Typing Methods: Aim, Attributes, Types

Characterization of an organism beyond its species level to determine relatedness. Useful for epidemiologist in outbreak investigations.

Phage Typing Method: Principle, Procedure, Results

When a panel of lytic phages is inoculated on a lawn inoculum of the bacteria, phages which are able to set up a lytic infection produce a clear zone.

Starch Hydrolysis Test: Principle, Procedure, Results

Some bacteria such as Bacillus sps can hydrolyze starch (amylose and amylopectin) using the enzymes α-amylase and oligo-1,6-glucosidase.

Anaerobic infections: Etiology, Characteristics, Diagnosis

Anaerobic bacteria are part of the normal flora but can cause abscess formation and tissue necrosis when enter into sterile sites.

Serotypes and Their Significance

Serotyping is the classic tools for epidemiological study of organisms having multiple serotypes: E. coli, Salmonella, Vibrio, Shigella, S. pneumoniae.

Gram-Positive Bacilli (Rods) and Diseases

Gram-positive bacilli are a diverse group of bacteria responsible for variety of infections such as gas-gangrene, tetanus, anthrax, etc.

Rapid Carbohydrate Utilization Test (RCUT) for Neisseria

Patterns of acid production from the carbohydrates – glucose, maltose, lactose, sucrose, (and fructose) – are used to identify Neisseria.

Furazolidone Disk Test: Principle, Procedure Results

Furazolidone disk test is used to differentiate staphylococci (sensitive) from micrococci (resistant).

Biological Safety Cabinet (BSC): Types and Working Mechanism

An engineering control to protect laboratory workers, laboratory environment, and work materials from exposure to infectious or biohazardous aerosols.

Lac Operon: Mechanism and Regulation

Lac operon is a well-known example of an inducible gene network that regulates the transport and metabolism of lactose in Escherichia coli.

Psychrophiles, Mesophiles, Thermophiles

Psychrophiles can grow at 0°C, mesophiles have optimum temperature near 37°C, and thermophiles grow best at 50-60°C.

Staphylococcus aureus Virulence Factors

Major virulence factors of S. aureus are capsule, teichoic acid, protein A, enterotoxin, TSST-1, coagulase, hyaluronidase, etc.

Glycopeptides (Vancomycin, Teicoplanin)

Glycopeptide antibiotics act by inhibiting cell wall synthesis of bacteria. Vancomycin, a glycopeptide drug is used to treat MRSA infections.

Bactec Automated Blood Culture System

BACTEC by BD diagnostics utilizes fluorescent technology and detects the growth of organisms in the blood culture bottles.

Ames Test: Mutagenicity Test for Carcinogens

Developed by Bruce Ames, this test is used to identify environmental carcinogens.

Antigens in disease diagnosis

Detection of specific antigens present in the sample (blood, urine, or CSF) using specific antibodies is the mainstay for the rapid diagnosis of infections.

Plasmids: Properties, Types and Functions

Plasmids are extra-chromosomal genetic elements that replicate independently of the host chromosome. The codes for drug resistance, virulence

Bacteriological Analysis of Water

Membrane Filtration Technique used for the presence of fecal contamination (fecal coliforms) is discussed here.

Kligler’s Iron Agar (KIA): Principle, Procedure, Results

Kligler Iron Agar is used for the differentiation of microorganisms on the basis of glucose and lactose fermentation and H₂S production.

Laboratory Diagnosis of Leptospirosis

Leptospirosis is diagnosed using dark-field microscopy, microscopic agglutination test (MAT) or using IgM ELISA.

Mycoplasma pneumoniae: Properties, Disease, Diagnosis

This smallest free-living bacteria does not have cell wall (so pleomorphic in shape) causes walking pneumonia.

Klebsiella pneumoniae: Properties, Diseases, Lab Diagnosis

This gram-negative capsulated rod-shaped bacteria causes hospital acquired pnuemonia, UTI and blood stream infection.

Proteus species: Properties, Diseases, Identification

Known for its swarming motility, Proteus is a gram negative rod of Enterobacteriaceae family and causing urinary tract infections.

Preparation of Gram stain Reagents

Reagents are primary stain (crystal violet), mordant (iodine), decolorizer (ethanol or acid-alcohol), and counterstain (safranin or dilute carbol-fuchsin).

Short Term Storage of Fastidious Bacteria

For short-term storage (<2 weeks) of fastidious organism enriched chocolate or blood agar is used and stored at 2-8°C.

Haemophilus Influenzae Virulence Factors

Capsule, adhesion proteins, lipooligosaccharides, pili, IgA protease, and phase variations of H.influenzae play major roles in pathogenesis.

Streptococcus Pneumoniae Virulence Factors

S. pneumoniae virulence factors include capsular polysaccharide, C carbohydrate antigen, pneumolysin, autolysin.

Pus Sample: Collection, Processing, Staining and Culture

Pus aspirate is the preferred sample. S. aureus, Strep pyogenes, and members of Enterobacteriaceae are major pathogens.

MRSA: Emergence, Types, Detection Methods

MRSA (methicillin-resistant Staphylococcus aureus) is resistant to all ß-lactam agents, including cephalosporins and carbapenems.

MALDI-TOF Mass Spectrometry: Principle, Applications in Microbiology

MALDI-TOF MS offers species-level identifications in minutes at low costs with accuracy that matches or even exceeds the conventional system.

Blood Culture: Indications, Timing, and Volume

The overall volume of blood cultured is more critical in increasing organism yield. More the blood volume cultured greater the chance of isolating pathogen.

SEM vs. TEM Electron Microscopy

SEM provides detailed images of the surfaces of cells whereas TEM provides details about internal composition, morphology, crystallization.

Travelers’ Diarrhea: Causes, Prevention, Treatment

Individuals who travel to areas of poor sanitation and limited access to clean water are at greater risk of developing travelers’ diarrhea.

Acinetobacter: Disease, Properties, Resistance

Acinetobacter are gram-negative coccobacilli, among them Acinetobacter baumannii accounts for most  infections in humans in hospital settings.

Blood Culture Test: Information for the Patient

Physicians may prefer blood culture in a number of suspected disease conditions such as enteric fever, infective endocarditis, meningitis, pneumonia, etc.

Spread Plate Technique: Principle, Procedure, Results

Bacterial culture method for estimating the viable bacterial count after serial dilutions (when required).

Most Probable Number (MPN) Test: Principle, Procedure, Results

The most probable number (MPN) is a statistical serial dilution method for estimating viable numbers of bacteria present in a food or water sample.

Antibiotic Resistance: Origin, Causes, Mechanism

Decreased permeability, efflux pump, altered target, and inactivation of antibiotics are major mechanisms of drug resistance.

Bacteria Associated with Intrinsic Antibiotic Resistance

There are innumerable species of bacteria which are innately resistant to particular drugs. For example, penicillin resistance of Mycoplasma.

WHO: List of antibiotic-resistant “priority pathogens”

Antibiotic-resistant "priority pathogens" is a catalogue of 12 families of bacteria that pose the greatest threat to human health. Organisms are divided as Critical Priority, High Priority and Medium Priority.

Pneumococcal Urinary Antigen Testing (UAT)

Pneumococcal urinary antigen testing is a rapid assay that detects Streptococcus pneumoniae antigen (C-polysaccharide) in the urine of patients.

Carbohydrate Fermentation Test: Uses, Principle, Procedure, Results

It tests for the presence of acid and/or gas produced from carbohydrate fermentation. and is useful in differentiating among bacterial groups or species.

Robertson’s Cooked Meat (RCM) Medium

The most widely used anaerobic culture medium containing chopped meat particles and used for maintenance of stock cultures.

World Antibiotic Awareness Week Celebration

Phenylalanine Deaminase Test: Principle, Procedure, Results

Some organism such as Proteus oxidatively deaminate phenylalanine to phenyl-pyruvic acid.

Microbes with Good and Bad Smell

Odor of colonies of bacteria may help in their identification but sniffing culture plates is not a good idea and you may contract a disease.

Pour Plate Method: Procedure, Uses, (Dis) Advantages

One of the best methods to determine the number of bacteria present per mL of liquid broth/specimen.

Capsule Stain: Principle, Procedure, Results

The best way to visualize capsule is to stain the background using an acidic stain and to stain the cell itself using a basic stain.

Thioglycollate broth: Composition, Principle, and Uses

Thioglycollate broth supports the growth of anaerobes, aerobes, microaerophilic, and fastidious microorganisms.

Urea Breath Test (UBT) for H.Pylori

Patients swallow 14C-urea capsule. Test urea will be broken down, if infected, and a lot of 14CO2 produced which is detected in the breathe.

Cary-Blair transport medium: Composition, Preparation, Uses

Cary-Blair transport medium is used to transport clinical specimens suspected to contain enteric pathogens, including Shigella, Salmonella, Vibrio.

McIntosh and Fildes’ Anaerobic Jar

McIntosh and Fildes' anaerobic jar works on the principle of evacuation and replacement, where the air inside the chamber is evacuated and replaced with mixture of gases 

Streak Plate Method: Principle, Procedure, Uses  

Routine method for the isolation of bacteria from clinical specimen or for obtaining individual isolated colonies from a mixed culture.

Preparation of McFarland Turbidity Standards

For performing AST using Kirby Bauer disc diffusion method, a cell suspension of organisms equivalent to a 0.5 McFarland standard is used.

X and V factor test for Haemophilus

Haemophilus species require accessory growth factors such as X (hemin), V (NAD) or a combination of both.

Löwenstein–Jensen (LJ) Medium: Preparation, Uses

M. tuberculosis gives rough, raised, dry, non-pigmented (cream/buff colored) colonies on Lowenstein Jensen (LJ) medium.

Pigment Producing Pathogenic Bacteria

Red pigment of Serratia, golden yellow of S. aureus and green (pyoverdin) and blue (pyocyanin) of Pseudomonas help in their identification.

Gram-Negative Cocci and Coccobacilli of Medical Significance

Gram-negative cocci of medical importance belong to the family Neisseriaceae which includes the genera Neisseria, Moraxella, Kingella, Acinetobacter.

TPHA: Principle, Procedure, Results, Interpretations

TPHA is a treponemal test for the serologic diagnosis of syphilis, based on the principle of passive hemagglutination. It detects IgG and IgM.

Oxidative fermentative (OF) test:  Principle, Procedure, Results

The oxidative-fermentative (OF) test is used to differentiate oxidative bacteria from fermentative bacteria based on acid production.

Streptococcus pyogenes Virulence Factors

Major virulence factors of S.pyogenes are adhesions, M protein, hemolysins, pyrogenic exotoxins and spreading factors.

Helicobacter Pylori Tests and Results

To diagnose H. pylori infections, urea breathe test, fecal antigen test and rapid urease test are most widely used.

GeneXpert MTB/RIF Assay

GeneXpert MTB/RIF assay is a NAAT that simultaneously detects DNA of M.tuberculosis complex and resistance to rifampin (i.e. mutation of the rpoB gene).

Quellung reaction: Principle, Procedure, Results

Quellung reaction is the gold standard technique for serotyping S. pneumoniae. Capsule get “swollen” and is more visible.

Fecal Transplant: Principle, Procedure, Uses

Fecal microbiota transplantation (FMT) also known as fecal bacteriotherapy is a novel approach used to treat Clostridioides difficile infections.

Widal Test: Principle, Procedure, Results, Limitation

Widal test is one of the oldest and most widely used serological tests for the diagnosis of enteric fever.

Clostridioides difficile: Characteristics, Disease, Lab Diagnosis

Gram positive obligate anaerobe responsible for a unique colonic disease, pseudomembranous colitis.

Staphylococcus vs. Micrococcus

Micrococcus is lysostaphin and furazolidone resistant, bacitracin sensitive and microdase positive. Find the results of Staphylococcus.

Neisseria gonorrhoeae vs. Neisseria meningitides

Neisseria meningitidis is capsulated and ferment maltose (MM), whereas Neisseria gonorrhoeae is non-capsulated and do not ferment maltose.

Elek Test: Principle, Procedure, Results

Elek test is an in vitro immunoprecipitation test to determine whether or not a strain of Corynebacterium diphtheriae is toxigenic.

Difference Between Prokaryotic Cell and Eukaryotic Cell

Eukaryotic cells contain a nucleus with a nuclear membrane enclosing multiple chromosomes, while prokaryotic cells have a single chromosome.

Streptococcus Pyogenes (GAS): Characteristics, Diseases, Tests

This group A beta-hemolytic streptococci is bacitracin sensitive and causes strep sore throat, rheumatic fever, and PSGN.

Staphylococcus vs. Streptococcus

Staphylococci are catalase positive, gram positive cocci in clusters but Streptococci are catalase negative and may appear in pairs or chains.

Key Phrases Used in Microbiology Lab Reports

Modified Oxidase Test (Microdase): Procedure, Uses

Microdase test is a rapid method to differentiate Staphylococcus aureus (negative) from Micrococcus luteus (positive).

Tests for Bacterial Motility: Procedure, Results

These tests determine if an organism is motile (possesses flagella).

Nagler Reaction (Lecithinase Test)

Lecithinase test is a biochemical test used to identify organisms that liberate phospholipases (lecithinases) e.g. Clostridium perfringens.

Tuberculin Skin Test (Mantoux test): Principle, Procedure, Results

Tuberculin skin test is the standard method of determining whether a person is infected with M.tuberculosis or has exposure to tubercle bacilli.

Albert Stain: Principle, Procedure and Results

Albert stain is a type of differential stain used for staining metachromatic granules or volutin granules found in Corynebacterium diphtheriae.

Acetate Utilization Test: Principle, Procedure, Uses

Acetate utilization test determines if an organism can use acetate as the sole source of carbon.

Butyrate Disk Test: Principle, Procedure, Results, Uses

Rapid test for identifying Moraxella (Branhamella) catarrhalis which produce butyrate esterase enzyme.

Cetrimide Agar: Composition, Preparation, Uses

Cetrimide agar test the ability of an organism to grow in the presence of cetrimide.

Endospore Staining: Principle, Procedure, Results

In Schaeffer-Fulton`s method, primary stain-malachite green is forced into the spore by steaming the smear, safranin is counterstain.

API 20E Test System: Results and Interpretations

API-20E test strip (from bioMerieux, Inc.) is used to identify the enteric gram negative rods.

Complement Fixation Test: Principle, Procedure, Results

In the presence of specific Abs to an infectious agent, any complement in the system is bound, leaving no residual complement for rxn with Abs to the RBCs.

Nitrocefin test: Principle, Procedure, Uses

The nitrocefin test is a sensitive technique for detecting beta-lactamase-producing strains of N. gonorrhoeae, H. influenzae, Enterococcus spp.

Auramine-Rhodamine Fluorochrome Staining

Auramine-rhodamine fluorochrome staining also known as "Truant method of staining", is used to visualize Acid-fast bacilli (AFB).

Voges Proskauer (VP) Test: Principle, Procedure, Results

Certain bacteria produce acetoin as the chief end product of glucose fermentation. Acetoin gets oxidized to diacetyl giving red color.

Decarboxylation Test: Types, Principles, Uses

The presence of lysine, ornithine, and arginine decarboxylase enzyme is routinely tested in the identification of Enterobacteriaceae.

Hippurate Hydrolysis Test: Principle, Procedure, Results

Hippurate test is used in the identification of Campylobacter jejuni, Listeria monocytogenes, Gardnerella vaginalis, and Streptococcus agalactiae.

Lancefield Classification of Streptococci

Beta hemolytic streptococci are arranged into twenty (20) groups A-U without I and J (i.e. A through H and K through V).

Tween 80 Hydrolysis Test: Principle, Procedure, Results

Mycobacterium species possess an enzyme-lipase, that splits Tween-80 and releases oleic acid and polyoxyethylated sorbitol.

Teixobactin: Introduction, Mechanism of Action, Uses

Teixobactin is an extract of β-proteobacteria named Eleftheria terrae. It has shown excellent activity against Gram-positive bacteria.

ONPG: β-galactosidase Test

Organism producing β-galactosidase hydrolyzes the ONPG producing visible yellow product (orthonitrophenol).

Leucine Aminopeptidase (LAP) Test

Gram-positive, catalase negative cocci which produce the enzyme leucine aminopeptidase gives positive LAP test results.

Gram Staining: Principle, Procedure, Results

Gram-positive bacteria retain the crystal violet-iodine complex and stain purple, whereas gram-negative bacteria stain pink.

Nitrate Reduction Test: Principle, Procedure, Results

Nitrate reduction test is used to determine the ability of an organism to reduce nitrate.

Culture media for Salmonella typhi and paratyphi

Common culture media are bismuth sulfite agar, MacConkey agar, deoxycholate citrate agar, xylose lysine deoxycholate agar, salmonella-shigella agar, etc.

String test for Lab diagnosis of Vibrio cholerae

V. cholerae emulsified in sodium deoxycholate, it lyses the cell wall and releases DNA giving a mucoid “string” when a loop is drawn away.

E-TEST (Epsilometer): Principle, Procedure, Results

Quantative method for detecting MIC by using the principles of both dilution and diffusion of antibiotics into the medium.

Modified Hodge Test (MHT) for Carbapenemase Detection

Modified Hodge test (MHT) is a simple phenotypic test for the detection of the presence of carbapenemase enzyme in bacteria.

Stokes Disc Diffusion Method: Principle, Procedure, Results

Stokes’ disc diffusion method allows each individual isolate to be compared with a sensitive control of the same or similar species.

DNase Test: Principle, Procedure, Results

DNase test determines the ability of an organism to hydrolyze DNA.

Atypical Mycobacterial Infections

Atypical mycobacteria include species such as M. avium, M. intracellularae, M. kansasii, M. xenopi, and M. fortuitum.

Hanging Drop Method for Bacterial Motility

The drop hangs from the coverslip, and the petroleum jelly forms a seal that prevents evaporation. This preparation gives good views of microbial motility.

Toluidine Blue Staining in Microbiology: Procedure, Uses

Bacteria are easier to detect in broth culture if the preparation is stained using toluidine blue rather than stained by the Gram staining technique.

Virulence Factors of Uropathogenic E. coli

Virulence factors of UPEC are adhesins (P fimbriae), K antigen, hemolysin and aerobactin system.

Specimen Collection for UTI Diagnosis

Clean-catch midstream urine, suprapubic aspiration and straight catheter techniques are common method of urine sample collection.

Etiology and Treatment of Urinary Tract Infections (UTI)

Majority of community-acquired UTIs in elderly women are caused by E coli. Preferred drugs are nitrofurantoin, trimethoprim-sulfamethoxazole, etc.

New York City Medium: Composition, Uses

New York City medium is primarily designed for the isolation of pathogenic Neisseria. It also supports the growth of genital mycoplasmas.

Methyl Red (MR) Test: Principle, Procedure, Results

Certain bacteria ferment glucose to produce stronger acids that take the media pH below 4.4 in which Methyl Red indicator turns red.

Gelatin Hydrolysis Test: Principle, Procedure, Results

Gelatin hydrolysis test determines the ability of an organism to produce gelatinases that liquefy gelatin.

Microbiology Laboratory Safety Rules and Procedure

Safety in a microbiology laboratory is important in the prevention of infection because virulent and/or potentially pathogenic microorganisms are cultured (grown) there. 

Bile-Esculin test for Enterococcus species

Bile-esculin test is widely used to differentiate Enterococci and Non-enterococcus group D streptococci from non-group D viridans group streptococci.

Salt Tolerance Test for Enterococcus species

Salt tolerance test determines the ability of an organism to grow in high concentrations of salt (6.5%).

Ziehl-Neelsen Technique-AFB Staining

Ziehl-Neelsen acid fast stain is designed to stain bacterial cells containing long chain fatty (mycolid acids) such as Mycobacterium.

Sodium Hypochlorite Centrifugation Technique to Concentrate AFB

Sodium hypochlorite centrifugation technique is used to concentrate the AFB present in the sputum, as it increases the chances of detecting AFB.

Broth Dilution Method for MIC Determination

MIC can be determined by broth dilution or agar dilution methods. Broth dilution testing allows the option of providing both quantitative MIC and qualitative results.

PYR Test: Principle, Procedure, Results

Some gram-positive cocci such as Enterococcus produces enzyme L-pyrroglutamylaminopeptidase that hydrolyze PYR substrate.

CAMP Test: Principle, Procedure, Results

Group B Streptococci produce CAMP factor that acts synergistically with beta-lysin of S. aureus.

Trans-Isolate (T-I) Medium

Tran-isolate medium is used to inoculate and transport CSF sample, If the CSF cannot be transported to a microbiology laboratory immediately.

Handwashing and hygiene: Why do we wash our hands

Proper Hand-washing technique. Learn when and how you should wash your hands to stay healthy.

Rose Bengal Plate Test (RBT) for Brucella

Rose Bengal test is a simple, rapid slide-type agglutination assay performed with a stained B. abortus to diagnose brucellosis.

Brucellosis: Etiology, Pathogenesis, Lab Diagnosis

Brucellosis, also known as “Undulant fever”, “Mediterranean fever” or “Malta fever” or “Bang’s disease”  is a zoonosis caused by Brucella melitensis.

Typhus Fever

Vibrio Cholerae: Lab Diagnosis

Chlamydia Infections: Causes, Symptoms, Diagnosis, Treatment

Q Fever: Etiology, Pathogenesis, Lab Diagnosis

Q fever is caused by the intracellular bacterium Coxiella burnetii and is endemic in nearly every country in the world.

Catalase test: Principle, Procedure, Results, Uses

Catalase test is used to distinguish among Gram-positive cocci. Staphylococci are catalase-positive but Streptococci are catalase-negative.

List of Major sexually transmitted diseases and their causative agents

Sexually transmitted diseases (STDs) or infections (STIs), are passed from one person to another through sexual activity including vaginal, oral, and anal sex.

Enterobacteriaceae Family: Common Characteristics

Enterobacteriaceae is a family of gram-negative rods which are catalase positive and oxidase negative.

Weil Felix Test: Principle, Procedure, Limitation

Weil-Felix is a nonspecific agglutination test that detects anti-rickettsial antibodies in patient serum using OX strains of Proteus vulgaris.

Bacterial Transformation: Mechanism

Process of random uptake of free DNA fragments by the competent bacteria from the surrounding environment.

Colony Morphology of Bacteria

A colony is defined as a visible mass of microorganisms. Colony characteristics of microorganisms help in their identification.

Infectious causes of Cancer: Bacteria, Virus and Parasites

Long-term storage of Bacterial Strains

Lab Diagnosis of Lower Respiratory Tract Infections

Microbiology Specimen Collection Guidelines

Blood Culture: Key points for Lab diagnosis

Modified Kirby-Bauer Disc Diffusion Method

Modified Kirby-Bauer disc diffusion test method is a reference method to test the susceptibility of a bacterial isolate in a clinical laboratory.

Antibiotics used in routine Antimicrobial susceptibility testing (AST)

What does Susceptible, Intermediate, and Resistant Mean?

Susceptible organism is likely to respond to treatment with this drug, at the recommended dosage but resistant wont respond.

Selection of Antimicrobials for Antimicrobial Testing

Preparation of Antibiotic Stock Solutions and Discs

How to store commercial antimicrobial discs

Satellitism Test for Haemophilus influenzae

Haemophilus spp may grow on sheep blood agar very close to the colonies of Staphylococcus aureus.

List of Bacterial Diseases transmitted by insects

RPR Test: Principle, Procedure, Interpretations

RPR test is a macroscopic, nontreponemal flocculation card test used to screen for syphilis. RPR test measures IgM and IgG antibodies to lipoidal material.

Gram-Positive vs. Gram-Negative Bacteria

Gram positive bacteria appear purple and gram-negative bacteria appear pink when stained by Gram-staining methods.

Anti-streptolysin O Titer: ASO Test

Rapid latex agglutination test for the qualitative and semi-quantitative determination of anti-streptolysin-O antibodies (ASO) in serum.

Lab Diagnosis of Meningitis-Key Points

Common etiologic agents of acute meningitis are enteroviruses and bacteria (S. pneumoniae, Neisseria meningitidis, Haemophilus influenzae).

Inducible Clindamycin Resistance (D Test)

Inducible clindamycin resistance should be checked in all staphylococci that are erythromycin-resistant and clindamycin susceptible or intermediate.

Laboratory Diagnosis of Haemophilus influenzae

Gram-negative, oxidase-positive, coccobacilli, which requires X and V factors for the growth.

How to identify Streptococcus pneumoniae?

Gram positive diplococci (lanceolate shaped), alpha hemolysis, optochin sensitive and bile soluble isolates are S.pneumoniae.

Biochemical Tests to identify Mycobacteria, NTM

Tests are; Tween-80 hydrolysis test, niacin test, nitrate reduction test, tellurite reduction test, urea hydrolysis test and citrate utilization test.

Novobiocin Susceptibility Test: Principle, Procedure, Results

Novobiocin test is used to differentiate CONS and presumptively identify the isolate as Staphylococcus saprophyticus (novobiocin resistant).

IMViC Tests: Principle, Procedure, Results

IMViC is an acronym that stands for four different tests; indole test, methyl red test, Voges-Proskauer test, and citrate utilization test.

MUG (Beta-Glucuronidase) Test for E. coli

Escherichia coli produces the enzyme beta-D-glucuronidase, which hydrolyzes a substrate giving blue fluorescence.

Common Cause of Bacteremia and Sepsis

Most common cause are E. coli, S. aureus, Salmonella, Klebsiella pneumoniae, S. pnuemoniae and H. influenzae.

Guidelines for Routine Antibiotic Susceptibility Testing (AST)

Triple Sugar Iron (TSI) Agar: Principle, Results, and Interpretation

TSI test determines whether a gram-negative rod utilizes glucose, and lactose or sucrose fermentatively and forms hydrogen sulfide.

Identification of Pseudomonas aeruginosa

Gram negative rods, catalase positive and oxidase positive. It produces pigments (pyocyanin and pyoverdin).

Neisseria gonorrhoeae: Disease, Pathogenesis, Lab Diagnosis

Neisseria gonorrhoeae is a gram-negative kidney-shaped diplococci. It causes gonorrhea, a sexually transmissted infection.

Neisseria meningitidis Virulence Factors

Major virulence factors of Neisseria meningitidis are capsular polysaccharide, outer membrane proteins, endotoxin and IgA protease.

Laboratory diagnosis of Syphilis

Syphilis is diagnosed by using dark field microscopy, non-treponemal tests (VDRL, RPR) or treponemal tests (TPHA, FTA-ABS).

FTA-ABS Test: Principle, Procedure, Results

FTA-ABS is an indirect fluorescent antibody technique used as a confirmatory test for syphilis. FTA-ABS is the first serological test to become positive following infection.

VDRL Test: Principle, Procedure, Results

Venereal disease research laboratory (VDRL) test is a nonspecific flocculation test for the screening of syphilis.

Clinical Specimens for Anaerobic Culture

Sample from sites known to have anaerobes as part of the normal flora (eg mouth) is unacceptable for anaerobic culture.

Importance of Gram Stain in Anaerobic Bacteriology

Positive gram stain with negative culture report gives information regarding the adequacy of sample collection, transport, and also of culture methods used.

Anaerobic Culture Media

Commonly used anaerobic culture media are; Robertson's cooked meat broth, anaerobic blood agar, egg-yolk agar, bacteroides bile esculin agar.

Extracellular and Intracellular Bacteria

Obligate intracellular bacteria cannot be grown in artificial media (agar plates/broths) in laboratories but requires viable eukaryotic host cells.

Chlamydia trachomatis: Properties, Disease, Lab Diagnosis

Chlamydia trachomatis, is an obligate intracellular bacteria which causes pelvic inflammatory disease and other infections (e.g. eye).

Shigella: Disease, Properties, Pathogenesis, Lab Diagnosis

The causative agent of Bacillary dysentery, Shigella is a member of family Enterobacteriaceae. It is non-motile, non-lactose fermenter.

Campylobacter Jejuni: Disease, Properties, Lab Diagnosis

The most common cause of gastroenteritis worldwide, Campylobacter is a curved, gram-negative rod. It is an oxidase-positive microaerophile.

Optochin Sensitivity Test: Principle, Procedure, Results

Optochin (ethylhydrocupreine hydrochloride) lyses pneumococci (positive) but alpha-streptococci are resistant (negative).

Bile Solubility Test: Principle, Procedure, Results

Bile solubility test differentiates S. pneumoniae (positive) from alpha-hemolytic streptococci (negative).

Citrate Utilization Test: Principle, Procedure, Results

Citrate test determines the ability of an organism to utilize sodium citrate as source source of carbon.

Bacitracin Test: Principle, Procedure, Results

Bacitracin test differentiates S. pyogenes (inhibited) from other beta-hemolytic streptococci.

Streptococcus pneumoniae (pneumococcus): Disease, Properties

Pneumococcus is lanceolate shaped gram-positive cocci and causes pneumonia and meningitis. Its is optochin sensitive and bile soluble.

Wolbachia Bacteria may make mosquitoes resistant to malaria parasite

Bacterial Growth Curve: Phases, Significance

Typical growth curve of microorganisms in a closed system consists of distinct phases called lag phase, log phase, stationary phase, and death phase.

Oxygen Requirements for Pathogenic Bacteria

Microorganisms can be classified as obligate aerobes, facultative, microaerophilic, aerotolerant and obligate anaerobes based on their oxygen requirements.

Biosafety level 1 (BSL1) guidelines for teaching laboratories

Work with microbes at the K–12 level, informal education settings and in undergraduate non-microbiology laboratories would almost always be at BSL1.

Biochemical Tests for Bacterial Identification

Catalase test, oxidase test, MUG test, optochin sensitivity test, bacitracin sensitivity test, coagulase test, etc are some of the common biochemical tests.

Size, Shape, Arrangement of Bacteria

Bacteria exist in four basic morphologies: cocci; rod-shaped cells, or bacilli; spiral-shaped cells, or spirilla; and comma-shaped cells, or vibrios.

E. coli: Only Bacteria that win records number of Nobel Prizes

E. coli is the preferred model organism for different experiments as it is easy to grow and work within the laboratory.

Culture Media: PH Indicators, Color of Colonies

Characteristics pigmentation observed in the culture media is because of the changes in the pH of the medium.

Motility Patterns of Bacteria

Motility patterns of Gram-negative bacteria are also used for their identification. Most of the Gram-positive bacteria are non-motile.

Peptidoglycan: Structure, Function

Peptidoglycan consists of carbohydrate backbone composed of alternating units of NAG and NAM molecules attached through β-1,4-glycosidic bonds.

Transposons: Definition, Types, Functions

Transposons, also called 'jumping genes' are mobile genetic elements. Barbara McClintock got Nobel Prize for the study of transposons.

Cytoplasmic Granules in Bacteria

Concentrated deposits of certain substances which are presented/located in the cytoplasm of certain bacteria.

Teichoic Acid: Structure, Functions

Teichoic acids are fibers of glycerol phosphate or ribitol phosphate and is located in the cell-wall of gram-positive bacteria.

Lipopolysaccharide (LPS) Layer

Lipopolysaccharide (LPS) layer also called the outer membrane is the outermost layer present in the cell wall of gram-negative bacteria.

Bacterial Pili (Fimbriae): Types, Functions

Pili or fimbriae are hair-like filaments that help pathogen in adherence to host cells. Sex pili play role in conjugation.

Differences between Exotoxins and Endotoxins

Bacterial toxins are broadly divided into two general categories: exotoxins (secreted outside the cell) and endotoxins (LPS).

Flagella: Structure, Arrangement, Function

Flagella are long, whiplike appendages that move the bacteria toward nutrients and other attractants

Bacterial Spores: Structure and Spore-Forming Bacteria

Bacterial spores are highly resistant, dormant structures formed in response to adverse environmental conditions

Bacterial Capsule: Importance, Capsulated Bacteria

Capsule is a gelatinous layer covering the bacterium and is a major virulence factor of S. pneumoniae, H. influenzae, etc.

Staphylococcus aureus: Disease, Properties, Lab Diagnosis

Frequent colonizer of skin, S. aureus is a major cause of surgical wound infection. This gram-positive cocci is catalase and coagulase +ve.

Salmonella: Properties, Disease, Lab Diagnosis

Escherichia coli (E. coli): Properties and Identification

Normal flora of GI tract, E.coli is a major cause of urinary tract infections. It is lactose fermenting, gram negative bacilli.

Pathogenicity Islands: Properties and Types

PAIs are large genomic islands located in the chromosome which codes for numerous virulence factors such as toxins, invasions, iron uptake.

Isolation of ESBL producing E. coli from Urine

Variations in Gram Staining Results

`Category A Infectious Microorganisms

Food Poisoning: Definition, Causative Agents

Enterohemorrhagic Escherichia coli (EHEC)

EHEC can cause severe foodborne diseases; diarrhea or hemorrhagic colitis. It can not ferment sorbitol. EHEC O157:H7 is a major strain.

Important Facts About Cholera

Collection and Transport of Stool Specimens

Urease Test: Principle, Procedure, Results

This test determines the ability of an organism to produce the enzyme urease which hydrolyzes urea.

Oxidase test: Principle, Procedure, Results

Organism having cytochrome oxidase oxidizes tetramethyl-p-phenylenediamine hydrochloride to indophenol (a dark purple-colored) compound.

Pseudomonas aeruginosa: Infections, Pathogenesis

Non-culturable Pathogenic Bacteria: Challenge to Lab Diagnosis

We can not culture T. pallidum, M. leprae, Chlamydia trachomatis, Coxiella burnetti and Rickettsia in in-vitro culture media.

Leprosy: Etiology, Pathogenesis, Lab Diagnosis

Also known as Hansen’s disease, leprosy is a chronic infectious disease caused by an acid-fast bacillus, Mycobacterium leprae.

Coagulase Test: Principle, Procedure, Results

Coagulase test detects clumping factors and bound coagulase and differentiates Staphylococcus aureus (positive) from CoNS (negative).

Indole Test: Principle, Procedure, Results

Indole test determines the ability of an organism to split tryptophan to form indole.

Cultivation of Aerobic and Anaerobic Bacteria

Membrane Filter Technique

Membrane filter technique is an effective, accepted technique for testing fluid samples for microbiological contamination.

Maintenance and Preservation of Pure Cultures of Bacteria

Isolation and Enumeration of Bacteria