Table 3.2 Appearance of colonies of some common pathogenic bacteria on two common media after 24 hours of growth. Organism Colony appearance after 24 h on blood agar Colony appearance after 24 h on MacConkey agar Bacillus cereus Dull grey, rough No growth Campylobacter jejuni Grey, smooth, crinkly edge No growth Clostridioides White with halo, swarming Green fluorescent Escherichia coli O157 White/colourless, mucoid, small halo Colourless or pink, smooth Haemophilus influenzae No growth No growth Klebsiella pneumoniae Greyish-white, mucoid Large, pink, mucoid Neisseria gonorrhoeae Very small, colourless No growth Pseudomonas aeruginosa Large, greyish-white, rough, metallic sheen Brownish-white, smooth, mucoid Salmonella typhi Large, white, smooth Large, colourless, smooth Shigella dysenteriae Large, greyish-white Colourless to pink, smooth, crinkly edge Staphylococcus aureus Yellow with halo No growth or very small, yellow Streptococcus pneumoniae Brownish-white with halo No growth Table 3.3 Some common bacterial pathogens from various body sites and the types of disease that they cause. Body site Pathogen Description Disease Skin/wound swab Staphylococcus aureus Gram-positive coccus Infection Streptococcus spp. Gram-positive coccus Infection Clostridioides spp. Gram-positive bacillus Abscess Pseudomonas aeruginosa Gram-negative bacillus Infection Streptococcus pneumoniae Gram-positive coccus Pneumonia Pseudomonas aeruginosa Gram-negative bacillus Chest infection Klebsiella pneumoniae Gram-negative bacillus Pneumonia Legionella spp. Gram-negative bacillus Legionellosis Staphylococcus aureus Gram-positive coccus Chest infection Haemophilus influenzae Gram-negative coccobacillus Chest infection Campylobacter spp. Gram-negative bacillus Diarrhoea Clostridioides difficile Gram-positive bacillus Diarrhoea Escherichia coli O157 Gram-negative bacillus Diarrhoea Salmonella spp. Gram-negative bacillus Diarrhoea Shigella spp. Gram-negative bacillus Diarrhoea Treponema pallidum Gram-negative spiral Syphilis Neisseria gonorrhoea Gram-negative coccus Gonorrhoea Streptococcus spp. Gram-positive coccus Inflammation Chlamydia trachomatis Gram-negative coccobacillus Chlamydial disease Staphylococcus aureus Gram-positive coccus Urinary tract infection Respiratory tract/sputum Gut/faeces Genitourinary tract/urethral swab Table 3.4 Bacterial catalase and oxidase and phenotypes. Bacterium Catalase Oxidase Enteric bacteria (e.g. Escherichia coli, Salmonella, Shigella) + − Bifidobacterium − + Campylobacter jejuni + + Citrobacter + − Clostridioides tetani − − Corynebacterium + − Enterococcus − −* Haemophilus influenzae + + Helicobacter pylori + + Lactobacillus acidophilus − − Neisseria gonorrhoea + + Pseudomonas aeruginosa + + Staphylococcus aureus + − Streptococcus pneumoniae − − Vibrio cholerae + + Ex. You should have noted some key media that would help in identification, shown below: Bacterium Media Notes Staphylococcus aureus Mannitol salt Golden colonies CNA Selective for Gram positives Streptococcus CNA Selective for Gram positives Clostridioides No specific media Pseudomonas aeruginosa CLED Blue agar Table 2.1 Major phyla of the human microbiota. Phylum Gram stain category and morphology Characteristics Notable human pathogens, conditions or diseases Actinobacteria Gram-positive rods or cocci with high GC content in DNA Many produce antimicrobials. Nocardia, an opportunistic pathogen causing respiratory illness or encephalitis. Bacteroidetes Gramnegative rods Obligate anaerobes. Largest and most stable component of the gut microbiota. Carry out many complex metabolic activities that are beneficial to humans. A few species linked to appendicitis, obesity, irritable bowel syndrome (IBS) and diabetes. Cyanobacteria Gramnegative rods or cocci Phototrophic and produce O2. Increased the atmospheric oxygen 1– 2 billion years ago to present levels. Origin of plant chloroplasts. Rarely pathogenic, but some produce toxic blooms in water that, if ingested, can damage the nervous system and liver. Firmicutes Gram-positive rods or cocci with low GC content in DNA Can form spores. Clostridioides (anaerobic) Fusobacteria Gramnegative rods Anaerobes that ferment cellulose. Periodontitis (gum disease), tissue necrosis, premature labour. Proteobacteria Gramnegative, highly diverse group; purple Alphaproteobacteria Brucella Bacillus (aerobic) Chlamydia Betaproteobacteria Neisseria Bordetella Gammaproteobacteria Pseudomonas Escherichia Haemophilus Vibrio Legionella, Klebsiella Deltaproteobacteria No known pathogens Epsilonproteobacteria Campylobacter Helicobacter Table 2.4 Actions of different classes of antibiotics. Class of antibiotic Example Target process Bactericidal or bacteriostatic? Beta-lactams Penicillin Cell wall synthesis Bactericidal Cephalosporins Cefotaxime Cell wall synthesis Bactericidal Glycopeptides Vancomycin Cell wall synthesis Bactericidal Carbapenems Meropenem Cell wall synthesis Bactericidal Lincomycins Clindamycin Protein synthesis Bacteriostatic but bactericidal at high doses Aminoglycosides Gentamicin Protein synthesis Bacteriostatic but bactericidal at high doses Macrolides Azithromycin Protein synthesis Bacteriostatic Tetracyclines Doxycycline Protein synthesis Bacteriostatic Quinolones Ciprofloxacin DNA synthesis Bacteriostatic and bactericidal Sulfonamides Sulfasalazine Other metabolic reactions (e.g. folic acid biosynthesis) Bacteriostatic and bactericidal Table 3.1 Some hazard groups and the associated requirements for their biocontainment and worker protection with PPE (data from Health and Safety Executive, 2013). Hazard group and definition Examples Containment level and requirements Group 1: Nonpathogenic Escherichia coli Containment level 1: Unlikely to cause human disease. Work allowed on open bench. Lab coat, safety glasses. Group 2: Campylobacter jejuni Containment level 2: Can cause human disease and may be a hazard to employees; it is unlikely to spread to the community and there is usually effective prophylaxis or treatment available. Helicobacter pylori Work in a controlled negative pressure air flow environment. Pseudomonas aeruginosa Lab coat, safety glasses/visors, gloves. Staphylococcus aureus Vibrio cholerae Epstein–Barr virus Influenza virus Mumps virus Norovirus Group 3: Bacillus anthracis Containment level 3: Can cause severe human disease and may be a serious hazard to employees; it may spread to the community, but there is usually effective prophylaxis or treatment available. Mycobacterium tuberculosis Work in a closed, sealable laboratory with biohazard signage and a controlled negative-pressure airflow. Work in suitable safety cabinet with HEPA-filtered exhaust. Rickettsia Yersinia pestis Hepatitis A virus Lab coat, safety glasses/visors, gloves, aprons. Rabies virus SARS-CoV-2 Yellow fever virus Group 4: Causes severe human disease and is a serious hazard to employees; it is likely to spread to the community and there is usually no effective prophylaxis or treatment available. No bacteria in this category Ebola virus Lassa fever virus Variola virus Containment level 4: Work with maximum protection and containment measures in isolated, sealable facilities, under health authority control. All material in and out must be sterilised. The air circulation must be isolated. Hazard suits. Table 1.2 Classification of some viruses pathogenic to humans.
