case study 1 microbiology

2014 Pathology Website

m1-1 . What is the MOST LIKELY diagnosis?

m1-2. The Gram stain from a skin pustule showed gram positive cocci in clusters. The organism grew on sheep blood agar (SBA) and was catalase positive. What is the most likely microorganism?

A. Staphylococcus aureus B. Staphylococcus epidermidis C. Streptococcus pyogenes D. Streptococcus pneumonia

Micro Case 2 (Path Slide 18) [ImageScope] [WebScope]

Clinical History: This 29-year-old male's illness began 10 weeks prior to death, with an episode of "flu". Two weeks later his urine became "smoky". He was found to have hematuria, albuminuria and elevated BUN (180 mg/dl). He died from a pulmonary embolus.

Image Gallery:

m2-1. What is the BEST diagnosis at the time of death?

m2-2. The throat culture obtained exhibited gram positive cocci in chains. It also showed beta-hemolysis on sheep blood agar (SBA) and was catalase negative. What was the most likely organism?

• Streptococcus pyogenes
• Streptococcus viridans
• Staphylococcus aureus

m2-3. An elderly wheelchair bound man had a history of recurrent urinary tract infections. He presents with new onset of fever, chills, and confusion. Blood cultures were drawn. The organism grown was non-hemolytic, catalase negative, and PYR positive. Gram stain showed gram positive cocci. What is the most likely organism?

• Staphylococcus epidermidis
• Staphylococcus saprophyticus
• Enterococcus species

m2-4. An elderly wheelchair bound man had a history of recurrent urinary tract infections. He presents with new onset of fever, chills, and confusion. Blood cultures were drawn. The organism grown was non-hemolytic, catalase negative, and PYR positive. Gram stain showed gram positive cocci. What is the MOST LIKELY organism?

Micro Case 3 (Path Slide 51) [ImageScope] [WebScope]

Clinical History: A 45-year-old male became ill approximately 2 to 3 weeks ago following an alcoholic spree. He had nausea, vomiting, dehydration, confusion and high fever. He died suddenly shortly after admission.

What is the MOST LIKELY diagnosis AND the likely causative agent?

m3-1. These images depict pneumonia in the stage of:

• Red hepatization
• Gray hepatization
• Abscess formation

m3-2. Community acquired atypical pneumonia can be caused by which of the following organisms?

• Legionella pneumophilia
• Klebsiella pneumoniae
• Mycoplasma pneumoniae
• Pseudomonas aeruginosa

Micro Case 4 (Path Slide 195) [ImageScope] [WebScope]

Clinical History: A 67-year-old male had rheumatic heart disease for thirty years. Three months prior to death he began to have episodes of fever and chills accompanied by signs of worsening congestive heart failure. Splinter hemorrhages and purpuric skin rashes were noted three weeks before death.

m4-1. What is the MOST LIKELY diagnosis?

m4-2. Most cases that present with these findings are caused by:

• Rickettsiae

m4-3. In this particular patient the MOST LIKELY causative organism was:

• Group A Streptococci
• Viridans Streptococci

m4-4. The organism MOST LIKELY to infect normal heart valves is:

• Group B Streptococci

m4-5. The organism MOST OFTEN associated with infective endocarditis in IV drug abusers is:

m4-6. The heart valve MOST OFTEN affected by infective endocarditis in IV drug abusers is the:

• Aortic valve
• Mitral valve
• Pulmonic valve
• Tricuspid valve

m4-7. Which of these organisms are normal flora of the throat and are associated with dental caries, brain abscesses, and endocarditis?

• Streptococcus pneumoniae
• Peptostreptococcus species

ANSWER  

m4-8. A patient with suspected infectious endocarditis has a St. Jude’s prosthetic aortic valve and a fever of 38.6°C (101.5°F). Blood culture shows non-hemolytic, small, white colonies. The organism was Gram positive, catalase positive and coagulase negative. What is the MOST LIKELY organism?

• Stapylococcus epidermidis

m4-9. A throat culture grows normal oropharyngeal flora. What alpha-hemolytic organism is most likely to be isolated on the blood agar?

A. Staphylococcus epidermidis B. Staphylococcus viridans C. Streptococcus pneumoniae D. Peptostreptococcus species

m4-10. A throat culture grows normal oropharyngeal flora. The coagulase test for the organism is positive. What is the genus and species of the organism?

A. Staphylococcus aureus B. Streptococcus agalactiae C. Streptococcus pyogenes D. Staphylococcus epidermidis

Micro Case 5

Clinical history: A 33-year-old female dairy farmer develops a severe headache and neck stiffness. On physical examination, her temperature is 38.2°C.  She has no papilledema.  A lumbar puncture is performed, and a Gram stain of the CSF obtained shows many short, gram-positive rods.

m5-1. Based on the clinical findings presented, what is the most likely causative agent in the case above?

m5-2. A sputum gram stain of an elderly person with cough and fever shows gram positive cocci in pairs. What is the most likely organism?

• Haemophilus influenzae
• Enterobacter species

m5-3. A 10-month-old child of a family from Mexico living in Durham was noted by his mother to have a grand mal seizure with shaking of arms and legs by the description given to the EMT. The EMTs found the child limp and unresponsive. In the emergency room the child’s fever was 39.5°C (103.1°F). Blood cultures and lumbar puncture were performed. CSF findings were as follows:

• cell count of 4000
• glucose 20mg/dl
• protein 125mg/dl.

Gram stain showed PMNs and occasional Gram-negative coccobacillary organisms. The organism grew on chocolate agar but not on sheep blood agar or MacConkey’s agar. What is the most likely organism in this case?

• Neisseria meningiditis
• Moraxella catarrhalis
• Streptococcus pneumonia

Micro Case 6 (Path Slide 123) [ImageScope] [WebScope]

Clinical History: A 25 year-old woman had pelvic pain, fever, and vaginal discharge for 3 weeks. On physical examination, she has lower abdominal adnexal tenderness and a painful, swollen left knee.  Laboratory studies show WBC count of 11,875/mm 3 with 68% segmented neutrophils, 8% bands, 18% lymphocytes, and 6% monocytes.

m6-1. What is the MOST LIKELY diagnosis AND the likely causative agent?

m6-2. What is a likely complication of this disease?

• Ectopic pregnancy
• Infertility
• Tubo-ovarian abscess
• ALL of the above

m6-3. What organisms are most likely to cause this disease?

m6-4. Which of the following statement about this disease is FALSE ?

• It is usually associated with endometriosis
• May be complicated by strictures and infertility
• May also involve the adjacent ovary
• May result in a hydrosalpinx
• May be complicated by septicemia
• ALL of the above statements are false regarding this disease.
• NONE of the above statements are false regarding this disease.

m6-5. The following organisms are commonly responsible for pelvic inflammatory disease EXCEPT :

• Aspergillus
• Streptococcus
• Staphylococcus

m6-6. A 25-year-old male presents with urethritis. The Gram stain shows intracellular gram positive cocci. What is the most likely organism?

• Chlamydia trachomatis
• Ureaplasma species
• Neisseria gonorrhoeae
• Haemophilus ducreyi

Micro Case 7 (Path Slide 9) [ImageScope] [WebScope]

Clinical History: A 51-year-old male had a " neurogenic bladder ", caused by a spinal cord tumor. He had multiple bladder infections which were treated with antibiotics. He had surgery to remove the tumor. Postoperatively, he developed fever and costovertebral angle tenderness which did not respond to antibiotics. He expired and an autopsy was performed.

m7-1. What is the BEST diagnosis?

• Acute pyelonephritis
• Acute glomerulonephritis
• Chronic pyelonephritis
• Chronic glomerulonephritis

m7-2 . ALL of the following are risk factors for this condition EXCEPT :

• Reflux nephropathy
• Congenital vesicoureteral reflux
• Posterior urethral valves
• Acetaminophen (Paracetamol) overdose
• Urolithiasis

m7-3 . A urine culture from an 18-year-old woman with similar symptoms also grew a pure culture of more than 100,000 colonies/ml of an organism on sheep blood agar (SBA) and MacConkey’s agar. The gram stain also showed gram negative rods. What is the most likely organism?

• Escherichia coli

Micro Case 8 ( Pathology Slide 39) [ImageScope] [WebScope]

Clinical History: 58-year-old African American female had been hemiplegic on the right side for 3 months prior to death. She developed malaise, fever and chills after visiting with her grandchildren. Her infection progressed. She developed dyspnea and expired.

Image Gallery

m8-1. Based on these clinical findings, what is the best diagnosis and likely causative agent ?

m8-2. What is the most likely cause of this disease in most adults?

M8-2. What organism would be most likely to cause a persistent infection in cystic fibrosis?

Micro Case 9

Clinical history: A 52-year-old homeless, alcoholic man had a fever and a cough productive of thick sputum that worsened over several days. His temperature is 38.2°C.   Diffuse crackles are heard at the right lung base. Laboratory studies are as follows:

• hemoglobin: 13.3 g/dL
• hematocrit: 40%
• platelet count: 291,8000/mm 3
• WBC count: 13,240/mm 3 with 71 segmented neutrophils, 7% bands, 16% lymphocytes, and 6% monocytes.

m9-1. Based on these clinical findings, what is the likely causative agent?

m9-2. An 18-year-old Duke freshman presented to student health with severe headache, fever, and disorientation. A lumbar tap was performed with the following results:

• cell count: 300 with 100% PMN
• glucose: 10 mg/dl
• protein: 100 mg/dl.

The gram stain of the spinal fluid revealed numerous PMNs with intracellular gram-negative diplococci. What is the most likely organism?

• H aemophilus influenza
• Neisseria meningitides

Micro Case 10

Clinical history: A 66-year-old man incurs extensive thermal burns to his skin and undergoes skin grafting procedures in the surgical intensive care unit.  Two weeks later, he has increasing respiratory distress.  Laboratory studies show hemoglobin of 13.1 g/dL, hematocrit 39.2%, platelet count 222,200/mm 3 , and WBC count 4520/mm 3 with 15% monocytes. A chest radiograph shows extensive bilateral infiltrates with patchy areas of consolidation. Image Gallery:

m10-1. Based on these clinical findings, what is the likely causative agent?

m10-2. A sputum specimen from a cystic fibrosis patient grew Gram negative rods on sheep blood agar and MacConkey’s agar. The organism was oxidase positive. What is the most likely organism?

Micro Case 11

Clinical history: A suspicious envelope arrived for sorting at rural post office. The envelope was opened and found to contain white powder. Approximately two days later, the postal worker who handled the letter developed cutaneous boils, which were and 1 to 5 cm in diameter with central necrosis and eschars. He and his wife also developed a mild nonproductive cough with fatigue, myalgia for 72 hours, followed by severe dyspnea, diaphoresis and cyanosis.  Temperature of 39.5°C, pulse 105/min, respiration 25/min, and blood pressure 85/45mm Hg.  Crackles were heard at the lung bases. A chest xray shows a widened mediastinum and small pleural effusions. WBC count of 13,130/mm 3 , hemoglobin 13.7g/dL, hematocrit 41.2%, MCV 91 um 3 , and platelet count 244,000/mm 3 . Both died despite antibiotic therapy. Several cattle, horses, and sheep on the postal worker's farm also died.

m11-2. In a somewhat related case, when Pharaoh did not heed Moses to the let the captive Hebrews go, a series of plagues fell upon the land of Egypt. In the fifth plague, large domesticated mammals including cattle, horses, and sheep died. This was followed by a plague in which the Egyptians developed cutaneous boils. Some developed a mild nonproductive cough associated with fatigue, myalgia, and low grade fever over 72 hours, followed by a rapid onset of severe dyspnea with diaphoresis and cyanosis. Despite antibiotic therapy with both ciprofloxacin and doxycycline (had they been available), many of those affected would die. Which of the following organisms is most likely to have produced these findings?

• Bacillus anthracis
• Herpes simplex virus
• Mycobacterium leprae
• Yersinia pestis

Micro Case 12 (UMich Slide 017) [ImageScope] [WebScope]

Clinical history : A 45-year-old woman is being treated in the hospital for pneumonia complicated by septicemia. She has required multiple antibiotics and was intubated and mechanically ventilated earlier in the course. On day 20 of hospitalization, she has abdominal distention. Bowel sounds are absent, and abdominal radiograph shows dilated loops of small bowel suggestive of ileus. She has a low volume of bloody stool.

m12-1. Based on these clinical findings, what is the likely causative agent?

m12-2. Which of the following are appropriate specimen samples for anaerobe culturing:

• blood, spinal fluid, abscess aspirate
• deep tissue biopsy, sputum, blood
• cerebrospinal fluid, tissue and debridement from decubitus ulcer, bile

Micro Case 13

Clinical history: A 25-year-old man is involved in an accident in which he is ejected from the vehicle. He sustains a compound fracture of the left humerus and undergoes open reduction with internal fixation of the humeral fracture.  Several days later, he has marked swelling of the left arm and crepitus . 

m13-1. In a similar case, a middle aged woman with type 2 diabetes presents to the emergency room with a very painful right lower leg. She has a wound on that extremity and stated that she stumbled on a fallen tree limb in her yard. You observe that her lower leg is discolored and swollen with several areas of crepitus . The abscess fluid was sent to the microbiology laboratory for aerobic and anaerobic culture. The organism grew best on anaerobic cultures and was lecithinase positive. Gram stain shows gram positive rods and the organism show anaerobic growth on egg yolk agar. What is the most likely organism?

• Fusobacterium nucleatum
• Bacteroides fragilis
• Clostridium perfringens
• Peptostreptococcus spp.

Micro Case 14 (Path Slide 451) [ImageScope] [WebScope]

Clinical History: A 4-year-old female had a gradual onset of fever, productive cough, anorexia and diarrhea about eleven days prior to death. The breath sounds were harsh, and a few cracking rales were heard over the right base posteriorly.

m14-1. Based on these clinical findings, what is the likely causative agent?

m14-1. Which of the following is the BEST diagnosis?

• Ghon complex
• Miliary (disseminated) tuberculosis
• Foreign body reaction to talcum powder
• Atypical pneumonia
• H1N1 influenza

Micro Case 15

Clinical history: A 35-year-old man with HIV complains that he has had a "bad" taste in his mouth and discoloration of his tongue for the past 6 weeks.

m15-1. What is the MOST LIKELY diagnosis?

m15-2. In a separate case, a blood culture from a neutropenic (<100 neutrophils/ul) 50-year-old woman on broad spectrum antibiotics grew a yeast. Tests for germ tubes were positive in the microbiology laboratory. What is the likely organism?

• Candida albicans
• Candida tropicalis
• Candida pseudotropicalis
• Candida parapsilosis

Micro Case 16

Clinical history: A 44-year-old diabetic woman developed facial pain over the past 24 hours.  She has become lethargic and obtunded. There is swelling with marked tenderness over the left and right maxilla, bilateral exophthalmos, diffuse abdominal pain, poor skin turgor, and dry mucous membranes. Her temperature is 37.7°C. She has tachycardia, but no murmurs, and tachypnea; the lung fields are clear.

m16-1. What is the MOST LIKELY diagnosis and the best treatment option?

m16-2. In a separate case, A 22-year-old with non-Hodgkins lymphoma was profoundly neutropenic after induction chemotherapy and developed fevers. Broad spectrum IV antibiotic therapy was administered, but fevers continued. Chest x-ray showed new bilaterial fluffy pulmonary infiltrates. A bronchoscopy was performed which showed hyaline, septate hyphae with acute-angle branching. What is the MOST LIKELY organism?

• Blastomyces dermatitidis
• Candida species
• Aspergillus spp

Micro Case 17

Clinical history: A 50-year-old resident of Phoenix, Arizona, has a cough that has persisted for 1 month.  On physical examination, his temperature is 38.1°C. A chest radiograph shows 3.5-cm opacity with central cavitation in the right apical region.  An open lung biopsy is performed to exclude cancer.

m17-1. Which of the following organisms is MOST LIKELY to be responsible for these findings?

• Aspergillus fumigates
• Coccidioides immitis
• Histoplasma capsulatum
• Mycobacterium tuberculosis

Micro Case 18

Clinical history: For the past 3 weeks, a 52-year-old man has had a chronic cough with a low-grade fever. On physical examination, his temperature is 37.4°C.  A chest radiograph shows bilateral, scattered, 0.3- to 2-cm nodules in the upper lobes and hilar adenopathy.  A fine needle aspirate of one of the nodules shows inflammation with mononuclear cells, including macrophages that, with PAS or silver stains, show intracellular, 2- to 5-um, rounded, yeast-like organisms.

m18-1. Which of the following infectious diseases is MOST LIKELY to produce these findings?

• Coccidioidomycosis
• Candidiasis
• Cryptococcosis
• Histoplasmosis
• Blastomycosis

Micro Case 19

Clinical history: For the past month, a 68-year-old patient has had painful oral abcesses, fever, and a cough productive of yellow sputum.  On physical examination, there is dullness to percussion at the left lung base. A chest radiograph shows areas of consolidation in the left lower lobe.  Despite antibiotic therapy, the course of the disease is complicated by abscess formation, and he dies.

m19-1. Based on these clinical findings, what is the BEST diagnosis AND the likely causative agent?

m19-2. In a separate case, a middle aged man presented to his physician with a persistent cough of two months following an extended overseas trip to visit relatives. He had also noted a 10 pound weight loss and night sweats. A sputum was sent to the microbiology laboratory for routine bacterial culture and AFB culture. Kinyoun stain of his sputum was positive. What is the likely causative agent?

• Actinomyces spp
• Nocardia spp.

Micro Case 20

Clinical history: A 50-year-old man post lung transplant was admitted to hospital with fever, chills and cough. Chest x-ray showed multiple small abscesses within a right middle lobe infiltrate. The patient had been treated with prednisone and azathioprine daily for rejection. Gram stain of a bronchoalveolar lavage of the right middle lobe shows gram positive rods. Modified acid fast stain shows partially acid fast bacilli.

m20-1. What is the most likely organism?

m20-2. Nocardia species are:

• branching, gram negative bacilli
• partially acid fast, beaded gram positive filaments
• acid fast, branching gram negative filaments
• partially acid fast, gram variable bacilli

Micro Case 21

Clinical history: An HIV positive male presented in clinic with confusion and disorientation. He had a fever 38.5°C and photophobia. His CD4 count was 80/ul. A lumbar puncture was performed. It showed 32 WBC/ul with 89% lymphocytes, and 6% monocytes, glucose of 22mg/dl, and protein of 89mg/dl. Gram stain showed yeast and India ink showed a thick capsule.

m21-1. Which of the following is the most likely pathogen?

• Cryptococcus neoformans
• Hemophilus infulenzae
• West Nile virus

m21-2. In a separate case, A 35-year-old man who received kidney transplantation was being treated with cyclosporine, azathioprine, and high doses of corticosteroids.  While on this regimen, the patient began to experience headaches and became lethargic.  A clinical diagnosis of meningoencephalitis was made.  He died 7 days later.  Autopsy showed a gelatinous meningeal exudate, and on sectioning of the brain, multiple small cyst-like areas were seen.  Microscopic examination showed areas containing rounded structures with a prominent capsule that stained brightly with mucicarmine. 

What is the most likely organism?

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Educational Resource Review : Clinical microbiology case studies

Graphical abstract.

LI, low-income countries; LMIC, low- and middle-income countries; HMI, high- and middle-income countries; HIC, high-income countries.

Resource web link:   http://clinmicro.asm.org/index.php/explore-the-profession/what-is-clinical-microbiology/418-clinical-microbiology-case-studies-clinical-microbiology-case-studies (Full classification scheme available at: http://bsac.org.uk/wp-content/uploads/2019/03/Educational-resource-review-classification-scheme.pdf )

WHO region and country (World Bank): Region of the Americas, USA (HIC)

Peer review commentary

These clinical microbiology case studies are available on the American Society for Microbiology website. Each of the case studies is humorously named and free to download and use. As of December 2020, there were 14 case studies on the website, with each case study available for individual download. Topics include malaria, Streptococcus pyogenes , Legionella , Salmonella and Nocardia , among others.

Each case study details a patient’s history and presentation, the action(s) of the doctor, lab test results, diagnosis and treatment, as well as the final patient outcome. The case studies are in PowerPoint (.ppt) format and contain, on average, 12 slides. Each case study was developed by a different author.

Overall, the case studies are straightforward and would be easy for teachers and other medical professionals to use as part of medical education. Contact information for each of the authors is provided at the end of the case study, should the educator want additional information before using the case study.

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Clinical Case Study

You are a pathologist working in the lab at Daigger Memorial Hospital (located in central Oregon). The emergency room is sending you cultures collected from patients. Your job is to determine:

• The pathogenic bacteria causing the disease
• What disease is being presented
• What is the best treatment given the patient’s unique symptoms and history

Review the patient assessment form provided. Consider the type of sample taken and determine the relevant primary and secondary symptoms. Generally, samples taken in a clinical setting contain multiple organisms. In this case study, the sample will contain one contaminant organism and one causative agent.

Note: Watch for allergies. These may affect the appropriate treatment you will prescribe for the patient.

For some diseases, an irregularity in pulse or respiration, for example, may be indicative of the seriousness of the illness or may even be a direct indicator of the disease presented. Therefore, it is important that you understand what is considered “Within Normal Limits” for all assessment areas on the patient assessment form. Familiarize yourself with the acceptable normal ranges for pulse, respiration, oxygen saturation, blood pressure, and temperature for the age group your patient falls within.

Clinical Case Study Flowchart »

Patient Assessment Form »

Normal Flora According to Body System

Adapted from: Strohl, W.A. et.al. Lippincott's Illustrated Reviews: Microbiology. Lippincott Williams & Wilkins. Baltimore, MD. 2001 and Forbes, B.A. et.al. Bailey and Scott's Diagnostic Microbiology. Eleventh Edition. Mosby. St. Louis, MO. 2002

Pathogenic Organisms According to Body System

Adapted from: Gilligan, P.H. et.al. Cases in Medical Microbiology and Infectious Diseases. 2nd ed. American Society for Microbiology, Washington, D.C. 1997. Murray, Patrick R. Editor. Manual of Clinical Microbiology. 8th ed. ASM Press. Washington, D.C. 2003. Strohl, W.A. et.al. Lippincott's Illustrated Reviews: Microbiology. Lippincott Williams & Wilkins. Baltimore, MD. 2001

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Case Studies: Microbiology

All microbiology case studies.

A Bioinformatic Investigation of a Mysterious Meningoencephalitis

By Sari Matar, Dyan Anore, Basma Galal, Shawn Xiong

Sarah’s Stomach

By Kelli M. Kinlen, David M. Zuckerman

Molly’s Medical Mission Maladies

By William M. Kolling, Catherine D. Santanello

A New York State of Mind

By Samantha N. Jewell, Julian A. Brix

What’s in Your Food?

By Bwalya Lungu

A Fatal Bite

By Obidimma Ezezika, Mona Jarrah, Shawanah Rahman

Troubled Waters

By Sebastian A. Schormann, James E. Boyett, Samiksha A. Raut

New Tricks for Old Drugs

By Carlos C. Goller, Stefanie H. Chen, Melissa C. Srougi

Stuck on You

By Brenda F. Canine, Michael L. Dini, Breanna N. Harris

Making Better Poison Eaters

By Kelsie J. Anson, Briana N. Van Treeck, Jake J. Flood

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9.1: Case Study - Environment

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Case study #2 – The Land is Sick

Disclaimer: This is a fictitious scenario created for the purposes of microbiome, health, disease, and environmental education. Any names, characters, places and incidents either are products of the author’s imagination or are used fictitiously. Any resemblance to actual events or locales or persons, living or dead, is entirely coincidental.

Part I – Background and Problem

Coffee production in South America has drastically decreased in the 2021-23 growing seasons. Specifically, the major farms in Columbia and Brazil which collectively contribute over half of each countries coffee (both specialty and commercial) production, have had severe crop failures. As a result, the price of a cup of coffee has noticeably increased, putting financial strain on suppliers and businesses.

Interestingly, the few years prior to this decline, coffee production was at an all-time high, with more coffee in the market than demanded. This dropped the price of coffee, and in many cases original farmers were not fairly compensated.

The International Coffee Organization (ICO) has tasked a team of researchers to identify potential problems to South American coffee plant failure and provide quick and efficient resolution.

Article 1 – The Bacterial Microbiome of Meloidogyne -Based Disease Complex in Coffee and Tomato

Article 2 – A review of three major fungal diseases of Coffea Arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya

Article 3 – Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei

Video 1 – The biggest threats to the coffee industry

Video 2 – #1 Specialty coffee and the price crisis | Producer Crossover 2019

• As a scientific researcher, what are some factors you would take into consideration when addressing this problem?
• What type of environmental microbiomes could be implicated in coffee plant crop failure and why?
• Should other coffee farms in countries besides those in South America be worried about similar failure in their crops? Why or why not?

Attributions

• Figure 1 – Coffee exports by country 2019-20 by Dylan Parks. Data source: International Coffee Organization
• Figure 2 – A world map of countries by coffee production, 2019 by Cbahrs licensed under CC BY-SA 4.0
• Article 1 – The Bacterial Microbiome of Meloidogyne -Based Disease Complex in Coffee and Tomato by Lamelas et al., 2020 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Article 2 – A review of three major fungal diseases of Coffea Arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya by Hindorf and Omondi, 2011 licensed under CC BY-NC-ND 3.0
• Article 3 – Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei by Mejía-Alvarado et al., 2021 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Video 1 – The biggest threats to the coffee industry by Startup to Storefront licensed under a Creative Commons Attribution License (reuse allowed)
• Video 2 – #1 Specialty coffee and the price crisis | Producer Crossover 2019 by Coffee Circle licensed under a Creative Commons Attribution License (reuse allowed)

Part II – Approach, Implementation, Reasoning

Upon initial inspection, the unhealthy coffee plants exhibited yellowing of leaves, appearance of red-brown lesions, abnormal shape, damaged coffee berries, and little new growth or production. Researchers decided to take samples of healthy and unhealthy leaves and berries, as well as soil and root samples.

Article 1 – Prokaryotic diversity in the rhizosphere of organic, intensive, and transitional coffee farms in Brazil

Article 2 – A metagenomics approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems

Video 1 – #2 Producer Crossover 2019

Video 2 – How countries farm and make coffee differently

Over the next year, other plantations in Columbia and Central American begin to experience similar declines in coffee plant health. Farmers were questioned about any changes in practices, and while there have been some adjustments do to the fluctuating coffee prices, traditional farming techniques have remained the same for the most part in smaller plantations. Larger plantations with intensive farming made more changes due to trader suggestions on improving yields including application of different fertilizers and hiring less experienced workers.

• What type of analytical techniques do you think were or should be performed on the samples taken?
• How could the observed symptoms of the unhealthy plants be connected to an associated microbiome?
• How could human intervention exacerbate or ameliorate this situation?
• Article 1 – Prokaryotic diversity in the rhizosphere of organic, intensive, and transitional coffee farms in Brazil by Caldwell et al., 2015 licensed under a Creative Commons Attribution-ShareAlike 4.0 International ( CC BY-SA 4.0 ) license.
• Article 2 – A metagenomics approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems by Rodriguez et al., 2020 licensed under a Creative Commons Attribution-NonCommercial 4.0 International License .
• Video 1 – #2 Producer Crossover 2019 by Coffee Circle licensed under a Creative Commons Attribution License (reuse allowed)
• Video 2 – How countries farm and make coffee differently by Startup to Storefront licensed under a Creative Commons Attribution License (reuse allowed)

Part III – Discussion

Analysis of the negatively affected plantations’ soil showed a decline in plant growth promoting bacteria and mycorrhizae and an increase in bacterial and fungal pathogens like Pseudomonas syringae and Cercospora coffeicola .

Over the next few years (2022-24) coffee plants still struggle to grow in Central and South America. Other parts of the world, such as Vietnam and other Asian countries, are seeing a decline in crop health also, further contributing to global coffee market troubles. Many of these farms switched from shade-grown to intense sun-grown coffee to try to meet needs for demand. Larger corporations and roasters have purchased many of the smaller family farms to try to recoup losses and implement ‘new and improved’ growing strategies for increased production. This included switching to primarily sun-grown coffee, and application of large amounts of synthetic nitrogen fertilizer.

Video 1- #3 The future of the price crisis

Video 2 – How coffee destroys the environment

Article 1 – Root endophytes of coffee ( Coffea Arabica ): Variation across climatic gradients and relationships with functional traits

Article 2 – Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario

Article 3 – Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil

• What factors could cause these changes in the soil microbiomes?
• Why do you think coffee plantations across the globe are beginning to fail as well?
• How does natural biodiversity benefit ecosystem health on both a micro and macro scale?
• Figure 1 – Shade grown coffee in Guatemala by John Blake under Public Domain
• Figure 2. Sun-grown coffee plantation in Brazil by Knase caption adapted by Dylan Parks licensed under the Creative Commons Attribution 3.0 Germany license.
• Video 1 – #3 The future of the price crisis by Coffee Circle licensed under a Creative Commons Attribution License (reuse allowed)
• Video 2 – How coffee destroys the environment by Startup to Storefront licensed under a Creative Commons Attribution License (reuse allowed)
• Article 1 – Root endophytes of coffee ( Coffea Arabica ): Variation across climatic gradients and relationships with functional traits by Fulthorpe et al., 2020 licensed under Creative Commons Attribution License (CC BY).
• Article 2 – Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario by dos Santos et al., 2021 licensed under the terms and conditions of the Creative Commons Attribution ( CC BY ) license.
• Article 3 – Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil by Veloso et al., 2020 licensed under the terms and conditions of the Creative Commons Attribution ( CC BY ) license.

Part IV – Resolution

In 2030, most varieties of coffee are extinct, and only small amounts of coffee are produced on shade grown farms further from the equator. It appears that coffee plantations were severely impacted by increasing global temperatures, which altered ecosystem dynamics and promoted pathogen and pest invasion. Fungi, bacteria, and arthropods devastated already struggling coffee farms and with a major switch to sun-grown coffee, soil microbiomes were depleted and disease spread rapidly through monoculture crops. This switchover was prompted by an energy drink corporation, KAPOW!, which wanted to corner the caffeine market and boost production, though their expertise in growing coffee was lacking and the excessive use of synthetic fertilizers on already sun baked land which requires much more watering further doomed plantations. At least they now produce a cheap “coffee” flavored energy drink. It tastes terrible.

Article 1 – Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Article 2 – Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

Article 3 – One health relationships between human, animal, and environmental microbiomes: A mini-review

Video 1 – Teaching coffee farmers about the birds and the bees

• In what ways are environmental microbiomes impacted by changing environmental factors and how can this promote diseases within an ecosystem?
• How could various environmental microbiomes be utilized to improve sustainable practices and technology?
• How are environmental and human microbiomes interconnected?
• Article 1 – Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review by Duong et al., 2020 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Article 2 – Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador by Rao et al., 2020 licensed under the Creative Commons CC0 public domain dedication.
• Article 3 – https://www.frontiersin.org/articles/10.3389/fpubh.2018.00235/full by Trinh et al., 2018 licensed under the terms of the Creative Commons Attribution License (CC BY).
• Video 1 – Teaching coffee farmers about the birds and the bees by VOA Learning English licensed under a Creative Commons Attribution License (reuse allowed)
• Hindorf, H., & Omondi, C. O. (2011). A review of three major fungal diseases of Coffea arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya. Journal of Advanced Research , 2 (2), 109–120. https://doi.org/https://doi.org/10.1016/j.jare.2010.08.006
• Lamelas, A., Desgarennes, D., López-Lima, D., Villain, L., Alonso-Sánchez, A., Artacho, A., Latorre, A., Moya, A., & Carrión, G. (2020). The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato. Frontiers in Plant Science , 11 . https://www.frontiersin.org/article/10.3389/fpls.2020.00136
• Duong, B., Marraccini, P., Maeght, J.-L., Vaast, P., Lebrun, M., & Duponnois, R. (2020). Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review. Frontiers in Sustainable Food Systems , 4 . https://www.frontiersin.org/article/10.3389/fsufs.2020.607935
• Fulthorpe, R., Martin, A. R., & Isaac, M. E. (2019). Root Endophytes of Coffee (Coffea arabica): Variation Across Climatic Gradients and Relationships with Functional Traits. Phytobiomes Journal , 4 (1), 27–39. https://doi.org/10.1094/PBIOMES-04-19-0021-R
• dos Santos DG, Coelho CCdS, Ferreira ABR, Freitas-Silva O. Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario. Microorganisms . 2021; 9(4):858. https://doi.org/10.3390/microorganisms9040858
• Caldwell AC, Silva LCF, da Silva CC, Ouverney CC (2015) Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil. PLoS ONE 10(6): e0106355. doi:10.1371/journal.pone.0106355
• Rodríguez, A. C.-, R. T.- Calzada, C. G.-D. la Peña, J. G. A.- Ávila, E. N.- Reyna, F. V.- Paniagua, C. D.- Velásquez, and C. A. M.- Herrera. “A Metagenomic Approach in the Evaluation of the Soil Microbiome in Coffee Plantations under Organic and Conventional Production in Tropical Agroecosystems”. Emirates Journal of Food and Agriculture , Vol. 32, no. 4, Apr. 2020, pp. 263-70, https://doi.org/10.9755/ejfa.2020.v32.i4.2092.
• Rao, M., Rice, R., Fleischer, R., & Muletz Wolz, C. (2020). Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador. PLOS ONE , 15 , e0231875. https://doi.org/10.1371/journal.pone.0231875
• Mejía-Alvarado, F. S., Ghneim-Herrera, T., Góngora, C. E., Benavides, P., & Navarro-Escalante, L. (2021). Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei. Frontiers in Microbiology , 12 . https://www.frontiersin.org/article/10.3389/fmicb.2021.639868
• Veloso, T. G. R., da Silva, M. de C. S., Cardoso, W. S., Guarçoni, R. C., Kasuya, M. C. M., & Pereira, L. L. (2020). Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil. Scientific Reports , 10 (1), 14692. https://doi.org/10.1038/s41598-020-71309-y
• Trinh, P., Zaneveld, J. R., Safranek, S., & Rabinowitz, P. M. (2018). One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review. Frontiers in Public Health , 6 . https://www.frontiersin.org/article/10.3389/fpubh.2018.00235