P11 Clinical microbiology II – examination in respiratory and GI infections To study: Infections of various organs and organ systems (from textbooks, www etc.), sampling, specimen transport (from textbooks, www etc.) From the spring term: Microscopy, culture, biochemical identification Examination in respiratory tract infections Task 1: Search for respiratory pathogens in clinical microbiology Look at the picture, already filled in for the double practical. Use this picture in the Task 2 and Task 3. Common pharyngeal flora consists mostly of a) oral streptococci appearance: colourless or greyish, viridation b) oral neisserias appearance: yellowish, no haemolysis or partial Task 2: Examination in acute bronchopneumonia For this casuistic, documented by the order form, try to examine the corresponding specimen (sputum), to find a possible pathogen, make a conclusion and interpret the result. Step by step, fill in the individual fields in “the screen of laboratory information system”. Antibiotic susceptibility test (bacterium C) Cefoxitin (FOX)* R < 22 S ≥ 22 Co-trimoxazole (SXT) R < 14 S ≥ 17 Erythromycin (E) R < 18 S ≥ 21 Tetracyclin** (TE) R < 19 S ≥ 22 Clindamycin (DA) R < 19 S ≥ 22 Chloramfenicole (C) R < 18 S ≥ 18 write S = susceptible, R = resistant, eventually I = intermediary *interpreted as oxacillin and other beta-lactams **result of this test is also valid for doxycycline Final conclusion and recommendation for treatment: _______________________________________________ a) Microscopy of sputum Look at the smear prepared from your specimen. Try to find the individual objects (bacteria, host cells). Fill in the field “Microscopy result”: +++ = more than 10 objects in the observation area ++ = less than 10 objects in the observation area + = only rare objects (one or less per an observation area) 0 = none b) Description of bacteria On the blood agar, describe the size, colour and haemolytic properties of the grown bacteria. Do not describe other characteristics. Take into account that there was no growth visible on Endo agar. Bacteria A and B should be bacteria considered to be parts of normal flora. Bacterium C will be a pathogenic bacterium that will be tested in detail in parts c) and d) c) Further tests Fill in the results of the catalase test, hyaluronidase test and of the growth on blood agar with 10 % NaCl for Bacterium C. d) Antibiotic susceptibility Fill in the antibiotic susceptibility test for Bacterium C. Always write down the name of the antibiotics and “S” or “R” (susceptible or resistant). Reference zones are written on your table. e) Final conclusion Try to formulate several words for the general practitioner. Especially try to find out (with the help of your teacher) which antibiotics would be the best choice. Task 3: Examination in acute tonsillitis Similarly as in the previous case, there is an order form. Try to examine the corresponding specimen (throat swab) to find a possible pathogen, make a conclusion and interpret the results. Step by step, fill in the individual fields in “the screen of laboratory information system”. The way of doing it is the same as in the previous task. Antibiotic susceptibility tests (bacterium C) Penicillin (P) R < 18 S ≥ 18 Chloramfenicol (C) R < 19 S ≥ 19 Erythromycin (E) R < 18 S ≥ 21 Tetracyklin* (TE) R < 20 S ≥ 23 Clindamycin (DA) R < 17 S ≥ 27 Vancomycin (VA) R < 13 S ≥ 13 write S = susceptible, R = resistant, eventually I = intermediary *interpreted as oxacillin and other beta-lactams **result of this test is also valid for doxycycline Final conclusion and recommendation for treatment: _______________________________________________ Task 4: Suitable specimens for various respiratory infections Using slideshow, find suitable way of examination for various clinical situations Suspicion for Type of specimen Suspicion for Type of specimen rhinitis bronchitis sinusitis acute pneumonia (expectoration of pus) pharyngitis subacute pneumonia (dry cough) influenza lung aspergilosis Examination in gastrointestinal system Task 5: Examination in acute diarrhoea In this case, stool was sent to the laboratory. We have to know, that stool normally contains strictly anaerobic flora, but this cannot be found during normal examination, as normal examination is only aerobic. Even enterococci are only found in blood agar is used, and this is not part of routine examination of stool. On the other hand, members of Enterobacteriaceae family are often found in stool – both parts of normal flora (with some strains with elevated virulence, for example EPEC for E. coli) and obligatory pathogens (Salmonella). – The stool specimens are observed after 24 hours (direct result of Endo agar and XLD agar) and 48 hours (direct result of Campylobacter examination on CCDA agar and Yersinia examination on CIN agar, and subcultures from selenite broth on Endo agar and MAL agar). The 24 h examination was already performed in your case. Fill in results of 48 h examination and try to make a final conclusion. Acute diarrhoea Cecilia Brown Stool for bacteriological examination Patient Cecilia Brown, *1984 Dg.: Accute diarrhoea Endo agar (24 h) XLD agar (24 h) Endo agar (subcultivation) MAL agar (subcultivation) CIN agar (48 h) CCDA agar (48 h) E. coli negative Final conclusion and interpretation More tests HAJNA medium Serotypisation Dental students do nto perform this part Task 6: Stool samples for different types of pathogens and toxins For some purposes, it is possible to send rectal swabs, while for others, it is necessary to send a piece of stool, sometimes even refrigerated. Watch the next table. For dental students it is already filled in. Stool sent for Type of specimen Stool sent for Type of specimen bacteriology Anal/rectal swab (Amies) virology – virus isolation Nut-sized piece of stool (cooling necessary!) mycology Anal/rectal swab (Amies or FungiQuick) parasitology Nut-sized piece of stool (cooling not necessary) virology – antigen detection Nut-sized piece of stool (cooling not necessary) detection of the Clostridium difficile toxin Nut-sized piece of stool (cooling not necessary) Task 1: Indications for microbiological examination For following casuistries, fill in the table – for the double practical do it just together with your teacher. Description of a case Solution a b c d Task 2: Swabs and vessels Observe the swabs in your table and fill in their “identity cards”. Name: Plain swab Stick material plastic, wood, aluminium Swab material synthetic cotton Practical use: Name: Swab with Amies transport medium Stick material plastic or aluminium Swab material synthetic cotton Medium Amies (Stuart, Cary Blair) Note: The medium may contain charcoal (then it is black); without charcoal, it would be colourless. Practical use: Variant with aluminium stick is used for Name: Fungi-Quick swab Stick material plastic Transport medium colour colourless Cap colour Practical use: Name: C. A. T. swab Stick material plastic Transport medium colour colourless Cap colour Practical use: Name: Common test tube for microbiology Sterile? (yes or no) Description made of polystyrene, 16 × 100 mm, 10 ml Practical use: Name: Sputum test tube Sterile? (yes or no) Description made of polystyrene or polypropylene, 26 × 92 mm, 30 ml Practical use: Name: Stool container Sterile? (yes or no) Description made of polypropylene, 26 × 82 mm, 30 ml Practical use: Name: Sampling vessel for urine Sterile? (yes or no) Description made of polypropylene, 45 × 70 mm, 120 ml Practical use: Task 3: Other sampling methods than swabs and vessels Fill in the following table: Sampling method Typical example(s) of use smear on a slide Fastidious microbes (gonococci, aktinomycetes etc.) imprint with an agar Examination of skin focuses moulage method Examination of infections of areal wounds uricult Examination of urine (primocultivation possible at patient) Task 14: The order form a) Filling in the order form Fill in the following order form with a patient name and data and the requested examination related to the disease, according to a card that has been given to you by the teacher. b) Order form common mistakes Oral students in the double practical session do not perform this task. Tissue for syphilis cultivation Task 15: Interpretation a) Direct diagnostic interpretation Using the table in the slideshow, write likely interpretation for first five of thirteen various findings written on cards available on your table. Use terms “pathogen”, “common flora”, “accidental finding”, “colonization” and “contamination” Finding Interpretation b) Indirect diagnostic interpretation Interpret several clinical situations with data given on the card. Do not forget to make your interpretation on the base of both clinical findings and laboratory results (clinical findings) Rewrite from the card (simplify the sentences) Conclusion Clinical situation Serology examination results