Urinary tract infection (UTIs) are common bacterial infections that occur in the urinary tract which is one of the most susceptible sites for bacterial infections. Bacterial infections caused by pathogens like Eschrichia coli also contribute to community acquired infections. In comparison to the hospital- acquired infections the community- acquired UTIs are more common.Females are mostly affected by Urinary tract infections when compared to males which is due to the differences in the anatomy of the urethra as well as the age, pregnancy, sexual activity and catheterisation. UTI occurs in twenty to thirty percent of females in latter life. The infections are extracellular infections that are short lived and appear to be an acute condition. However, the morbidity rate of the UTI is significant in the population as the kidneys can be infected by the pathogen which can lead to a very serious infection. Prolonged infections can result in extreme consequences. Therefore, it is essential to identify the organism(s) that lead to UTIs, in order to provide patients with the correct antibiotics to treat their infection. UTI in females occur in the bladder known as Cystitis, in urethra known as urethritis and in the vagina known as vaginitis. The bacterial infection occurs in the urinary tract along the urethra and moves to the kidneys.
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This experiment involved the mid stream urine samples (MSU) collected from patients affected with UTIs. The MSU is often collected from the middle of the bladder as contamination might take place at the initial part of the urine that flows through the baldder. MSU is important for a culture and the MSU test allows a confrimed diagnosis for a urine infection and allows the treatment by determining the most suitable antibiotics required to act against the bacteria.
There aims of the three practicals (A, B and C) were to:
Examine samples using a microscope,
Identify and examine the clonies present in CLED agar,
Identify the bacterial strains present in the six clinical samples,
Identify isolated bacterial pathogens by ID test,
Use Cowan and Steels Manual to determine the genus of the bacterial pathogens.
Use the two commercial systems (API-20E and BBL Enterotube II) to determine the enterobacteriae species.
There were no changes made to the method section. Laboratory coats and gloves were worn when handeling the samples during the experiment. Please refer to the schedules provided for the method of the three practicals.
The MSU were changed so change the results, ask ema about the antibiotics table..
Number of red blood cells (RBCs/ml)
Number of white blood cells (WBCs/ml)
Description of microscopic examination and observation by eye
Colonies forming units/ml on CLED agar
Description of colonies observed on CLED agar
7.0 x 106
10.6 x 106
Uric acid crystals observed; Dark brown coloured urine,
>100,Green colonies with white streak, shiny texture, irregular shape of colonies
2.5 x 104
Yellow, small colonies
4.0 x 105
2.5 x 105
3.0 x 105
Few epithelial cells present;
Dark coloured urine
Green, different sizes of colonies,
The result table of the urinary tract infection practical B (Identification) is attached to this practical report.
Cowman and Steel ID
Enterobacteriaceae: Escherichia coli
Enterobacteriaceae: Klebsiella Pneumoniae
CHECK : MSU 4: Enterococcus saecalis
By using the results the six studies can be solved.
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Case 1: The genus of the bacteria in MSU 1 is found to be Escherichia coli. The pathogen belongs to Enterobacteriaceae family. By carrying the API-20E commercial test the species was found to be E.coli based on the API-20E. The infection might be transmitted by touch for example contacting restrooms. The results indicate that the patient is affected with impaired renal function.
Case 2: The genus of the bacteria determined in the MSU 2 sample is found to be Staphylococcus and the species is the S.aureus. Due to the pregnancy of the patient, her immune system could have been weak and this might have led to the women being susceptible to this infection.
Case 3: The genus of the bacteria in the MSU 3 sample is Klebsiella which is found to belong to the Enterobacteriaceae family. Based on the results found from the BBL Entertube II commercial test the species is found to be K. Pneumoniae. The possible disease of this patient can be pneumonia. The cause of this infection can be due to burn on the patientâ€™s leg which may have resulted in cellulitis or sepsis. Cathetherisation might have increased the possibility of UTI in the patient. The patient might have been affected by Gram positive aerobes in the past as the patient was treated with amoxicillin (when looking at the patientâ€™s history).
Case 4: MSU 4 was identified as Streptococus, Enterococcus or Lactococcus, the patient is a 30 year old woman, who has abdominal pains, frequency and dysuria. Enterococcus faecalis is the possible pathogen, it is a common cause of UTIs, as it is normally found in the gastrointestinal tract, but can enter the urinary tract during intercourse. Streptococcus is causes haematuria there was no evident of this in the macroscopic investigation, there was also no evident to indicant that Lactococcus causes UTIs. They believe they might be pregnant; a pregnancy test would need to be carried out to determine this.
The genus of the bacteria found in MSU 4 sample is Enterococcus and the species is E. Faecalis which is one of the main causes of nasocomial infections.
This pateint is expected to be affected with Cystitis which can be diagnosed in this patient. The factors that can cause this type of infection includes sexual intercourse which might have entered the urethra from vagina or anus. By the wiping following bowel movement can lead to bacteria from passing into the urethra.
Case 5: The genus of the bacteria in MSU 5 sample is found to be Mycobacterium and the species is M. tuberculosis. The disease that can be diagnosed in the patient is Renal tuberculosis. White blood cells as well red blood cells present in the sample when examined microscopically indicates pyuria and haematuria (blood present in the pateintâ€™s sputum) that refers to an infection.
Case 6: The genus of the bacteria in MSU 6 sample is found to be Pseudomanas and the species is P.aeruginosa. Due to the history of recurrent of UTI of the patient, there is a possibility that the patient is immunocompromised.
Example for MSU 1
White blood cells(WBC)= 1136 cells counted
= 1136 x 10= 11360
= 11360 x 1000
= 11360000 WBCs/ml
Red blood cells (RBCs)= 700 cells counted
= 700 x 10= 7000
= 7000 x 1000
= 7000000 RBCs/ml
The number of colonies observed in CLED agar for the MSU 1,2,3,4 and 6 samples were >1.0x105 . This indicates the presence of an infection.
Case 4: The bacterium in this case was found to be gram negative, rod shaped, grew both in anaerobically and in air. The results indicated that the bacteria belongs to Enterobacteriae family. By carrying out the commercial test the species was identified as Escherichia coli. The high probability (96.5%) agrees with the type of species identified. By examining the sample through microscope indicated haematuria and pyuria which is related to cystitis. Beta-lactam antibiotics
Case 2: Staphylococcus aureus
The pathogen identified in MSU 2 was a spherical shaped, positively stained bacteria which grew both in air and anaerobically. The results indicate that the bacteria belongs to Staphylococcus genus. Therefore, by doing a catalase test the bacterium was found to be Staphylococcus and not Enterococcus bacteria.
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Case 3: Klebsiella Pneumoniae
The bacteria identified in this case study was a negatively stained, rod shaped bacteria which grew in air and anaerobically. The results indicated that the bacteria is K. Pneumoniae. Vesicoureteric reflux in the patient is one of the possible cause that led to renal damage. However, symptoms such as fever and pain on micrurition maybe indicative of pyelonephritis in the patient.
Case 4: Enterococcus saecalis
This species is a commensal bacterium that is found in the intestinal tract. The species is a gram negative bacteria which is spherical shaped. By futher doing the catalase test and oxidase test, the bacteria resulted negative which are consistent its characteristic. The symptoms of the patient ( dysuria, abdominal pain and dysuria) in this case study is common in UTI.
Case 5: Mycobacterium tuberculosis
The pathogen found in MSU 5 is M.tuberculosis which cannot be visible on a routined standard media. Therefore, there was no growth observed on the CLED agar. The identification of the species was supported by observing the non-sporing acid fast bacilli with Ziehl-Neelsen stain. The coughing of blood by the pateint indicates that the patient is affected with renal tuberculosis which associated with painless haematuria.
Case 6: Pseudomonas aeruginosa
Due to different sizes of the colonies on the CLED agar, there were four genus identified which included Janthinobacterium, Agrobacterium and Achromobacter. A gram negative bacili observed was identified as pyocanin by P.aeruginosaâ€™s (green colonies). The bacteria can be further identified by testing the fruity odour of the bacteria. The bacteria is able to colonise on cathethers which in the patient can lead to a high risk of UTI.
Alternative methods:Additional tests and the importances of ID and antibiotic sensitivity tests
Polymerase chain reaction (PCR) is an effective method used in detecting pathogens. In addition, bacteria such as M.tuberculosis can be identified by this technique. It does this by amplifying the DNA in a bacteria and producing several millions of copies of the certain DNA sequence. Coagulase test must be used besides it to confirm the presence of Staphylococcus. If positive results are produced the bacteria is identified as S.aureus meanwhile if a negative result is produced the species is identified as S.saprophyticus or S. epidermidis. If positive result obtained, a further oxacillin test can be carried out to determine if methicillin-resistant Staphylococcus aureus (MRSA) is present. Meanwhile, vancomycin can be used in the antibiotic sensitivity testing to identify the presence of vancomycin-resistant enterococcus. In the other hand, K. pneumoniae has a typical characteristic which is resistance to ampicillin. Antibiotic sensitivity testing is crucial to investigate the susceptibility of a pathogen to a range of potential effective agents. A particular antibiotic or a range of antibiotics which inhibit the growth of the bacteria may provide additional information on the identification and act as a confirmatory test for the presumptive identifications. Possible human errors might have occurred throughout these experiments which may have influenced the results obtained.