4.Systematicbacteriology(A)...............................................................................

systemic bacteriology..................................................................................................................................................

1. Chapter 4 SYSTEMATIC BACTERIOLOGY (A) Dr Sonal Saxena Dr Arpita Saxena

2. GENERAL CONCEPTS Classification, nomenclature, and taxonomy of bacteria General concepts of pathogenesis and disease spectrum

3. NOMENCLATURE AND TAXONOMY OF BACTERIA Enable easy i dentification of microbes Bergey’s manual — systematic classification Carolus linnaeus introduced classification system consisting of domain, kingdom, phylum, class, order, family, genus and species Subspecies and serotypes are based on antigens Clone — derived from a single cell; almost all are identical Colony – represents one clone Strain – derived from a single source Kingdom → Division → Class → Order → Family → Tribe → Genus → Species

4. CLASSIFICATION 1) Phylogenetic R epresented as a branching tree One characteristic- for division at each branch or level 2) Adansonian classification Numerical Taxonomy All characteristics are taken into account Several characteristics are compared 3) Molecular or genetic classification Degree of genetic relatedness Based on the genes, DNA relatedness G:C ratio ( guanine:cytosine ): Constant within same species Used for classifying viruses. 4) Intraspecies classification Beyond species level Diagnostic and epidemiological Classified as: Biotypes: Biochemical properties Serotypes: Antigenic features Phage types: Bacteriophage susceptibility Colicin types: Production of bacteriocins

5. MOLECULAR EPIDEMIOLOGY Intraspecies typing by newer techniques to the evolution of molecular epidemiology Phenotypic – (expressed characteristics) b y: Electrophoretic typing Immunoblotting Genotypic (direct analysis of genes, chromosomal and extra-chromosomal DNA) by: Plasmid profile analysis Restriction endonuclease analysis Southern blotting Polymerase chain reaction Nucleotide sequence analysis

6. TYPE CULTURES Representatives of all species Maintained by International Reference Labs Made available for study and comparison ATCC (American Type Culture Collection) NCTC — National Collection of Type Cultures (Public Health England)

7. GENERAL CONCEPTS OF PATHOGENESIS AND DISEASE SPECTRUM

8. PATHOGENESIS Fig. 4.2 diagram showing the entry, invasion and damage to host tissue by pathogenic bacteria

9. PATHOGENESIS Exposure to the pathogen(bacteria) and route of entry Bacteria enters through an appropriate route Encounter host phagocytes  exhibit tissue tropism  multiplication  production of toxin and enzymes  cell destruction  tissue damage  prevention of host defence  disease manifestation  clinical features Routes of entry of some disease-causing bacteria

10. PATHOGENESIS Incubation period: time between exposure (entry of pathogen) to the first manifestation of symptoms (and clinical signs)

11. OVERVIEW OF IMPORTANT BACTERIA ASSOCIATED WITH HUMAN HEALTH AND DISEASE Gram-positive cocci Staphylococcus, Streptococcus, Pneumococcus, Enterococcus Anerobic Gram-Positive Cocci

12. OVERVIEW OF IMPORTANT BACTERIA ASSOCIATED WITH HUMAN HEALTH AND DISEASE Gram-positive cocci : Staphylococcus, Streptococcus, Pneumococcus, Enterococcus Gram-positive bacilli: Bacillus, Corynebacterium, Actinomycetes, Clostridium Gram-negative cocci : Neisseria, Moraxella Gram-negative bacilli : Enterobacterales , Vibrios , Non- fermenters Miscellaneous bacteria: Mycobacteria, Spirochetes, Mycoplasma, Chlamydia, Rickettsia

13. GRAM-POSITIVE COCCI Staphylococci Spherical, 1 µm diameter Arrangement: Grape-like clusters Grows in ordinary culture media Produce potent toxins, enzymes and other metabolites Develops resistance to antibiotics Gram-positive cocci in clusters: Staphylococcus aureus (Source: Department of Microbiology, Pondicherry Institute of Medical Sciences[PIMS], Puducherry)

14. Classification Staphylococci are classified on basis of the coagulase test as coagulase-positive or -negative. Staphylococcus aureus is coagulase-positive. Culture characteristics Staphylococci grow readily on ordinary media Temperature range of 10–42°C, the optimum being 37°C pH- 7.4–7.6

15. GRAM- POSITIVE COCCI Common infections by Staphylococcus aureus  Localised suppurative lesions: Skin and mucosa  Disseminated: Bloodstream infections, osteomyelitis, meningitis, pericarditis pneumonia Coagulase negative Staphylococci ( CoNS )  S .epidermidis , S.lugdenunsis , S.haemolyticus , S.hominis  Commensals in the body  S.epidermidis : Most common CoNS infection in humans - Biofilm formation: important in pathogenesis - Healthcare-associated infections in immunocompromised hosts

16. Coagulase-negative staphylococci ( CoNS ) S. epidermidis S. lugdunensis S. haemolyticus S. hominis Habitat: Commensals in the throat, anterior nares, the skin of the perineum, and the web- spaces of the hands. Virulence of CoNS Biofilm formation is an important factor in the pathogenesis of infections by S. epidermidis . A biofilm is an extracellular polysaccharide matrix , which protects bacteria from antibacterial agents and aids colonisation and resistance of infections.

17. Common pathogenic species S. saprophyticus may be present on healthy human skin and the periurethral area and can cause urinary tract infection, particularly in sexually active young women. S. epidermidis Most common cause of CoNS infections in humans Cause disease when the host’s defences are breached or healthcare-associated infections in immunocompromised hosts

18. GRAM- POSITIVE COCCI 2) Micrococci Gram-positive cocci in tetrads, pairs or irregular clusters Rarely cause infection in healthy hosts

19. 3) Streptococci Morphology: Streptococci are gram-positive cocci arranged in chains or pairs. Culture characteristics: R equire blood or serum for growth and are nutritionally more exacting. Growth is better under 5–10% CO2, optimum temperature is 37°C (range 22–42°C). Habitat: Part of the normal flora of human and animal bodies. Some of them are human pathogens.

20. Classification of Streptococci 1. Based on oxygen requirement , they are classified as : Facultative anaerobes Obligate anaerobes 2. Based on hemolysis produced on sheep or horse blood agar , streptococci are classified as: Alpha hemolytic :greenish discolouration around colonies (partial hemolysis). E.g. viridans group of Streptococci, Pneumococci Beta hemolytic : clear zone of complete hemolysis. E g. Streptococcus hemolyticus Non- hemolytic: Fecal Streptococci (Enterococcus)

21. Classification of beta hemolyitic streptococci Lancefield’s grouping Based on the carbohydrate antigen (C) on the cell wall, Rebecca Lancefield (1933) serologically grouped beta ( β ) - hemolytic streptococci. These groups are known as Lancefield’s groups. So far, 20 of these groups have been identified, named A–H and K–V (without I and J). Griffith typing: It is used for the further classification of S. pyogenes . Based on the M proteins on the cell surface, they are subdivided into eighty M types (types M1, M2, M3, and so on).

22. Hemolytic streptococci Alpha ( α) - hemolytic streptococci They produce a greenish discolouration with partial hemolysis around the colonies. The zone of lysis is small( 1or2mmwide). Most alpha-hemolytic streptococci are commensals in the throat and may cause opportunistic infections in rare cases. Examples : Members of the viridans group of streptococci and pneumococci. Beta ( β)- hemolytic streptococci They produce a sharply defined, clear, colourless zone of complete hemolysis, 2–4 mm wide, around their colonies. The term ‘hemolytic streptococci’ applies strictly to beta-hemolytic strains. Most pathogenic streptococci belong to this group.

23. Infections caused by streptococci Streptococcus pyogenes & Streptococcus agalactiae are important ones

24. Infections Streptococcus pyogenes or Group A Streptococcus These are human pathogens , which produce a diverse array of diseases, ranging from self-limited conditions (pharyngitis, impetigo, and erysipelas) to severe, invasive infections ( bacteremia , necrotising asciitis , myositis, and streptococcal toxic shock syndrome. Streptococcal pharyngitis or skin infections may have lasting sequelae such as post-streptococcal rheumatic disease or glomerulonephritis respectively.

25. Group B streptococci (GBS)—Streptococcus agalactiae It is normal inhabitant of the vaginal tract and is associated with neonatal meningitis and septicemia . It is also an important pathogen of cattle, producing bovine mastitis . Nine capsular serotypes have been identified, antibodies to which confer type-specific protection.

26. Pneumococci ( S. Pneumoniae) Gram-positive diplococci; capsulated Flame-shaped/lanceolate appearance India ink stain: Capsule visualisation Culture characteristics S. pneumoniae have complex growth requirements. They grow only in enriched media such as sheep blood agar and chocolate agar with 5–10% CO2. Growth appears as 0.5–1 mm, dome-shaped, glistening colonies showing alpha-hemolysis , which subsequently become flat with raised edges, central umbonation , and concentric rings ( Draughtsman or carom coin appearance). Habitat S. pneumoniae is found in the throats of approximately half the population sampled at any time. Enterococci- electron micrograph showing oval cells arranged in pairs (Source: Public Health Image Library, ID266/ Janice Haney Carrr / CDC)

27. Infections and virulence factors Infections Meningitis Lobar pneumonia Bacteremia

28. Enterococci Enterococcus group has E. faecalis, E. faecium, E. durans Oval diplococci (cocci at an angle to each other), non-capsulated. Usually non-hemolytic (can be alpha or beta hemolytic) Habitat E. faecalis is most often isolated from human sources; it is a part of the microbiota of the human gut. Identification They are identified by their ability to grow on bile and cause esculin hydrolysis, do not grow in 6.5% NaCl, grow on can tellurite blood agar, on which they produce black colonies. Infections Urinary tract infection Wound infection Endocarditis Infections of biliary tract, septicemia and intra- abdominal abscesses complicating diverticulitis and peritonitis

29. ANAEROBIC GRAM- POSITIVE COCCI Peptostreptococci : Normal flora of vagina, intestines and mouth Morphology : Relatively small cocci (0.2– 2.5 μ m). Culture: Many of them are aerotolerant and grow well under 10% CO 2 in an aerobic atmosphere. Species: Peptostreptococcus anaerobius P. magnus . P. asaccharolyticus , P. tetradius , and P. prevotii . Infections Puerperal sepsis ( Peptostreptococcus anaerobius ) other genital infections Wound infections, UTI Osteomyelitis Abscesses of internal organs ( P. magnus )