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Bacteriology in medical microbiology, Lecture notes of Medical Microbiology

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2023/2024

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Dr. W.O. Emitaro
SYSTEMIC BACTERIOLOGY
GRAM NEGATIVE BACTERIA
GRAM NEGATIVE DIPLOCOCCI
GENUS: NEISSERIA
Characteristics:
They are non-motile, gram-negative intracellular diplococci.
Rapidly killed by drying, sunlight, heat, and disinfectants.
Ferment carbohydrate producing acid but not gas.
Each coccus is kidney-shaped with adjacent concave sides.
Grow best on complex media under aerobic conditions containing 5% CO.
They are Oxidase positive.
The main species of medical importance are: N. meningitidis and N. gonorrhoea.
N. gonorrhoea
Characteristics:
An obligate parasite of the human urogenital tract.
Antigenic structure:
Antigenically heterogeneous and capable of changing its surface structures.
1. Fimbriae: Hair-like appendages extending from bacterial surface and enhance attachment
to host cells and evade human defence. The fimbriae of almost all strains of N.
gonorrhoea are antigenically different, and a single strain can make many antigenically
distinct forms of fimbriae.
2. Por (Protein I): Pores on the surface of bacteria through which nutrients enter the cell.
3. Opa (Protein II): Important for attachment of bacteria to host cells.
4. RMP (Protein III): Reduction-modifiable protein. It is associated with por in the
formation of pores in the cell.
5. Lipooligosaccharide (LOS): Responsible to damage epithelial cells. Toxicity in
gonococcal infection is largely due to the endotoxic effects of LOS
6. LiP (H8): Gonococcal surface exposed Heat-Modifiable like Opa
7. Fbp (Iron binding protein): Expressed when there is limited available iron supply
8. IgA1 protease: Splits and inactivates major mucosal IgA (IgA1)
Clinical manifestation:
Route of infection: Sexual contact
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SYSTEMIC BACTERIOLOGY

GRAM NEGATIVE BACTERIA

GRAM NEGATIVE DIPLOCOCCI

GENUS: NEISSERIA

Characteristics:

  • They are non-motile, gram-negative intracellular diplococci.
  • Rapidly killed by drying, sunlight, heat, and disinfectants.
  • Ferment carbohydrate producing acid but not gas.
  • Each coccus is kidney-shaped with adjacent concave sides.
  • Grow best on complex media under aerobic conditions containing 5% CO.
  • They are Oxidase positive. The main species of medical importance are: N. meningitidis and N. gonorrhoea. N. gonorrhoea Characteristics: An obligate parasite of the human urogenital tract. Antigenic structure : Antigenically heterogeneous and capable of changing its surface structures.
  1. Fimbriae: Hair-like appendages extending from bacterial surface and enhance attachment to host cells and evade human defence. The fimbriae of almost all strains of N. gonorrhoea are antigenically different, and a single strain can make many antigenically distinct forms of fimbriae.
  2. Por (Protein I): Pores on the surface of bacteria through which nutrients enter the cell.
  3. Opa (Protein II): Important for attachment of bacteria to host cells.
  4. RMP (Protein III): Reduction-modifiable protein. It is associated with por in the formation of pores in the cell.
  5. Lipooligosaccharide (LOS): Responsible to damage epithelial cells. Toxicity in gonococcal infection is largely due to the endotoxic effects of LOS
  6. LiP (H8): Gonococcal surface exposed Heat-Modifiable like Opa
  7. Fbp (Iron binding protein): Expressed when there is limited available iron supply
  8. IgA1 protease: Splits and inactivates major mucosal IgA (IgA1) Clinical manifestation: Route of infection : Sexual contact

Male : Gonococcal urethritis. If complicated: Urethral stricture, Gonococcal epididymitis, Gonococcal epididymo-orchitis Infertility. Female: Gonococcal cervicitis, Gonococcal salpingitis. If complicated: Gonococcal tubo-ovarian abscess, Pelvic peritonitis, Infertility Infant (When delivered through the infected birth canal) causes Gonococcal ophthalmia neonatorum. If untreated and complicated leads to blindness. Laboratory diagnosis : Specimen: Urethral swab, cervical swab, eye swab Smear: Gram-negative intracellular diplococci. Culture: Requires an enriched media like chocolate agar or thayer-martin agar. Grows best in CO 2 enriched aerobic atmosphere with optimal temperature of 35- 37 OC. Fastidious- Dies with exposure to sunlight, room temperature and drying. Small glistening colonies. Culture of urethral exudate from men are not necessary when the gram stain is positive but culture should be done for women. Treatment: Gonorrhoea is difficult to treat because of resistance to lots of antibiotics, especially in developing countries. Penicillin is the drug of choice for susceptible strains. The alternate drugs in penicillin resistant infection or penicillin sensitive individuals include spectinomycin, tetracycline, doxycycline and ceftriaxone. Prevention and control

  • Avoid multiple sexual partner
  • Using mechanical protection methods (condom)
  • Early diagnosis and prompt treatment of cases
  • Contact tracing
  • Screening of high risk population groups
  • Ophthalmic ointment application of erythromycin or tetracycline to the conjunctiva of all new borns Neisseria meningitidis Characteristics:
  • Gram-negative intracellular diplococci.
  • Present in the nasopharynx in 5-10% of healthy people. Antigenic structure :
  1. Capsular carbohydrate: It is important for serogrouping of meningococci and there are 13 serogroups. The most important serogroups associated with disease in humans are A, B, C, Y and W
  1. Capsular polysaccharide. There are six serotypes of H. influenzae, A-F. It is the main virulence factor which provides anti-phagocytic property.
  2. Outer membrane protein.
  3. Lipo-oligosaccharide Clinical features: The bacteria cause diseases most commonly in young children.
  • Acute pyogenic meningitis.
  • Acute epiglottis.
  • Pneumonia.
  • Otitis media.
  • Siusitis.
  • Cellulitis.
  • Acute pyogenic arthritis Laboratory diagnosis : Specimen: Cerebrospinal fluid, sputum, blood, pus Smear: Gram-negative short rods. Culture: Chocolate agar contain both X and V factor; blood agar contain only X factor. Treatment: Ampicillin, Chloramphenicol, Cotrimoxazole, Third generation cephalosporins H. ducreyii
  • Slender, gram-negative, ovoid bacilli, slightly larger than H. influenzae.
  • It causes chancroid (tender genital ulcer).
  • Cultured in special enriched media (20-30% rabbit blood agar) with colonic morphology of small grey glistening colonies surrounded by zone of haemolysis.
  • It is treated by erythromycin, cotrimoxazole and third generation cephalosporins. GENUS: BORDETELLA Characteristics: Minute strictly aerobic non-motile gram-negative rods. Bordetella species of medical importance: B. pertussis Is the causative agent of pertussis or whooping cough Antigenic structure:
  1. Fimbriae: Adheres to ciliated epithelial cells of respiratory tract.
  2. Filamentous haemagglutinin: Adheres to ciliated respiratory tract.
  3. Pertussis toxin: ✓ Lumphocytosis promoting factor. ✓ Histamine sensitizing factor. ✓ Insulin secretion enhancing factor. ✓ Adenylyl cyclase toxin. ✓ Dermonecrotic toxin. ✓ Haemolysin. ✓ Tracheal cytotoxin: Inhibits DNA synthesis in ciliated respiratory epithelial cells. ✓ Lipopolysaccharide: Damages respiratory epithelial cells. Clinical features: Incubation period: 2 weeks Route of transmission is respiratory from early cases and possibly carriers. It has three stages:
  4. Catarrhal stage: During catarrhal stage, the patient is highly infectious but not very ill manifesting with mild coughing and sneezing.
  5. Paroxysmal stage: During paroxysmal stage, the patient presents with explosive repetitive cough with characteristic ‘whoop’ upon inhalation leading to exhaustion, vomiting, cyanosis and convulsion.
  6. Convalescence stage: During convalescence stage, the patient presents with prolonged cough Laboratory diagnosis: Specimen: Saline nasal wash (Preferred specimen), Nasopharyngeal swab or cough droplets on cough plate Smear: Small, non-motile, capsulated, gram-negative cocobacilli singly or in pair, and may show bipolar staining. Culture: Inoculate the primary specimen on Bordet-Gengue agar medium and incubate for 2- 6 days at 37o^ C in a moist aerobic atmosphere which produces small, raised, shiny, mucoid colonies. Treatment: Erythromycin. Administration of erythromycin during the catarrrhal stage of disease promotes elimination of the organism and limits rate of transmission. Treatment after the onset of paroxysmal stage does not alter the clinical course of the disease.

GRAM NEGATIVE RODS

It comprises the following bacterial groups

  1. Oxidase negative
    • Enterobacteriaceae ✓ Lactose-fermenters: Escherichia spp., Klebsiella spp., Enterobacter spp. Citrobacter spp. ✓ Non-lactose fermenters: Salmonella spp. Shigella spp. Proteus spp.
  2. Oxidase Positive.
    • Pseudomonas.
    • Vibrio.
    • Campylobacter.
    • Helicobacter ENTEROBACTERIACEAE Characteristics
  • Named, as well coliforms or enterobacilli
  • Found as normal flora in intestinal tract of humans and animals.
  • Gram-negative, non-spore forming, aerobic and facultative- anaerobic bacteria.
  • Most are motile.
  • Grow over a wide range of temperature in ordinary media.
  • All ferment glucose with acid production.
  • Oxidase negative.
  • Release endotoxin from their cell wall.
  • Some release exotoxin.
  • Most of them have possessed three types of antigens. These are:
  1. H antigen-. Flagellar protein ➢ Found in the flagella. ➢ Possessed by motile enterobacteriaceae. ➢ Heat labile and sensitive to alcohol. May interfere with agglutination by O antisera.
  2. K antigen- Capsular polysaccharide or protein. ➢ Surrounds the cell wall. ➢ Heat labile and may be associated with virulence. May interfere with agglutination by O antisera.
  3. antigen- Outer membrane lipopolysaccharide. ➢ Found in the cell wall of enterobacteriaceae. ➢ Resistant to heat and alcohol, and usually detected by bacterial agglutination. ➢ Antibodies to O ags are usually IgM

GENUS: ESCHERICHIA.

Main species of medical importance is Escherichia coli. Escherichia coli Characteristics :

  • Normal flora in human and animal gastrointestinal tract.
  • Found in soil, water and vegetation.
  • Most are motile; some are capsulated. Clinical features:
  • Urinary tract infection- cystitis, pyelonephritis
  • Wound infection- appendicitis, peritonitis
  • Neonatal septicaemia and meningitis
  • E. coli - associated diarrheal disease
  1. Enteropathogenic E. coli (EPEC): causes outbreaks of self-limiting infantile diarrhoea. They also cause severe diarrhoea in adults. Antibiotic treatment shorten the duration of illness and cure diarrhoea
  2. Enteroinvasive E. coli (EIEC): Non-motile, non-lactose fermenting E.coli invade the mucosa of the ileum and colon, and causes shigellosis-like dysentery in children in developing countries and travellers to these countries
  3. Enterotoxigenic E.coli (ETEC): Colonization factor of the organism promote adherence to epithelial cells of small intestine followed by release of enterotoxin which causes toxin-mediated watery diarrhoea in infants and young adults.. It is an important cause of traveller’s diarrhoea. Antibiotic prophylaxis can be effective but may increase drug resistance (Should not be uniformly recommended)
  4. Entero haemorrhagic E.coli (EHEC): Cytotoxic verotoxin producing E.coli serotype O157:H7. causes haemorrhagic colitis (severe form of diarrhoea), and haemolytic uremic syndrome characterized by acute renal failure, haemolytic anaemia and low platelet count.
  5. Enteroaggressive E.coli ( EAEC): Adhere to human intestinal mucosal cells and produce ST-like toxin and haemolysin, and causes acute and chronic diarrhoea in persons in developing countries. Produce food-borne illness in developed countries Laboratory diagnosis :
  • Specimen: Urine, pus, blood, stool, body fluid
  • Smear: Gram-negative rods
  • Culture: Lactose-fermenting mucoid colonies on MacConkey agar and some strains are haemolytic on blood agar. Treatment: Base on antibiotic sensitivity pattern

GENUS: CITROBACTER

  • It is gram-negative lactose fermenting motile rods, and opportunistic pathogen.
  • Medical important species is Citrobacter freundii.
  • Citrobacter freundii is associated with urinary tract infection, wound infection and septicaemia in immunocompromised and chronically deblitated patients. GENUS: SALMONELLA
  • Most isolates of salmonellae are motile.
  • It grows readily on simple media
  • It never ferment sucrose or lactose
  • Form acid +/- acid from glucose or mannose
  • Species of medical importance are: ✓ S. typhiS. paratyphiS. enteritidis Clinical features:
  1. Enteric fever : It is caused by S. typhi and S. paratyphi , and transmitted by faecal-oral route via contaminated food and drinks. Incubation period: 10-14 days. Predisposing factors: ✓ Reduced gastric acidity. ✓ Disrupted intestinal microbial flora. ✓ Compromised local intestinal immunity Both manifest with persistent fever, headache, malaise, chills, enlargement of liver and spleen, and skin rashes. Paratyphoid fever is milder than typhoid fever Complications: ✓ Intestinal perforation ✓ Lower gastrointestinal bleeding ✓ Dissemination to different body organs including meninges and brain Mortality rate ✓ Untreated cases: 10-15% ✓ Treated cases: < 1% 2.
  2. Bacteremia with focal lesions Causative agent: S. choleraesuis Manifests with blood stream invasion with focal lesions in lungs, bones and meninges Intestinal manifestation are often absent
  3. Gastroenteritis

It is caused by S. enteritidis, S. typhimurium IP= 8-48 hrs. It manifests with initial watery diarrhoea, and later bloody mucoid diarrhoea associated with crampy abdominal pain and tenesmus. Bacteremia is rare (2-3 % of cases) and it usually resolves in 2-3 days Laboratory diagnosis: Specimen:

  1. Blood, Bone marrow, stool, urine and serum for enteric fever. Blood – 80% positive in the first week. Stool- 70 - 80% positive in the second and third week.. Urine- 20% positive in the third and fourth week. Serum for widal test- positive after the second week of illness.
  2. Stool for gastroenteritis. Gram reaction: Gram-negative rods Culture: Bacteriologic methods for salmonella isolation 1. Differential medium. For rapid isolation of lactose non-fermenters Prevention and control ✓ Sanity measures like hygienic food and drink handling, and avoid carriers from food handling until properly treated ✓ Provision of vaccine ✓ Injectable acetone-killed S. typhi suspensions GENUS: SHIGELLA Species of medical importance are:
  • Subgroups ✓ S. dysenteriae A ✓ S. flexneri B ✓ S. boydiiS. sonnei C D In developing countries, shigellosis (bacillary dysentery) is caused by S. flexneri and S. dysenteriae. It is found in human intestinal tract as pathogen. Pathogenesis and Clinical features :
  • Route of infection is fecal-oral route
  • Inoculum dose: 103 organisms
  • Pathogenicity determinant: ✓ Endotoxin: irritate the bowel wall Exotoxin: ✓ Enterotoxin and neurotoxin S. dysenritiae type 1 (shiga bacillus) produce heat labile exotoxin mediated diarrhea. IP: 1- 2 days It causes shigellosis (bacillary dysentery) characterized by sudden onset of bloody mucoid diarrhea, abdominal cramp, tenesmus, fever, generalized muscle ache and weakness.

Specimen: Urine, pus, blood, ear discharge Smear: Gram-negative rods Culture: Produce characteristic swarming growth over the surface of blood agar. Treatment: Based on sensitivity testing. GENUS YERSINIA General characteristics:

  • Animals are natural hosts of yersinia, and humans are accidental hosts of yersinia infection
  • Short, pleomorphic microaerophilic or facultatively anaerobic gram negative rods exhibiting bipolar staining with special stains
  • Important human pathogens ✓ Y_. pestis_ ✓ Y. pseudotuberculosisY. enterocolitica Yersinia pestis. Plague bacillus with gram negative, non-motile, facutatively anaerobe possessing bipolar granules Antigenic structure :
  • LPS: ✓ Endotoxic effect Envelope protein (Fraction I) ✓ Antiphagocytic property V-W antigens: ✓ Plasmid gene-encoded virulence factor ✓ Exotoxin (lethal for mice/unknown role in humans) Pathogenesis and clinical features : Rat flea ( Xenopsylla cheopis ) gets infected by biting an infected rodent → infected rat flea bites human (accidental host) → organism migrate to regional lymph nodes from the site of bite (bubonic plaque) and gets into the blood via lymphatics (septicaemic plaque), or Primary pneumonic plaque results from inhalation of infective droplets, usually from an infected coughing person. IP=2-6 days. Human Plaque: 3 types
  1. Bubonic plague: Fever, vomiting, painful lymphadenitis(buboes) in the groin or axillae
  2. Pneumonic plague: Ip is 1-3 days. Profuse mucoid or bloody expectoration with signs of pneumonia
  1. Septicaemic plague. Fever, vomiting, diarrhoea, hypotension, altered mentation, renal and heart failure, intra vascular coagulopathy Lab. Diagnosis : Specimen: Lymphnode aspirate, CSF, blood Smears: Wright’s stain, immunofluorescence stain, methylene blue stains, basic fuchsin stain Wayson’s stain to demonstrate bipolar granules Culture: Grow in blood agar or MacConkey agar NB: All cultures are highly infectious and must be handled with extreme caution Biochemical reaction: Treatment : Streptomycin Tetracycline Streptomycin + tetracycline or chloramphenicol Prevention and control : Chemoprophylaxis for contacts of patients. Formalin-killed vaccine for travellers to hyperendemic areas and high risk persons Yersinia enterocolitica and Yersinia pseudotuberculosis
  • Non-lactose fermenting gram negative rods, Urease positive, Oxidase negative
  • Human infection occurs by contaminated food and drinks from domestic animals or rodents Antigenic structure.
  • Invasion locus.
  • AIL (attachment invasion locus) Pathogenesis and clinical feature : Route of transmission: Contaminated food and drinks Inoculum dose: 108-109 org IP=5-10 days Yersinosis : Enterocolitis. Fever, abdominal pain, toxin and invasion-mediated diarrhoea. Usually self-limited disease. Post-diarrheal diseases. Arthritis. skin rash/nodules. Complication: Sepsis/ Meningitis Lab. Diagnosis : Specimen: Stool, blood, rectal swab Culture: Grow in routine enteric media Treatment: Fluid replacement for enterocolitis (Antibiotics not required). Cephalosporin (3rd generation) + Aminoglycosides for sepsis/ meningitis Prevention and control: Conventional sanitary precautions GENUS: PSEUDOMONAS

Prevention and control :

  • Special attention to sinks, water baths, showers and hot tubs
  • Polyvalent vaccine to high risk groups. GENUS: VIBRIOS Actively motile, gram-negative curved rods. Species of medical importance is Vibrio cholerae - 01 Vibrio cholerae Characteristics :
  • Found in fresh water, shellfish and other sea food.
  • Man is the major reservoir of V. cholerae - 01, which causes epidemic cholera.
  • Readily killed by heat and drying; dies in polluted water but may survive in clean stagnant water, esp. if alkaline, or sea water for 1-2 weeks. Antigenic structure : O antigen. Six major subgroups. All strains possess a distinctive O antigen and belong to subgroup I with subdivision into three serotypes; Ogawa, Inaba, Hikojima Clinical features : Route of infection is faecal-oral route. After ingestion of the V. cholerae - 01, the bacteria adhere to the intestinal wall without invasion then produces an exotoxin causing excessive fluid secretion and diminished fluid absorption resulting in diarrhoea (rice water stool) which is characterized by passage of voluminous watery diarrhoea containing vibrios, epithelial cells and mucus; and result in severe dehydration. Laboratory diagnosis : Specimen: Stool flecks Smear: Gram-negative motile curved rods. Motility of vibrios is best seen using dark-field microscopy. Presumptive diagnosis: Inactivation of vibrios in a wet preparation after adding vibrio antiserum. Culture: TCBS (thiosulphate citrate bile salt sucrose agar) media Selective media for primary isolation of V. cholerae. Treatment: Sensitive to tetracycline and chloramphenicol. Fluid and electrolyte replacement are the first line of management for cholera.

GENUS: CAMPYLOBACTER

Characteristics :

  • Small, delicate, spirally curved gram-negative bacteria.
  • Motile bacteria with single polar flagellum.
  • Strictly microaerophilic bacteria requiring 5-10% o2 and 10% co2 enriched environment.
  • Oxidase and catalase positive.
  • Species of medical importance ✓ Campylobacter jejuniCampylobacter coli Campylobacter jejuni and Campylobacter coli Characteristics:
  • Gram-negative non-spore forming motile rods with comma, S or ‘gull-wing’ shapes.
  • Requires selective media like skirrow’s and Butzler’s media for isolation of the bacteria from faecal specimen.
  • Antigenic structure:. ✓ Lipopolysaccharide. ✓ Cytopathic extracellular toxin. ✓ Enterotoxin Clinical features :
  • Inoculum dose: 104 organisms
  • Source of infection is contaminated food, drinks and unpasteurized milk.
  • The organism multiply in small intestine, invade the epithellium and produce inflammation Campylobacter enteritis manifests with fever, headache, malaise, crampy abdominal pain and bloody mucoid diarrhoea, and usually self-limited enteritis in a week period Laboratory diagnosis : Specimen: Stool Microscopy: Typical ‘gull-wing’ shaped gram-negative rods. Typical darting motility of the bacteria under dark field microscopy or phase contrast microscopy Culture: Grow best at 42oC on selective media but can be cultured at 37 oC. Treatment: Erythromycin Shorten the duration of faecal shedding of bacteria HELICOBACTER PYLORI General characteristics:
  • Spiral-shaped gram negative, microaerophilic, motile rods with polar flagella
  • Antigenic structure: Pili Protease Ureae

✓ Proteins: Elicits the tuberculin reaction and antibody production. ✓ Polysaccharides. Induce the immediate type of hypersensitivity. Clinical manifestation :

  • Incubation period: 4-6 weeks.
  • Source of infection: Tuberculous patients
  • Route of infection: Respiratory- Inhalation of droplet nuclei, Ingestion of infected milk
  • Disease: Pulmonary and extrapulmonary tuberculosis. The disease generally manifests with low-grade persistent fever, night sweating, significant weight loss, fatigue and generalized weakness. Laboratory diagnosis: Identification of M. tuberculosis Specimen: Sputum; pleural, peritoneal and cerebrospinal fluid Smear: Acid fast bacilli from primary specimen. Cord forming acid-fast bacilli from culture. Culture: Semisynthetic agar media. New techniques: ✓ Molecular probes (DNA probes)- It detects Mycobacterial RNA sequence. ✓ High-performance liquid chromatography ✓ Polymerase chain reaction. ✓ Enzyme immunoassay Treatment: Anti-tuberculosis drugs ✓ First-line drugs. Isoniazid, Rifampin, Streptomycin, Ethambutol, Pyrazinamide ✓ Second-line drugs. Kanamicin, Cycloserine, Capreomycin, Ethionamide, Ofloxacin, Para-aminosalicylic acid (PAS) Prevention and control:
  • Prompt and effective treatment of patients with active tuberculosis and careful follow up of their contacts with tuberculin test and CXR.
  • Immunization with BCG (Bacillus-Calmette-Guerin) vaccine
  • Pasteurization of milk and milk products

Mycobacterium leprae Characteristics:

  • Typical acid-fast bacilli, arranged in singly, parallel bundles or in globular masses.
  • Not grown in non-living bacteriologic media.
  • Characteristic lesions are grown in laboratory animals. Eg. Foot pads of mice, Armadillos Clinical features :
  • Incubation period is months to years.
  • Route of infection is through nasal mucus secretion.
  • Disease: Hansen’s disease or leprosy. The lesion involves the cooler parts of the body, Eg. Ear lobes. Clinical triads: Anaesthetic skin patches, Peripheral neuritis, Presence of acid- fast bacilli from skin lesion
  • Two major types of leprosy
  1. Lepromatous leprosy
  2. Tuberculoid leprosy Laboratory diagnosis : Specimen: Skin scrapings from the ear lobe. Smear: Acid fast bacilli from the primary specimen. SPIROCHETES Characteristics:
  • Long, slender, helically coiled, spiral or cork-screw-shaped gram-negative rods.
  • Move by bending and rotating body movements.
  • Spirochete consist of protoplasmic cylinder bounded by a cell wall and outer membrane.
  • There is an axial filament or endoflagella between the cell wall and outer membrane.
  • Spirochetes of medical importance: ✓ Treponema ✓ Borellia ✓ Leptospira GENUS: TREPONEMA Species of medical importance:
  1. T_. pallidum_ causes syphilis
  2. T. pertenue causes yaws
  3. T. carateum causes pinta
  4. T. endemicus causes bejel
  5. Treponema pallidum