Clinical Microbiology

A 23-year-old woman presents to the emergency department with a 24-hour history of right loin pain, fever, chills, and general malaise. She describes the pain as sharp and constant, radiating towards her flank. She also reports recent dysuria and increased urinary frequency. She has a history of a recurrent urinary tract infection (UTI), which was treated by her general practitioner with trimethoprim 24 hours ago. Despite the treatment, her symptoms have worsened. She has no significant past medical history, does not use any regular medications, and is not pregnant. On examination, she appears febrile with a temperature of 38.7°C, tachycardic with a pulse rate of 110 beats per minute, and hypotensive with a blood pressure of 90/60 mmHg. Her abdomen is soft, but there is tenderness in the right lower quadrant and costovertebral angle. Urinalysis shows positive leukocyte esterase, nitrites, and blood. Blood cultures are pending. Given her sepsis and symptoms, which of the following organisms is the most likely cause of her infection?

A 45-year-old male with a history of recurrent urinary tract infections (UTIs) is admitted to the hospital with fever, dysuria, and hematuria. His urine culture reveals a Gram-negative bacillus, which is identified as Escherichia coli. The infection is deemed to be complicated due to the patient’s history of kidney stones and an indwelling catheter. He is started on intravenous antibiotics, and the physician selects ciprofloxacin due to its effectiveness against E. coli. As part of his treatment, the pharmacist explains the mechanism by which ciprofloxacin works. What is the most likely mechanism of action of ciprofloxacin?

A 30-year-old aid worker, recently returned from a mission at the site of a devastating earthquake, begins to feel unwell shortly after working in the relief efforts. Initially, he experiences vomiting, which is soon followed by the onset of extremely watery and loose diarrhea. The diarrhea is profuse, and he is unable to retain fluids. He is brought to the clinic where he is noted to be severely dehydrated. The patient reports that he had been drinking water from a local supply, which may have been contaminated due to the disruption caused by the disaster. What is the most likely infective organism responsible for his symptoms?

A 28-year-old chef presents to the emergency department with complaints of profuse, bloody diarrhea. He also reports feeling an intense urge to pass stools (tenesmus), even after having already gone to the bathroom. He states that he recently returned from a food festival where he prepared and served food to a large number of people. He also mentions having had some abdominal cramping and a fever. A sigmoidoscopy is performed, revealing necrosis and ulceration of the descending colon mucosa. Given his occupation and recent symptoms, what is the most likely cause of his condition?

A 27-year-old man presents to the hospital with a five-day history of high fever, malaise, and abdominal discomfort. On examination, his temperature is 39.5°C (103.1°F), and his pulse rate is 78 beats per minute. The physician notes a few faint, pink macules on his abdomen. Laboratory investigations reveal mild leukopenia and mildly elevated liver enzymes. Blood cultures grow Salmonella typhi. Which of the following is true regarding Salmonella species?

A 45-year-old male presents to the emergency department with severe pain and swelling in his right lower leg following a traumatic injury while working on a construction site. The injury occurred several hours ago, and the wound is deep with signs of extensive tissue damage. On examination, the affected limb is swollen, pale, and there is a pronounced foul odor emanating from the wound. The patient is febrile and tachycardic. An X-ray shows the presence of gas within the tissues, and the wound is discolored with a purplish hue. Given the clinical signs, what is the most likely diagnosis, and what treatment should be prioritized?

A 50-year-old woman with a history of rheumatoid arthritis presents with acute knee pain, swelling, and fever. Examination reveals a warm, erythematous, and tender knee joint with a limited range of motion. A diagnostic joint aspiration is performed, and the synovial fluid is sent for microbiological analysis. Which of the following organisms is most likely to be responsible for her condition?

A 58-year-old man undergoes a difficult colonoscopy for the assessment of a cecal cancer. Forty-eight hours after the procedure, he develops sepsis and is admitted to the hospital. His abdomen is soft and non-tender. Blood cultures grow gram-positive cocci. What is the most likely underlying organism?

A 62-year-old woman with a history of hypertension and type 2 diabetes mellitus undergoes an emergency laparoscopic cholecystectomy for acute calculous cholecystitis. Intraoperatively, there is significant gallbladder inflammation with multiple stone spillage into the peritoneal cavity. The procedure is prolonged, and she is started on intravenous ciprofloxacin postoperatively due to concerns about infection.
Four days after surgery, she develops worsening lower abdominal cramping and profuse, foul-smelling watery diarrhea. She is febrile (38.5°C), and her vital signs reveal tachycardia (110 bpm) with mild hypotension (BP: 98/65 mmHg). On examination, her abdomen is mildly distended but non-peritonitic. Laboratory results show leukocytosis (WBC: 18,000/mm³) and elevated C-reactive protein. Stool studies are ordered, and blood cultures are negative. A flexible sigmoidoscopy reveals pseudomembranous colitis.
Which of the following organisms is most likely responsible for her condition?

A 32-year-old woman undergoes a mastectomy with latissimus dorsi flap reconstruction for breast cancer. To achieve optimal cosmesis, a McGhan implant is placed under the myocutaneous flap. Three weeks postoperatively, she develops recurrent wound infections that persist despite multiple courses of antibiotics. Wound cultures show bacterial growth. Which of the following organisms is most likely responsible?

A young woman is admitted to the hospital with Escherichia coli O157 infection after returning from Germany during an outbreak. She presents with abdominal pain, bloody diarrhea, and dehydration. Laboratory tests reveal anemia, thrombocytopenia, and elevated creatinine levels. Which of the following statements regarding E. coli O157 is not true?

A 68-year-old man with poorly controlled diabetes presents with severe otalgia (ear pain) and headaches. On examination, there is the presence of granulation tissue within the external auditory meatus. What is the most likely underlying infective agent?

A 22-year-old woman presents one week postpartum with a tender, indurated mass in her right breast. She is breastfeeding her first child. What is the most likely infective organism responsible for this condition?

A 72-year-old male with a history of peripheral vascular disease presents to the emergency department with complaints of severe pain and swelling in his right foot. He reports that over the past 48 hours, his right great toe has developed discoloration, becoming dark purple and cold to the touch. He is a known diabetic and has struggled with poor circulation for several years. On examination, the affected toe is found to be gangrenous, with noticeable swelling and tenderness spreading to the
surrounding tissues. During palpation of the infected area, crepitus is noted, and the skin appears tense with a distinct foul odor. The patient’s vital signs are stable, but his blood sugar is elevated at 220 mg/dL. He is immediately started on broad-spectrum intravenous antibiotics and prepared for surgical debridement. Which of the following is the most likely infective organism responsible for this condition?

A 28-year-old woman presents to her general practitioner with complaints of discomfort and swelling in her right breast while breastfeeding her first child. She reports tenderness in the area, which has gradually worsened over the past few days. On clinical examination, erythema and a fluctuant area are noted on the right breast, indicative of a possible abscess. The patient is otherwise healthy but has had some difficulties with breastfeeding, including cracked nipples. Aspiration and culture of the fluid from the fluctuant area are performed. Which of the following organisms is most likely to be identified?

A 35-year-old woman, a heavy smoker, presents to her gastroenterologist with a long-standing history of increased stool frequency and crampy abdominal pain. Her symptoms have been persistent for several months. A colonoscopy is performed, and the procedure reveals macroscopically normal findings. To further investigate the cause of her symptoms, pan-colonic biopsies are taken. The histological analysis of the biopsies demonstrates a thickened sub-apical collagen layer along with an increased number of lymphocytes in the lamina propria. Based on the histological findings, what is the most likely diagnosis?

A 45-year-old man with a history of poor dental hygiene presents with chronic multiple abscesses in his jaw and neck area. He has been treated multiple times for skin abscesses but the lesions persist and recur. On examination, the abscesses are deep, draining, and have a characteristic sulfur-like appearance. A differential diagnosis is being considered, including actinomycosis. Which of the following statements regarding actinomycosis is false?

A 65-year-old male with type 2 diabetes and poor glycemic control presents with forefoot cellulitis. His foot is tender, swollen, and warm to the touch, but there is no visible skin breakdown or ulceration. An X-ray of the foot shows evidence of osteomyelitis affecting the 2nd ray. The overlying skin remains healthy with no signs of necrosis or gangrene. What is the best initial treatment for this patient?

A 45-year-old male with a history of intravenous drug use presents with localized pain and swelling in his left tibia. He has a low-grade fever, and laboratory tests reveal an elevated white blood cell count and C-reactive protein. After confirming the diagnosis of osteomyelitis, the patient is started on intravenous antibiotics. Which of the following statements regarding osteomyelitis is false?

A 72-year-old male with a history of diverticular disease is scheduled for a sigmoid colectomy. He is considered to be at increased risk for post-operative wound infection due to age and co-morbidities. Which of the following interventions is most likely to reduce his risk of developing a post-operative wound infection?

A surgical trainee is incising a groin ‘abscess’ in an intravenous drug abuser. Unfortunately, the ‘abscess’ turns out to be a false aneurysm, and torrential bleeding ensues. In the panic of the situation, the doctor stabs himself in the finger. It later transpires that the patient is a Hepatitis B carrier and the doctor has not been immunized. What type of virus is Hepatitis B?

A 77-year-old female with diabetes and peripheral vascular disease presents with a non-healing ulcer on her right foot. Despite receiving initial treatment with antibiotics, the ulcer continues to worsen, and blood cultures grow methicillin-resistant Staphylococcus aureus (MRSA). The patient is already on vancomycin. Which of the following antibiotics would you consider adding to vancomycin to improve the management of this infection?

A 23-year-old man is admitted to the hospital with complaints of diarrhoea and severe abdominal pain. He has been otherwise healthy, but his symptoms have persisted for the last 18 hours. What is the most likely cause of his illness?

A 28-year-old man undergoes a laparotomy for a perforated duodenal ulcer and is started on broad-spectrum antibiotics post-operatively. He develops hearing impairment shortly after the procedure. Which of the following agents is the most likely underlying culprit?

A 34-year-old man from Zimbabwe presents to the Emergency Department with a 2-week history of abdominal pain, intermittent hematuria, and fatigue. He has a history of recent travel to his home country, where he swam in freshwater lakes. On examination, he is noted to have mild abdominal tenderness, and his urine is visibly blood-stained. An abdominal x-ray is performed and reveals calcifications in the bladder region. What is the most likely cause of his symptoms?

A 70-year-old man who underwent a revision total hip replacement presents 30 days post-operatively with increased pain and swelling in the hip. He also reports pus discharging from the wound. On examination, he is systemically unwell with a fever of 38.5°C and a white blood cell count (WCC) of 19. What is the most appropriate course of action?

A 70-year-old man who underwent a revision total hip replacement presents 30 days post-operatively with increased pain and swelling in the hip. He also reports pus discharging from the wound. On examination, he is systemically unwell with a fever of 38.5°C and a white blood cell count (WCC) of 19. What is the most appropriate course of action?

A 22-year-old chef presents with abdominal pain localized to the right iliac fossa. The patient also has a fever and diarrhea. The on-call CT1 believes the patient is suffering from acute appendicitis and proceeds with an appendicectomy. However, upon inspection, the appendix appears normal. The terminal ileum is noted to be thickened and engorged. Which of the following infections is most likely responsible?

A 60-year-old male with perforated sigmoid diverticular disease undergoes a Hartmann’s procedure. The patient is hemodynamically stable but has evidence of significant fecal contamination at the time of surgery. What is the risk of developing a wound infection in this case?

A 45-year-old man, who recently underwent a total hip replacement, is recovering in the hospital. He develops profuse and watery diarrhea, and several other patients on the same surgical ward are experiencing similar symptoms. What is the most likely underlying cause of the infection?

A 25-year-old man recently returned from a backpacking holiday in India. He presents with symptoms of coughing and episodic abdominal discomfort. Perianal examination is normal. Stool microscopy reveals both worms and eggs within the feces. What is the most likely infective organism?

A 23-year-old man is readmitted to the hospital three days after a complicated appendicectomy. He initially presented with acute abdominal pain and fever, and after diagnostic imaging, an appendicectomy was performed. The surgery was more difficult than expected, with dense adhesions and a perforated appendix. Post-operatively, he was started on broad-spectrum antibiotics. On day three, the patient develops increasing pain at the surgical site, accompanied by erythema, swelling, and a high fever (38.7°C). The wound is drained, and foul-smelling pus is noted. The surgical team suspects an infection, and cultures are sent for analysis. Which of the following organisms is most likely responsible for this infection?

A 22-year-old man presents to the emergency department with a 5-day history of sore throat, malaise, and fatigue. He describes progressively worsening throat pain, difficulty swallowing, and a feeling of
fullness in the back of his throat. On examination, the patient has a fever of 38.2°C, and there is evidence of a large, swollen tonsil with a shifting uvula, suggestive of a peritonsillar abscess (quinsy). Given the symptoms and clinical findings, what is the most likely underlying infective organism?

A 54-year-old female is admitted one week following a cholecystectomy with profuse diarrhea. The procedure was uncomplicated, except for a minor intra-operative bile spillage during the removal of the gallbladder. What is the most likely diagnosis?

A 55-year-old man with diabetes presents with severe pain, redness, and swelling in his left thigh. The area is warm to the touch and has an expanding, red-purple discoloration. On examination, the patient is febrile and tachycardic. The wound appears to have a “dirty dishwater” appearance. Which of the following statements regarding necrotizing fasciitis is false?

A 48-year-old man, a watercress farmer, presents with a 2-month history of severe abdominal pain, fevers, and progressively worsening jaundice. His symptoms have been accompanied by malaise and weight loss. An ultrasound scan reveals mildly dilated bile ducts with hyperechoic areas within them. Considering his occupation and the ultrasound findings, what is the most likely cause?

A 38-year-old woman presents with a respiratory infection caused by Streptococcus pneumoniae. She is prescribed an antibiotic to inhibit the growth of the bacteria. Which of the following best describes the mechanism of action of macrolides, the class of antibiotics used for this infection?

A 34-year-old man with a history of HIV presents with severe diarrhea lasting 3 months. His CD4 count is <50. Which of the following organisms is most likely responsible for his symptoms?

A 58-year-old man, who received a successful cadaveric renal transplant one year ago, is seen in the clinic for follow-up. He has resumed his work as a swimming instructor and has been generally well until the past week, when he developed recurrent episodes of diarrhea. He reports feeling increasingly lethargic and exhausted. Stool microscopy reveals cysts.

What is the most likely source of his infection?

A group of consultant surgeons is attending a symposium. During the event, they consume canapés prepared by a chef
who has an infection on his finger. Approximately 40 minutes after eating the canapés, the group is struck by severe vomiting.
What is the most likely underlying explanation for this process?

A 22-year-old man presents with crampy abdominal pain, diarrhea, and bloating. He recently returned from a holiday in Egypt, where he had been swimming in the local pool a few weeks ago. He reports having bowel movements 5 times a day, and his stool is greasy and floats in the toilet water, though there is no blood.
What is the most likely cause of his symptoms?

A 14-year-old boy presents with enlarged tonsils that meet in the midline. On oropharyngeal examination, you observe petechial hemorrhages affecting the oropharynx. Additionally, systemic examination reveals splenomegaly.
What is the most likely cause of these findings?

A 29-year-old female undergoes a subtotal thyroidectomy due to a large benign multinodular goiter that was causing compressive symptoms. The surgery was initially uncomplicated, and she was discharged on the third postoperative day with instructions to follow up in one week. Five days after the procedure, she presents to the emergency department with a fever of 38.5°C (101.3°F), increased pain at the surgical site, and erythema around the incision. On examination, there is purulent drainage from the wound, and the surrounding tissue appears inflamed. There is no history of neck trauma, and the patient’s thyroid function is stable post-surgery. Blood cultures are obtained, and the surgical team is consulted for wound management.
What is the most likely causative organism of this wound infection?

A 27-year-old male presents to the urology department with symptoms of pyelonephritis, including malaise, pyrexia, and flank pain. He also reports lymphadenopathy and a maculopapular rash. Given the clinical picture, there is a concern for an HIV seroconversion illness, especially since the patient has a history of recent high-risk sexual behavior. The Monospot test is negative, and the urologist is now asking for appropriate investigations to rule out HIV infection.
What is the most appropriate investigation to confirm or exclude HIV seroconversion?

A 68-year-old man with a history of diabetes presents to the emergency department with an area of necrosis at the base of his scrotum, extending to the perineum. The affected area is surrounded by erythema, and the patient appears systemically unwell, with hypotension. The clinical team is concerned about a severe, rapidly progressing soft tissue infection.
Which of the following organisms is likely to be accountable for this condition?

A 43-year-old woman is scheduled for an elective laparoscopic cholecystectomy due to uncomplicated biliary colic. She has no history of biliary infections or other significant comorbidities. The procedure is expected to proceed without complications. Her preoperative care team is evaluating the risk of surgical site infection.
What is the risk of wound infection occurring in this patient?

A 68-year-old woman with a history of rheumatic fever is admitted with a fever of unknown origin. She appears generally unwell, with a persistent fever over several days. Her blood cultures return negative for bacterial growth, but a transoesophageal echocardiogram reveals vegetations on the mitral valve. The clinical team is concerned about infective endocarditis.
Infection with which of the following organisms is most likely?

A 23-year-old male undergoes an elective inguinal hernia repair. His past medical history is unremarkable, and he is otherwise healthy. The surgery is performed under sterile conditions without complications. Postoperatively, the patient is advised on wound care and follow-up.
What is the likely risk of surgical wound infection in this patient?

A 10-year-old boy presents to the clinic with a three-day history of fever, sore throat, and difficulty swallowing. His mother reports that he has had no cough or nasal congestion. On examination, his temperature is 38.5°C, and he has erythematous tonsils with exudates, tender anterior cervical lymphadenopathy, and no signs of respiratory distress. A rapid antigen detection test is positive for Streptococcus pyogenes.
Which of the following antibiotics is Streptococcus pyogenes still largely susceptible to?

A 4-year-old child presents with a 4- to 5-day history of feeling generally unwell and having a sore throat. His parents report that he has had difficulty swallowing and a mild fever. On examination, there is marked cervical lymphadenopathy and a thick, greyish membrane covering the oropharynx, which bleeds upon attempted removal. The child also has mild respiratory distress, and his voice sounds muffled.
What is the most likely diagnosis?

A 29-year-old man presents with a five-day history of sore throat that has progressively worsened. Over the past 24 hours, he has developed severe, throbbing pain localized to the right tonsil, along with difficulty swallowing and trismus (inability to fully open his mouth). He has a fever and feels generally unwell. On examination, there is a unilateral swelling of the right peritonsillar region, with deviation of the uvula towards the left. His voice has a characteristic “hot potato” quality.
What is the most likely cause?

A 25-year-old man presents to the emergency department with fever, generalized malaise, crampy abdominal pain, and diarrhea. His symptoms began three days ago, starting with fever and fatigue, followed by progressively worsening watery diarrhea that later became bloody. He denies recent antibiotic use but reports consuming undercooked chicken at a restaurant a few days ago. On examination, he has mild right lower quadrant tenderness without rebound or guarding.
Which of the following is not a feature of Campylobacter jejuni infection?

A 22-year-old man undergoes an inguinal hernia repair. Seven days postoperatively, he presents with an erythematous, tender wound that is discharging purulent material. He has no systemic symptoms such as fever or chills, and there is no evidence of deep abscess formation. Examination reveals localized erythema, warmth, and induration around the surgical site, with purulent drainage.
What is the most likely cause?

A 6-year-old boy presents with symptoms of recurrent pruritus ani. On examination, a small worm-like structure is observed protruding from the anus. The child’s parents report frequent scratching and discomfort in the anal region. Based on these findings, which of the following organisms is most likely responsible for the infection?Q54

A 22-year-old man presents with a painless ulcer on his penis and significant inguinal lymphadenopathy. He denies fever, dysuria, or penile discharge. His sexual history reveals multiple partners in the past year, and he does not consistently use barrier protection. There is no history of recent trauma or insect bites. Examination reveals a solitary, indurated ulcer with a clean base and no signs of purulent discharge. A sample from the lesion is sent for microscopy.
Which organism is most likely to be visualized?

A 48-year-old woman is admitted with crampy abdominal pain and diarrhea that started 12 hours ago. She reports feeling generally unwell but denies fever or vomiting. Upon further questioning, she mentions that her milk bottles have been repeatedly pecked by birds, but she has made no other recent dietary changes. She has no history of recent antibiotic use or travel. Physical examination reveals mild abdominal tenderness but no peritoneal signs.
Which of the following is the most likely causative organism?

A 23-year-old woman presents to the gastroenterology clinic with an eight-month history of persistent diarrhea, occurring up to four times daily. She reports occasional crampy abdominal pain but denies blood or mucus in her stools. Over this period, she has unintentionally lost 2 kg. Her past medical history is unremarkable, and she denies recent travel, sick contacts, or antibiotic use. On further questioning, she admits to using herbal supplements for weight loss but is reluctant to disclose further details. Physical examination is unremarkable, with no signs of dehydration, abdominal tenderness, or lymphadenopathy. Laboratory investigations, including complete blood count, inflammatory markers, and stool cultures, are normal. A colonoscopy is performed and reveals diffuse dark pigmentation of the colonic mucosa, consistent with melanosis coli. Histopathological examination confirms the presence of lipofuscin-laden macrophages.
What is the most likely cause?