Medical Microbiology - Urinary Tract Infections - Essay Example

?Microbiology report First Sur Registration number Introduction Definition of terms and abbreviations: DST-diagnostic sensitivity test, MSU-mid stream urine, Antibiotic-this is a chemical agent that kills or inhibits bacterial growth. UTI- Urinary tract infection, AST-antibiotic sensitivity test, Trimethoprim (W), Ampicillin (AMP), Gentamicin (CN), Colistin (CT), Chloramphenicol (C), Ciprofloxacin (CIP), PCR-polymerase chain reaction, MIC-minimum inhibitory concentration, S-sensitive, I-immediately sensitive, R-resistant. MIC- minimum inhibitory concentration. CLED- cysteine lactose electrolyte deficient agar, WBC-white blood cells, RBC-red blood cells, MRSA-methicillin resistant S. aureus, MRSA- methicillin resistant S. aureus. Urinary tract infections (UTIs) are infections of the urinary tract acquired either externally (from the urethral orifice) or internally (systemic septicemia). They affect the female gender more than the male gender and are mostly caused by normal microbial flora inoculated into/unto the urogenital mucosa. Methods The collection and division of urine samples was done by the asceptic method ensuring that there was no external contamination. The urine used was the mid -stream urine free of urethral bacterial contamination, otherwise known as Clean catch mid-stream urine (CCMSU). The study of the samples was divided into 4 parts; 1) Examination of samples: macroscopic and microscopic examinations were done. Macroscopic examination was done by viewing the sample using naked eyes. This was for presence of blood stains, opacity/ turbidity, colour and particulates. Microscopic exam was done to establish presence of WBCs and RBCs. 2) Isolation and culture of pathogens; CLED agar was used for the culture. The samples were incubated at 37 degrees Celsius for 24 hours. The bacterial colonies were examined and identified by colony morphology (size, shape, colour, pattern, height, texture) 3) Identification of the bacteria present. Gram stain was the preferred stain. Gram stain procedure: inoculate a slide with a sterile loop. A thin homogenous smear is preferred for proper and easy staining. Dry the slides and ensure proper fixation. Flood the slides with Chrystal violet and wait for 30 seconds. Proceed to flood with lugol’s iodine solution and set aside for another 30 seconds. Wash off using iodine acetone. Wash with running water afterwards and counterstain with Safranin of carbol fuschin. Wash with running water for a second time. Proceed to microscopy for identification of individual bacterial strains. Gram positive= blue, gram negative=red Further methods of bacterial strain classifications were done. These were more specific for certain bacterial strains. They included; 1) THE API20E and ROCHE ENTEROTUBE II 2) CARBOHYDRATES (F/O/-) 3) GLUCOSE (ACID) 4) OXIDASE TEST 5) CATALASE TEST 6) GROWTH IN AIR/GROWTH ANAEROBICALLY 7) MOTILITY 8) ACID FAST STAIN 9) ZIEHL NEELSEN The identification of the bacterial strains was then followed by antibiotic sensitivity tests. Three methods were used 1) Stokes method 2) Tube dilution method 3) Using the E-test strip. Results Table 1: Graph of antibiotic sensitivity values The graph is a graph of antibiotic sensitivities by values of test radii. The y-axis thus represents the sensitivity of samples thus giving an idea of the antibiotic efficacy across the multiple test bacteria. By inference, ciprofloxacin has the highest efficacy, while Colistin has the lowest. Across the x-axis, the individual sensitivity values of the antibiotics are represented as color coded portions (refer to graph legend). It can therefore be seen that the bacteria in MSU 1 and 4 have the highest sensitivities, while those in MSU 3 and 6 have the lowest. By inference, the bacteria in MSU 3 and 6 are more resilient and likely more pathogenic than those in MSU 1 and 4. They are thus more likely to exhibit antibiotic resistance if not well monitored and subjected to thorough antibiotic chemotherapy. MSU 2 does not appear, as the antibiotic sensitivity test was not done. The x axis also represents the individual antibiotics. Table 1: Graph of MIC Ampicillin versus Gentamycin The x-axis represents the two antibiotics Ampicillin and Gentamycin. The y axis represents the cumulative MIC determined by the E-test strip method, as well as the individual samples (MSU 1-6). The cumulative MIC gives an idea of the efficacy of the antibiotic. As can be seen form the graph, gentamycin has a higher cumulative MIC compared to Ampicillin, and thus less efficient. It can also be deduced that the sample in MSU 6 has the highest MIC compared to MSU 4 that has the lowest. It is also possible to see that the bacterium in MSU 6 is more susceptible to ampicillin than gentamycin. It can therefore be inferred that the bacterium in MSU 6 is more resilient than that in MSU 4. Again, MSU 2 does not appear as the test was not carried out. Staphylococcus species do not produce beta lactamases unless they acquired the gene from another bacterium, or by viral transfer/ infection. The S. aureus has an MIC of 0.1 to ampicillin. The results show that the Klebsiella pneumoniae are highly sensitive to most antibiotics. The pseudomonas aeruginosa is resistant to most antibiotics except ciprofloxacin. The E coli, S. aureus and E. faecalis are highly sensitive to antibiotics. Conclusion The individual genus groups of the bacteria are as follows; Klebsiella pneumoniae-MSU 1, M. tuberculosis- MSU 2, pseudomonas aeruginosa- MSU 3, S. Aureus- MSU 4, E. coli- MSU 5, E. faecalis- MSU 6 The MSU 1 belonged to a patient who experienced a recurrent vesicoureteric reflux; this is a condition characterized by a backflow of urine from the bladder to the kidneys. The most likely diagnosis was an infection by a bacterium of the enterobacteriace family. According to the laboratory results, the bacterium would be the Klebsiella pneumoniae. In this case, the most suitable antibiotics would be trimethoprim and ciprofloxacin, as they provide the highest efficacy according to the AST. The recurrent UTI may also be due to the Ureaplasma urealyticum or Proteus Mirabilis. It would most likely be the Proteus due to their ability to lodge in struvite stones (Gomez-nunez NG 2009). This confers the bacteria the ability to cause a recurrent UTI. The recurrence may also be attributed to antibiotic resistance caused by improper chemotherapeutic management, or antibiotic usage. The second MSU, it may also be Mycobacteria. The most probable is M. Tuberculosis. The patient has a history of sleeping rough, and thus may have acquired the mycobacterium spores from the ground. It is also evident there was jail time involved. This also predisposes the individual to the disease due to the nature of squeezed and improperly ventilated quarters in some jails. The presence of hemoptysis is characteristic of the bacterium’s pathology in the lungs. The laboratory tests also show specific characteristics such as acid fast positive rods. This characteristic is reserved for the nocardia and Mycobacterium species. The nocardia species causes pulmonary or systemic nocardiosis. The pulmonary disease does not manifest with hemoptysis. It is therefore M. Tuberculosis. The best treatment would be ethambutol, rifampicin, or pyrazinamide. The bacterium does not respond well to many other antibiotics. It may also be secondary to fungal infection in the lungs. An example is the Histoplasma capsulatum. This is associated with immunocompromised states and spelunking. The patient was homeless, and thus may have also been exposed to practices that led to immunocompromised states. These include infections or drug abuse with possibility of shared needles. The fungus is also capsulated and associated with hemoptysis. Furthermore, the fungal pathogenesis and manifestation are closely related and similar to those in M. tuberculosis. In the MSU 3, the cause may be enterobacteriaceae. They include pseudomonas, Salmonella, citrobacter and serratia. This is because most nosocomial infections are as a result of the enterobacteriaceae. The presence of a catheter that is still in place is an important factor in the acquisition of nosocomial infections. This is due to the presence of bacteria on the human skin that use the catheter as a tract for direct inoculation into the urethra and bladder. The laboratory tests on the bacteria obtained confirm the characteristics of the offending bacteria as enterobacteriaceae-Pseudomonas aeruginosa. This specific bacterium is associated with serious nosocomial infections and complications such as gas gangrene especially in burn victims or surgical patients. This is due to their immunocompromised states. It also has intrinsic characteristics that confer its ability to be highly resilient and thus even present on improperly sterilized surgical implements. According to the AST results, ciprofloxacin would be best for treatment. In MSU 4, there may be normal microbial flora. These include Mycolasma hominis, Lactobacillus spp and the E.coli. This is because UTIs caused by NMF are frequently seen in pregnant women. The susceptibility is mainly due to the physiological changes that they undergo during pregnancy (Abhay Rane 2013). Treatment is by trimethoprim, ampicillin, chloramphenicol (though not often used) or gentamycin. It is sensitive to these antibiotics. Some forms exist that are methicillin and vancomycin resistant. (MRSA, VRSA) In the fifth MSU, the honeymoon cystitis may be caused by bacteria such as: E.coli, S. saprophyticus, E. faecalis, and klebsiella species (John L Brusch 2013). This is because the cystitis is associated with increased sexual activity (John L Brusch 2013) characterized with direct inoculation of bacteria into the vaginal area from the peri-anal area. Tests show that the bacterium is indeed the E.coli present on peri-anal skin as a NMF. It can be pathogenic if it somehow finds its way onto the urethral mucosa. Treatment is by trimethoprim and ciprofloxacin, as they show the greatest efficacy on the AST. In MSU 6, it may be due to E. faecalis, Ureaplasma urealyticum and proteus due to ammonia production. This is because the bacteria are urealytic. The bacterial tests indicate that it is in fact E. faecalis. The bacterium causes UTIs, though rarely. It is associated with a type of UTI that is characterized by strong urine odor, cloudy urine, burning sensation on urination and supra pubic pain. The symptoms of dysuria, abdominal pain, cloudy urine and odor are spot on for the bacterium. The most suitable treatment would be the use of trimethoprim. Discussion The presumptions made; there were no underlying conditions that led to increased bacterial load. The conditions were caused by bacteria and not fungi or protozoa. The last assumption was that there was no contamination of samples by external factors like fomites. The practical was highly informative. It included aspects of clinical procedures that interweave with routine medical management and practices. These included the bacterial diagnostic tests and the antibiotic sensitivity tests that reinforce the practice of routinely carrying out combined therapy. Possible errors include machinery calibration errors, human errors in observation and calculation, contamination, and use of expired reagents. Improvements would include the addition of PCR tests to identify strains. Confirmatory tests done would be such as PCR and haemograms. References Gomez-nunez NG., Alvarez UM., Fernandez F., Aceves JG., Loske Am (2009) ‘Interaction of intracorporeal lithotripters with Proteus Mirabilis inoculated inside artificial calcium and struvite stones.’ www.ncbi.nlm.nih.gov/m/pubmed/19216637/ [30/11/2013] Rane Abhay., Dasgupta Ranan (2013) ‘Urinary tract infections: clinical perspectives on UTIs’ 1st edition. PP. 26, Springer science and business. John L Brusch., Mary F Bavaro., Burke A Cunha (2013) “Cystitis in females.” http://emedicine.medscape.com/article/233101 [1/12/2013] Read More