Meet the ESKAPE pathogens: Le Minh Nguyen

Assigned ESKAPE Pathogen: Pseudomonas aeruginosa

Why is this ESKAPE Pathogen of interest
Pseudomonas aeruginosa is a common opportunistic pathogen that can cause disease not only in plants and animals but also in humans. This ESKAPE Pathogen is of utmost importance because it is a multidrug-resistant pathogen, with very advanced antibiotic resistance mechanism, that can survive under various environmental conditions. According to the Centers for Disease Control and Prevention (CDC), it is the most common disease-causing species. P. aeruginosa affects different sites within the body, including urinary tract, skin (burn or surgical wounds), and the respiratory tract and causes severe acute and chronic infections in immunocompromised patients with cancer and patients suffering from severe burns and cystic fibrosis. It is often associated with hospital-acquired infections because there is a higher risk for infection if you have surgical wounds or burns or if you are being treated with a mechanical ventilator and other medical devices such as urinary or intravenous catheters.

General Cellular and Morphological Characteristics of the Organism 
Pseudomonas aeruginosa is a Gram-negative, rod-shaped, asporogenous, and monoflagellated bacterium (Wu, 2014). Its size is about 0.5 to 0.8 µm, and it belongs to the bacterial family Pseudomonadaceae (Putty, 2007).

Pseudomonas aeruginosa is often identified by its pearlescent appearance and grape-like or tortilla-like odor (Putty, 2007). P. aeruginosa strains can produce one or more pigments: pyocyanin (blue-green), pyoverdine (yellow-green and fluorescent), and pyorubin (red-brown) (Wu, 2014).

Pseudomonas aeruginosa has simple nutritional requirements as it is often observed to grow in “distilled water” (Putty, 2007). It grows well at 25°C to 37°C, but it is its ability to grow at 42°C that help us differentiate it from many other Pseudomonas species (Wu, 2014).

Like most environmental bacteria, P. aerugionosa lives predominantly in slime-enclosed biofilms adherent to available surface from which it periodically releases (Putty, 2007). It is present in soil and aquatic environments. However, as mentioned before, it is tolerant of a variety of environmental conditions. It is also capable of growing in diesel and jet fuel, where it is known as a hydrocarbon utilizing microorganism (or “HUM bug”), causing microbial corrosion (Putty, 2007). Furthermore, it is resistant to high concentrations of salts and dyes, weak antiseptics, and many antibiotics (Putty, 2007).

Clinical Importance and Prevalence
The most difficult challenge when facing P. aeruginosa is its ability to rapidly develop resistance to multiple classes of antibiotics during treating an infection, ability to survive on minimal nutritional requirements and ability to tolerate a variety of physical conditions. These contribute to the organism’s capacity of persisting in hospital settings.

Data collected by the CDC National Nosocomial Infections Surveillance System from 1986 to 1998 reveals that P. aeruginosa was the fifth most frequently isolated nosocomial pathogen, accounting for 9% of all hospital-acquired infections in the United States; the second leading cause of nosocomial pneumonia (14 to 16%); third most common cause of urinary tract infections (7 to 11%); fourth most frequently isolated pathogen in surgical site infections (8%), and seventh leading contributor to bloodstream infections (2 to 6%) (Lister et al., 2009). In addition, more recent studies continue to show it is the leading cause among pediatric patients in the intensive care unit (Lister et al., 2009).

Infection
In hospital settings, infections by P. aeruginosa can be transmitted in hospitals by nursing staff, medical equipment, sinks, disinfectants, and food (Lister et al., 2009). Transmission occurs from improper hygiene, by patient contact with a contaminated reservoir or by ingestion of contaminated materials.

As described before, P. aeruginosa affects different sites within the body, including urinary tract, skin (burn or surgical wounds), and the respiratory tract and causes severe acute and chronic infections in immunocompromised patients with cancer and patients suffering from severe burns and cystic fibrosis (Wu, 2014).

Furthermore, exposure to contaminated water can also cause mild P. aeruginosa infections. For example, inadequately chlorinated hot tubs and swimming pools can cause ear infections and skin rashes. P. aeruginosa can also cause eye infections in users of contact lenses (Bennington-Castro, 2015).

Pathology
Bloodstream infections can cause:
• Fever and chills
• Body aches
• Light-headedness
• Rapid pulse and breathing
• Nausea and vomiting
• Diarrhea
• Decreased urination

Pneumonia can cause:
• Fever and chills
• Difficulty breathing
• Cough, sometimes with yellow, green, or bloody mucus

Urinary tract infections can cause:
• Strong urge to urinate frequently
• Painful urination
• Unpleasant odor in urine
• Cloudy or bloody urine

Wound infections can cause:
• Inflamed wound site
• Fluid leakage from wound

Ear infections can cause:
• Ear pain
• Hearing loss
• Dizziness and disorientation
(Bennington-Castro, 2015)

Ineffective Antibiotics
P. aeruginosa currently shows resistance to the following antibiotics: penicillin G; aminopenicillin, including those combined with beta-lactamase inhibitors; first and second generation cephalosporins; piperacillin; piperacillin and tazobactam; cefepime; ceftazidime; aminoglycosides; the quinolones; the carbapenems; colistin and fosfomycin (Hancock, 2000).

 

Effective Antibiotics
P. aeruginosa is most susceptible to the following antibiotics: cefepime, amikacin, ceftazidime, tobramycin, the combination of piperacillin and tazobactam, meropenem, imipenem, piperacillin, ciprofloxacin, gentamicin, and fosfomycin (Yayan et al., 2015).

Corresponding Safe Relative
The corresponding relative safe to P. aeruginosa is Pseudomonas putida. P. putida is a rod-shaped, flagellated, gram-negative bacterium that is found in most soil and water habitats where there is oxygen. It grows optimally at 25-30°C and can be easily isolated. Unlike P. aeruginosa, P. putida has a nonpathogenic nature; therefore, researchers find P. putida beneficial to research as it also happens to be very versatile and easy to handle (Marcus, 2003). For example, as P. putida assists in promoting plant development, researchers use it in bioengineering research to develop biopesticides and to the improve plant health (Espinosa-Urgel, 2000).

Works Cited
Bennington-Castro, Joseph. “What Is Pseudomonas Aeruginosa?” Stroke Center, Everyday Health, 7 Aug. 2015.
Espinosa-Urgel, Manuel, and Amparo SalidoJuan-Luis Ramos. “Genetic Analysis of Functions Involved in Adhesion of Pseudomonas Putida to Seeds.” Journal of Bacteriology, American Society for Microbiology Journals, 1 May 2000.
Hancock, R E, and D P Speert. “Antibiotic Resistance in Pseudomonas Aeruginosa: Mechanisms and Impact on Treatment.” Current Neurology and Neuroscience Reports., U.S. National Library of Medicine, Aug. 2000.
Lister, Philip D., et al. “Antibacterial-Resistant Pseudomonas Aeruginosa: Clinical Impact and Complex Regulation of Chromosomally Encoded Resistance Mechanisms.” Current Neurology and Neuroscience Reports., U.S. National Library of Medicine, Oct. 2009.
Marcus, Adam. “Versatile Soil-Dwelling Microbe Is Mapped.” GNN – Genome News Network, 10 Jan. 2003.
Putty, Murali. “Pseudomonas Aeruginosa.” EMLab P&K, Mar. 2007.
Wu, Weihui, et al. “Pseudomonas Aeruginosa.” Molecular Medical Microbiology, Academic Press, 29 Sept. 2014.
Yayan, Josef, et al. “Antibiotic Resistance of Pseudomonas Aeruginosa in Pneumonia at a Single University Hospital Center in Germany over a 10-Year Period.” PLOS ONE, Public Library of Science, 2 Oct. 2015.

 

Meet the ESKAPE pathogens: Carly Burns and Sofia Boswell

Assigned ESKAPE Pathogen: Klebsiella pneumoniae

Why is this ESKAPE Pathogen of interest (in brief)
Klebsiella pneumoniae is a common nosocomial (originating in a hospital) pathogen that accounts for about 10% of all infections acquired within a hospital setting (1). It is also a common pathogen responsible for community-acquired infections, as well as a number of other diseases such as meningitis, septicemia, purulent abscesses, and pneumonia (1). Additionally, as some strains are nitrogen-fixing, K. pneumoniae is of agricultural interest because it has been observed to increase crop yields in certain agricultural conditions.

General Cellular and Morphological Characteristics of the Organism (taxonomic classification, nutrition, cell shape, habitat)
K. pneumoniae is a Gram negative, non-motile, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. It is a part of the Enterobacteriacae family (6). K. pneumoniae is commonly found in the normal flora of the mouth, skin, and intestines, but can become destructive and cause damage if inhaled, specifically to the alveoli. K. pneumoniae occurs naturally in the soil and about one third of strains are nitrogen-fixing in anaerobic conditions.

https://chrislima90.weebly.com/blog/top-advice-on-klebsiella-pneumoniae

http://faculty.ccbcmd.edu/courses/bio141/labmanua/lab12/Mac_kpneumoniae.html
(Grows very well on MacConkey agar)

Clinical Importance and Prevalence
K. pneumoniae originated in a hospital setting and is now globally prevalent in hospital and community settings (6). Infections are more common in the young, the old, and the immunocompromised (6). Enterobacteriacae are becoming more and more difficult to treat because of their increasing resistance to antibiotics through the production of different enzymes such as extended-spectrum beta-lactamases and carabapenemases (6).

Infection (How does the infection occur and where is it localized?)
K pneumoniae infections are typically seen in individuals with a compromised immune system, and most infections are seen in middle-aged or older men who already have debilitating diseases. Healthy people typically do not get Klebisella pneumonia infections (3). Humans serve as the primary reservoir for this pathogen, and the pathogen is typical transmitted between individuals through fecal matter and nasal secretions. K. pneumoniae is rarely carried on the skin (2). Carrier rates of the pathogen increase significantly in hospital patients (2). Klebisella pneumonia is spread through contact, either person-to-person contact (i.e. touching the hands of an infected individual) or environmental contact (i.e. touching a contaminated surface). The bacteria cannot be spread through the air (3). Certain medical tools such as ventilators and catheters may cause an individual to be exposed as well (3). K pneumoniae are capable of infection because of fimbrial adhesins and a thick capsule that is comprised of two layers of polysaccharide fibers (6).

Pathology (What disease is caused? What are the symptoms?)
The most common disease caused by Klebisella pneumoniae is pneumonia. This occurs when Klebisella bacteria enter the respiratory tract and setting in the air sacs of the lungs, causing infection and inflammation (3). The most common symptoms of pneumonia are fever, cough, chest pain, difficulty breathing, and abnormal mucus production (4). Without treatment, pneumonia can become a very serious infection, especially in the elderly and those who are immunocompromised (4). Other diseases that can be caused by Klebisella pneumonia are septicemia, meningitis, endocarditis, and cellulitis (4).

Ineffective Antibiotics (Antibiotics to which the organism has acquired resistance)
Some K. pneumonia have become very resistant to a class of antibiotics called carbapenems (3). Resistant bacteria produce an enzyme called carbapenemase which renders carbapenems ineffective (3). These resistant bacteria are also known as KPC-producing organisms and are very difficult to treat (3).

Effective Antibiotics (Antibiotics known to inhibit the organism)
There are many effective antibiotics to treat K. pneumoniae (5). Beta-lactams, aminoglycosides, and quinolones are effective antibiotics against Klebsiella infections (5). Cephalosporins have also been used alone and in conjunction with aminoglycosides but should not be used if ESBL strains are present (5).

Corresponding Safe Relative
The corresponding safe relative is Escherichia coli (6). Most E. coli are commensal and make up about 0.1% of the of the normal intestinal flora, however some are pathogenic and has shown marked resistance to multiple antibiotics in the past decade (6).

Sources:
1. Guo, S., J. Xu, Y. Wei, Y. Li, and R. Xue. 2016. Clinical and molecular characteristics of Klebsiella pneumoniae venitllaor-associated pneumonia in mainland China. BMC Infec Dis. 16: 608
2. Yu, W.L., Y.C. Chuang. UpToDate. Clinical features, diagnosis, and treatment of Klebsiella pneumoniae infection. 2018. https://www.uptodate.com/contents/clinical-features-diagnosis-and-treatment-of-klebsiella-pneumoniae-infection
3. Centers for Disease Control and Prevention. Klebsiella pneumoniae in Healthcare Settings. 2012. https://www.cdc.gov/hai/organisms/klebsiella/klebsiella.html
4. WebMD. What is Klebsiella Pneumoniae Infection?. 2018. https://www.webmd.com/a-to-z-guides/klebsiella-pneumoniae-infection#1
5. S. Qureshi. Medscape. Klebsiella Infections Medication. 2017. https://emedicine.medscape.com/article/219907-medication#showall
6. Pendleton, J. N., Gorman, S. P., & B. F. Gilmore. Medscape. Clinical Relevance of the ESKAPE Pathogens. 2013.

Meet the ESKAPE pathogens: Staphylococcus aureus (Nicole B)

About 30% of people have staph bacteria, usually living commensally on the skin and in the nostrils. Occasionally, staph can break the skin and cause infections ranging in seriousness from small boils to sepsis and pneumonia.

Staphylococcus bacteria are named so because they are round, or coccus shaped, and they are arranged in grape shaped clusters (the Greek word for grapes is transliterated to staphule). On plates, S. aureus usually create yellow or golden colonies. They grow readily between 18 and 40 degrees Celsius, and are faculitative anaerobes, meaning they will use oxygen if available but can live without it.

Staphylococcus aureus is believed to be living peacefully on the skin or in the nose of 1/3 of the world’s population. In 2006, it was found that for every 10,000 visits to the hospital, 410 of those visits were for a staph skin infection such as abscesses and cellulitis; the number of skin infections in general might be much higher due to the relative lack of seriousness of some skin problems like impetigo and boils. Staph bacteremia, or presence of staph bacteria in the blood, is the cause of an estimated 23% of all cases of sepsis, and can lead to infection of the heart and infection of the bones. Staph is also a common complication of pneumonia, and S. aureus is implicated in more than 40% of healthcare acquired pneumonias. As you can see, staph infections can occur from a variety of ways; the best prevention is simply commonsense risk mitigation, such as cleaning open wounds and having good hygiene.

The antibiotic-resistant form of staph that everyone is afraid of is MRSA (methicillin-resistant Staphylococcus aureus). MRSA infections are commonly acquired in health care settings, but up to 12% of MRSA infections now are from the broader community. Oddly, MRSA refers to staph resistant against other antibiotics, though most antibiotics it is commonly resistant to is in the beta-lactam class, which includes methicillin and penicillin. Resistance happens when staph creates the enzyme beta-lactamase to cleave an important bond in the antibiotic. It recently became resistant to vancomycin, the antibiotic doctors usually go for when they treat MRSA. The antibiotics Bactrim, clindamycin, minocycline, and doxycycline are still effective and are still widely prescribed to patients.

Instead of playing with Stapholococcus aureus in the lab, we are using Staphylococcus epidermidis.

 

https://www.ncbi.nlm.nih.gov/books/NBK441868/

https://www.cdc.gov/mrsa/community/index.html

https://cmr.asm.org/content/10/3/505.long

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451395/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367609/

https://en.oxforddictionaries.com/definition/staphylococcus

https://en.oxforddictionaries.com/definition/aureus

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372331/

https://www.the-hospitalist.org/hospitalist/article/125986/what-best-treatment-adult-patient-staphylococcus-aureus-bacteremia

https://academic.oup.com/femsre/article/41/3/430/3608758

https://www.uptodate.com/contents/methicillin-resistant-staphylococcus-aureus-mrsa-beyond-the-basics

Meet the ESKAPE Pathogens – Alexa and Kara

Acinetobacter baumannii  is a multi-drug resistant, pathogenic bacteria that is commonly found in hospital settings.  Being that is an emerging source of nosocomial infection, and is becoming more prevalent, Acinetobacter baumannii is of interest to the medical and scientific communities (1).

A. baumannii is gram negative, aerobic, and coccobacillus in shape (Figure 1) (3).  The genus Acinectobacter was first discovered in 1911, when a Dutch scientist isolated microorganisms from soil. Originally “Acinectobacter” was used to designate non-motile bacteria. However, today it is currently the genus for “gram-negative, strictly aerobic, nonfermenting, nonfastidious, nonmotile, catalase-positive, oxidase-negative bacteria with a DNA G+C content of 39% to 47%” (2).  Differences in the carbapenemase and gyrB genes of A. Baumannii distinguish it from its close relatives. A. baumannii’s “safe” relative is A. baylyi (2). A. baumannii, Acinetobacter genomic species 3, and Acinetobacter genomic species 13TU are extremely similar, and cannot be distinguished from one another using commercial methods.  Therefore, the 3 species are often lumped together as a complex, and treated as one (2).  Acinectobacters are commonly found in soil and water in nature, and some are part of the flora of human skin. However, virtually no individuals have tested positively for A. baumannii outside of hospital settings and combat zones, so the natural habitat of A. Baumannii is currently unknown (2). Very few individuals in China and tropical Australia have been tested positively for A. baumannii (5).  In the laboratory setting, A. Baumannii  grows well on Luria-Bertani broth (LB) (1).

As mentioned prior, A. baumannii is rarely found outside of the hospital setting.  One notable exception to this is the prevalence of A. baumannii in skin infections among soldiers and other military personnel (1).   Additionally, A. baumannii is well documented in burn units and ICUs.  Immunocompromised individuals, as well as individuals with prolonged hospital stays are at the greatest risk for infection of A. baumannii (1). Hospital-acquired pneumonia and bloodstream infections, as well as post-neurosurgical meningitis, are the diseases commonly associated with A. baumannii. In 2003 the CDC reported that 7% of ICU-acquired pneumonias were caused by A. baumannii, and between 5 and 10% of cases of ICU-acquired pneumonia were due to A. baumannii (2).  It is hypothesized that soldiers returning from Afghanistan and Iraq brought this pathogen into U.S. hospitals.  A. baumannii has thrived in this setting due to its antibiotic and antiseptic resistance (2).  Infections typically begin when an external device, such as a ventilator, is used in the treatment of a patient.  The external device provides an entry site for A. baumannii, where it can then colonize (and can form biofilms)—for this example, in the lungs (1). Figure 2 below shows how A. baumannii spreads in the hospital setting, and Figure 3 shows how it affects the human body (6). Symptoms of an infection caused by A. baumannii are hard to distinguish among already ill individuals, however, they typically include fever, chills, and cough (5).

A. baumannii is known to be resistant to cephalosporins (can degrade beta-lactam), aminoglycosides, quinolones and, lately, carbapenems (3).  When A. baumannii was first treated in the 1990’s, carbapenems were effective antibiotics, but are becoming less effective over time (3). Modified efflux pumps, porins, and lactamases enable A. baumannii to be resistant to several classes of drugs (4). The World Health Organization reports that A. baumannii is susceptible to polymyxins, but academic research has focused on new developments to combat gram-negative bacteria. Outer membrane proteins of gram-negative bacteria are being targeted experimentally as potential antibiotics (3). Additionally, bacteriophages are also being investigated as potential antibiotics, due to their ability to selectively target bacteria (1).

ESKAPE Pathogen Fig 1-27hgnn4

ESKAPE Pathogen Fig 2-18eokb8

ESKAPE Pathogen Fig 3-1t4ue2e

References:

(1)   Howard, Aoife, et al. “Acinetobacter Baumannii.” Virulence, vol. 3, no. 3, 2012, pp. 243–250., doi:10.4161/viru.19700.

(2)   Peleg, A. Y., et al. “Acinetobacter Baumannii: Emergence of a Successful Pathogen.” Clinical Microbiology Reviews, vol. 21, no. 3, 2008, pp. 538–582., doi:10.1128/cmr.00058-07.

(3)   Soojhawon, Iswarduth, et al. “Discovery of Novel Inhibitors of Multidrug-Resistant Acinetobacter Baumannii.” Bioorganic & Medicinal Chemistry, vol. 25, no. 20, 2017, pp. 5477–5482., doi:10.1016/j.bmc.2017.08.014.

(4)   Vila, Jordi, et al. “Porins, Efflux Pumps and Multidrug Resistance in Acinetobacter Baumannii.” Journal of Antimicrobial Chemotherapy, vol. 59, no. 6, 2007, pp. 1210–1215., doi:10.1093/jac/dkl509

(5)   “WPRO | Multidrug-Resistant Acinetobacter Baumannii (MDRAB).” World Health Organization, World Health Organization, 7 July 2017, www.wpro.who.int/mediacentre/factsheets/fs_20101102/en/.

(6)  Dijkshoorn, Lenie, et al., “An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii”, Nature Reviews Microbiology, vol. 5, 2007, pp. 939-951

https://doi.org/10.1038/nrmicro1789

Meet the ESKAPE Pathogens – Elizabeth

Assigned ESKAPE Pathogen: Enterococcus faecium

Why is this ESKAPE Pathogen of interest:

Enterococcus faeciumis normally found in human and other mammal gastrointestinal tracts as part of the gut microbiota. However, when located elsewhere, it can cause infections. This has become a large problem in hospitals, causing about 3% of sepsis cases in NICUs­4. The emergence of VRE, or vancomycin resistant enterococci, in the early 2000s made this infection a larger issue, further compounding the growing problem of antibiotic resistance worldwide4.

General Cellular and Morphological Characteristics of the Organism (taxonomic classification, nutrition, cell shape, habitat):

This is a gram-positive aerobic bacterium that grows best on Columbia blood agar at thirty-seven degrees Celsius for twenty-four to forty-eight hours1. It typically grow as diplococci, meaning they grow in pairs of round colonies, or as short chains of round colonies and will exhibit hemolysis on some blood medias8.

As previously mentioned, they typically live in the intestines. The Enterococcus genus used to be classified as group D of the Streptococcus genus; however, genetic analysis proved too large a difference between Streptococci and Enterococci to classify them in the same genus8.

Clinical Importance and Prevalence:

Nosocomial infections are a growing problem given both antibiotic resistance and the aging of the Baby Boomer population causing an influx of ill, elderly patients in hospitals. This organism is usually resistant to penicillin (about 90% of cases in one Australian hospital) and resistance to vancomycin has hit about 50% worldwide3. Over twenty-eight percent of people with these infections in the same hospital died within 30 days3. Some research has shown that fluoroquinolone use against these infections should be reduced, as it may play a role in the development of linezolid resistance6.

Infection:

E. faecium, along with its close relative Enterococcus faecalis, cause endocarditis, urinary tract infections, prostatitis, intra-abdominal infection, and cellulitis5. These infections typically occur from lack of correct hygiene methods in hospitals, such as handwashing4.

Pathology:

Symptoms vary based on the location of the infection:

  • Endocarditis: fever, chills, fatigue
  • UTI: pain during urination, foul smelling and/or dark/cloudy urine, polyuria
  • Prostatitis: pain during urination, excessive night urination, urinary retention
  • Intra-abdominal infection: fever, chills, fatigue
  • Cellulitis: red skin, swelling, tenderness to the touch

Ineffective Antibiotics:

Strains isolated from humans have been shown to be resistant to vancomycin and linezolid (see above referenced sources). There is also evidence of strains resistant to chloramphenicol, tetracycline, ciprofloxacin, and erythromycin isolated from pigs in Malaysia5.

Effective Antibiotics:

The current recommendations include streptogramins, oxazolidinones, and Daptomycin5,6.

Corresponding Safe Relative:

The safe relative for E. faeciumis Enterococcus raffinosus. This organism has also been found to be vancomycin resistant and can cause endocarditis2. However, these infections are rare and the human immune system is normally able to withstand infection. Since the safe relative is in the same genus, it behaves similarly, but is less commonly the cause of infection in humans and less commonly resistant to antibiotics.

Sources:

  1. Culture Collections. Public Health England. Accessed October 5 2018.
  2. Dalal, Aman MD,Urban, Carl PhD, Rubin, David MD, Ahluwalia, Maneesha MD. Vancomycin-Resistant Enterococcus raffinosus Endocarditis: A Case Report and Review of Literature. Infectious Diseases in Clinical Practice. May 2008.
  3. Kelvin W. C. Leong, Louise A. Cooley, Tara L. Anderson, Sanjay S. Gautam, BelindaMcEwan, Anne Wells, Fiona Wilson, Lucy Hughson, & Ronan F. O’Toole. Emergence of Vancomycin-Resistant Enterococcus faeciumat an Australian Hospital: A Whole Genome Sequencing Analysis.Scientific Reportsvolume 8, Article number: 6274 (2018).
  4. Lakshmi Srinivasan, Jacquelyn R. Evans, in Avery’s Diseases of the Newborn (Tenth Edition), 2018
  5. Larry M. Bush, MD, Charles E. Schmidt, and Maria T. Perez, MD. Enterococcal Infections. Merck Manual. Accessed Oct 5 2018.
  6. Shiang ChietTanChun Wie ChongCindy Shuan Ju TehPeck Toung OoiKwai Lin Occurrence of virulent multidrug-resistant Enterococcus faecalisand Enterococcus faecium in the pigs, farmers and farm environments in Malaysia. PubMed. August 2018.
  7. Thomas E. Dobbs, Mukesh Patel, Ken B. Waites, Stephen A. Moser, Alan M. Stamm, Craig J. Hoesley. Nosocomial Spread of Enterococcus faeciumResistant to Vancomycin and Linezolid in a Tertiary Care Medical Center. Journal of Clinical Microbiology. June 2018.
  8. Enterococcus. Accessed Oct 5 2018.

Eskape Pathogens- Kelsey and Nicole D

Assigned ESKAPE Pathogen

#6 Enterobacter Species

 

Why is this ESKAPE Pathogen of interest (in brief)

The Enterobacter species is of interest due to the high rates of hospital-acquired infection that it causes. A study from the National Nosocomial Infections Surveillance System showed that the Enterobacter species is the third most common cause of pneumonia in ICUs. It is of increasing interest because the species has extremely high rates of antibiotic resistance. This is of concern due to the prevalence of infection and the mortality rates associated with the infections it causes. Crude mortality rates range from 15-87%. This is an extremely wide range, making the infections caused by the Enterobacter species highly unpredictable.

 

https://www.britannica.com/science/Enterobacter

https://emedicine.medscape.com/article/216845-overview

https://www.hopkinsguides.com/hopkins/view/Johns_Hopkins_ABX_Guide/540201/all/Enterobacter_species

 

General Cellular and Morphological Characteristics of the Organism (taxonomic classification, nutrition, cell shape, habitat)

The Enterobacter species is a rod-shaped bacteria that is gram negative. The size of each colony is 0.6-1.0 micrometers by 1.2-3.0 micrometers. The species is not capable of forming spores. It is motile due to flagella. The taxonomic classification is Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae. The species are facultative anaerobes; meaning the presence of oxygen is not required. They are capable of fermenting glucose and lactose. Through this fermentation, gases are produced. They are commonly found in intestinal tracts and in soil, water, and sewage. They are not harmful when found in the gut. Less commonly, they are found in urine, pus, and bodily fluids.

 

https://microbewiki.kenyon.edu/index.php/Enterobacter

https://www.britannica.com/science/Enterobacter

 

Clinical Importance and Prevalence

This Eskape pathogen is known to cause nosocomial infections. A nosocomial infection is caused due to a bacterium’s prevalence in certain locations. A nosocomial infection can also be called a hospital-acquired infection. The Enterobacter species is prevalent in ICUs and also commonly survives in equipment with water. This is because the species is able to live for a long time on surfaces. In wet environments, it is able to replicate rapidly. The most common source of spreading the bacteria is a lack of cleanliness, i.e. a lack of handwashing. This is a major source of infection in hospitals, with about 50% of infection in the ICU caused by the Enterobacter species. The species causes infections in the respiratory tract, urinary tract, intra abdominal cavity, intravascular devices, and can lead to sepsis.

 

https://www.healthline.com/health/hospital-acquired-nosocomial-infections

 

Infection (How does the infection occur and where is it localized?)

The Enterobacter species cause nosocomial infections in immunocompromised patients. The most common types of Enterobacter that cause human infection are E. cloacae, E. aerogenes, E. gergoviae, and E. agglomerans. Infections occur endogenously or exogenously. Endogenous sources of infection are the most common type of nosocomial infections caused by the Enterobacter species. The endogenous sources include the skin, respiratory tract, urinary tract, and gastrointestinal tract. The endogenous source tend to be the site of localization for the species.

 

https://emedicine.medscape.com/article/216845-overview

 

Pathology (What disease is caused? What are the symptoms?)

An infection caused by the Enterobacter species include a heart rate exceeding 90 bpm, a respiration rate greater than 20, and a fever above 100.4 °F or below 96.8°F. Other symptoms include hypotension, septic shock, cyanosis, and hypoxemia. Diseases and conditions that can be caused by this species are eye and skin infections, meningitis, bacterial blood infections, pneumonia, and urinary tract infections.

 

https://emedicine.medscape.com/article/216845-overview

http://www.antimicrobe.org/b97.asp

https://www.britannica.com/science/Enterobacter

 

Ineffective Antibiotics (Antibiotics to which the organism has acquired resistance)

Effective Antibiotics (Antibiotics known to inhibit the organism)

This species has developed resistance to a number of different antibiotics, especially in hospital settings. Infections and diseases caused by the Enterobacter species have been treated with an aminoglycoside, a fluoroquinolone, a cephalosporin, or imipenem. Over time, however, Enterobacter species has developed resistance to most beta lactam drugs and many other different drug types. Another source suggests that “third generation” cephalosporins, penicillins, and quinolones have become ineffective antibiotics as a result of increasing resistance. However, there are some antibiotics that are still effective. “Fourth generation” cephalosporins and carbapenems remain a viable option for treatment. Aminoglycosides are noted to be viable as well, but need to be combined with another type of antibiotic to allow for successful treatment. Lastly, quinolones are able to be used against many strains of the Enterobacter species, but similar to the trend of other drugs, emerging resistance is of concern. More specifically, Polymyxin B, Levofloxacin, Doripenem, Imipenem, Meropenem, Cefepime, Ciprofloxacin, Trimethoprim-sulfamethoxazole, Ertapenem, and Tigecycline are all examples of antibiotics that seem to remain effective and are largely avoiding resistance for now.

 

http://www.antimicrobe.org/b97.asp

https://www.britannica.com/science/Enterobacter

https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/Enterobacter.htm

 

Corresponding Safe Relative

The corresponding safe relatives are the Enterobacter aerogenes and the Erwinia carotovora.

 

(Source: Lab handout)

 

Images:

 

Enterobacter cloacae

https://jamanetwork.com/journals/jamadermatology/fullarticle/413232

 

https://www.researchgate.net/figure/A-localized-infection-of-Enterobacter-cloacae-developed-on-the-patients-left-forehead_fig4_258503948

 

Sources:

https://microbewiki.kenyon.edu/index.php/Enterobacter

http://www.antimicrobe.org/b97.asp

https://www.britannica.com/science/Enterobacter

https://emedicine.medscape.com/article/216845-overview

https://www.hopkinsguides.com/hopkins/view/Johns_Hopkins_ABX_Guide/540201/all/Enterobacter_species

https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/Enterobacter.htm

 

Davin-Regli, Anne, and Jean-Marie Pagès. “Enterobacter Aerogenes and Enterobacter Cloacae; Versatile Bacterial Pathogens Confronting Antibiotic Treatment.” Frontiers in Microbiology 6 (2015): 392. PMC

 

Davis, Elizabeth et al. “Antibiotic Discovery throughout the Small World Initiative: A Molecular Strategy to Identify Biosynthetic Gene Clusters Involved in Antagonistic Activity.” MicrobiologyOpen 6.3 (2017): e00435. PMC

 

Santajit, Sirijan, and Nitaya Indrawattana. “Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens.” BioMed Research International 2016 (2016): 2475067. PMC

 

Fun with Soil – Elizabeth

Where did you obtain your soil sample?

I got my soil from the path that walks up the right side of the football field behind Alumni Gym. The exact coordinates are Lat 42.816563, Long -73.926441. There was a layer of mulch on top that I moved out of the way and then I dug down about two inches. The soil was moist, but not wet, and dark. There were more ants in the soil than I expected once I got down into it.

Why did you choose this location?

I chose this location because I feel like it hasn’t been disturbed in a while. Most of the bushes in this area are just tended by facilities; not really replanted each year. The soil and the bacteria in it have probably been sitting long enough to have seen competition and (hopefully) some antibiotic production.

Do you expect a lot of isolates? Why or why not?

I expected the least-diluted plates to be covered, so I guess that’s one way to quantify “a lot of isolates.” However, given that its a soil sample and it was under a layer of mulch with at least some exposure to water, there’s probably a fair amount of anaerobic organisms there that we won’t grow at all, so I would expect very few of those isolates.

Have you initial observations supported this?

Yes – when I saw the plates, the ones with 1/100 dilutions were covered. They also looked like the serial dilutions were somewhat successful, as the numbers of colonies on each one decreased (based on rough estimate – I didn’t count them).

What media did you choose? What dilutions?

I chose to work with LB, 10% TSA, and R2A using dilutions of 1/100, 1/1000, and 1/10000. I used the LB as standard and then chose the 10% TSA as a “medium richness” media and the R2A as a bit of a less nutritious media. I thought this range of nutritional value would provide good comparison between plates. My dilution choices were based on our protocol from the test plates (the first lab); we weren’t seeing countable plates until the 1/10000 dilutions, so I made sure to get a 1/10000 plate for each media.

Will you need to redo any?

None of them initially seemed like they needed to be redone. They all had some growth on them and the lowest dilutions seemed countable.

How did your sample differ on the different media?

Honestly, I didn’t look at them too much. For personal reasons, my time in the lab has been limited and I haven’t been able to compare them in detail.

Fun with Soil – Tommy

Where did you obtain your soil sample?

My soil sample was collected under a tree on the North side of the Rugby field at Union. I dug down underneath a layer of mulch to reach the soil, which was held together by lots of roots. It was a dark, damp soil and contained wood chips from the relatively fresh mulch above.

 

Why did you choose this location?

Before inauguration, I saw groundskeepers putting fresh mulch around the trees and bushes around campus. I figured these frequently cared for soils might contain diverse microbe populations because of the recent layers of material deposited upon them. Part of the reason I was attracted to this soil was because its dark color reminded me of topsoil which I think of as being fertile with rich microbial life.

 

Do you expect a lot of isolates? Why or why not?

Hopefully some. It is encouraging that Penicillin-resembling molds grew on my PDA plates because if this antibiotic producing fungus lives in the soil, then possibly microbes that produce antibiotics will be selected for. The dark colour of the soil leaves me hoping for diverse microbial life some of which could be antibiotic producing. However, the fact that it was damp implies that some anaerobic microbes most likely were present, and I don’t expect these will grow on the plates much.  

 

Have you initial observations supported this?

Yes, lots of diverse colonies grew even though plates were mostly filled with one or two predominant types of colonies. PDA plates grew mold, R2A plates grew swarmers and mycoides, and LB plates grew big white colonies, but all plates had some unique colonies and even ones with rings of no growth around them indicating inhibition of other colonies. One small white colony with a distinctive texture on an R2A plate showed clear inhibition of a larger colony, but didn’t seem to inhibit another smaller colony nearby. I patched any colony that seemed to show inhibition and also any colony that looked unique, so hopefully some of these patched colonies turn out to be antibiotic producers. I calculated 170 cfu’s per gram from the 10^-3 dilution sample.

 

What media did you choose? How did you sample differ on the different media?

I chose PDA, R2A and LB because I wanted to use less nutritious media in addition to LB. In PDA and R2A, my dilutions were 10^0, 10^-1, and 10^-2, while in LB my dilutions were 10^-1, 10^-2, and 10^-3 because I didn’t want the LB plates to be too crowded nor the less nutritious plates to lack growth. Plates with higher dilutions showed less growth, but seemed more diverse – for example the 10^-3 dilution for the LB was the most diverse plate I had. The distinctions between dilutions blurred with time – by 6 days of growth all plates had a lot going on. PDA plates grew SERIOUS mold which resembled Penicillin producing molds. I even had to seal these plates up so I couldn’t patch much from these. This mold probably grew because of the mulch content in the soil. The R2A plates were overrun by small pinpoint colonies and swarmers, but this was less apparent in the most dilute sample. These also showed mycoides. LB plates were the most diverse and less dominated by only one or two types of colonies (although a large white type of bacteria enjoyed growth). 170 cfu/g in largest dilution. Most varied pigments showed up in LB – orange, brown, white, yellow. LB had the most colonies yielding inhibition.

What dilutions? (see above)

Will you need to redo any?

All plates had too many colonies to count, except LB at 10^-3 dilution which was also the most diverse plate. Thus, I plated two of each media at this dilution in hopes that I will be able to get CFU counts and more inhibiting colonies. At two days growth, R2A was more diverse than LB or PDA – interesting! Also, each plate (regardless media) showed around 40 colonies at 2 days growth.

Fun with Soil – Alexa

Where did you obtain your soil sample?
I obtained my soil sample from Peeble’s Island which is near Waterford, New York. I live in Waterford and I go to Peeble’s Island all the time when I can. I went to the beginning of one of the trails on the island, and decided to go a couple feet away from the trail and collect my soil sample there. I collected the dirt in between a tree and many smaller plants. I collected the sample about 2 inches below the surface since there was a lot of leaf litter on the top layer.

Why did you choose this location?
Since Peeble’s Island is home to many different kinds of trees, plants, and wildlife, I thought it would have very rich soil. I was also curious to see what kind of bacteria I could find in a place that I had spent so much time walking around!

Do you expect a lot of isolates? Why or why not?
I expected a lot of isolates because I expected the soil to be rich since it supported such a wide variety and large amount of plants. The soil also seemed like it would get enough oxygen to support aerobic bacteria which is the kind we are growing in the lab.

Have you initial observations supported this?
My initial observations have supported this. I was only able to determine a cfu for one plate which was on PDA and a dilution of 1:10000. All of the other plates had way too many colonies to even count, even after incubating for only 48 hours. The 1:100 dilutions were completely covered with bacteria on all the different medias I used.

What media did you choose? How did you sample differ on the different media?
I chose LB, AC, and PDA for my media. Everybody had to use LB, but I wanted to use another rich media to see how many different bacteria I could grow. I realized that since my soil was likely rich, I would need to use the weakest dilutions on LB and AC since they would support the most growth. I knew I needed to use a minimal media, so I chose PDA as my third media. I noticed there were more potential antibiotic producers on the rich media compared to the minimal media, but there was significantly more diversity on the minimal media. The most common colors on the rich media were off-white and there was occasionally a yellow colony. On the strongest dilution of PDA most of the colonies were pretty small and close to white. On the weaker dilutions there were more colors including pure white, off-white, yellow, orange, purple, dark brown, and green. There’s also fuzzy bacteria (or potentially mold) growing on the PDA plates which hasn’t grown on the rich media plates.

What dilutions?
I plated the 10-2, 10-3, and 10-4 dilutions for all of the media since I guessed the 10-1 dilution would have too much bacteria in it.

Will you need to redo any?
I am redoing the 10-4 dilution on PDA since it was my most interesting plate. I am also plating a 10-5 dilution on LB and AC since I couldn’t get a cfu on any of those plates.

Fun with Soil- Sofia Boswell

Where did you obtain your soil sample? Why did you choose this location?
I obtained my soil from a flower bed located outside of my house. I chose this location partially out of convince, but also because it seemed like it would be a fairly rich soil, seeing as it was supporting a substantial amount of plant growth. To obtain my sample, I dug down about 1.5-2 inches, to collect some of the darker and wetter soil, and avoid some of the mulch on top.

Do you expect a lot of isolates? Why or why not?

Seeing as this is fairly rich soil, I was expecting a good amount of isolates to grow. The soil I chose was much more clay like, and was fairly wet since it had just rained. Since we had learned that clay-like soils tends to support the growth of more anaerobic microbes.
Have you initial observations supported this?

So far, I have observed a lot of growth on all of my plates. Each one of my plates produced growth, and there is a lot of diversity of color, shape, and size among the colonies on each plate!
What media did you choose? How did you sample differ on the different media? What dilutions? 

Initially, I chose to use LB, AC, and R2A, my reasoning being that the richer and more nutrient dense medias would support the rich and presumed microbe dense soil. I chose to plate my 10^-2, 10^-3, and 10^-4 dilutions on each type of plate. After a few days of incubation, observations indicated that R2A grew the most diversity of microbes, however there was significant growth on the LB and AC plates as well. The 10^-2 plates of all three media were fairly overgrown, but still had some very interesting colonies. The 10^-3 plates were all very diverse and gave me the most useable colonies for my patch plates. The 10^-4 plates all had low amounts of growth, however this allowed my to obtain a definitive colony count, from which the cfu could be calculated.


Will you need to redo any? 

I chose to redo all three of my 10^-3 plates to see if I got anymore interesting growth. I also decided to make two more 10^-3 plates, using the PDA and 10% TSA medias, since these are both minimal medias and my R2A plate had yielded the best results. I wanted to see if these media types would result in similar growth.

2. Fun with Soil – Brianna Cummings

Where did you obtain your soil sample?Why did you choose this location?

I collected my soil sample between the pyramid and the bank of the Hans Groot Kill.  I dug about an inch down, and tried to avoid the grass and roots that were in the soil.  I chose this location for two reasons. The first being out of sheer convenience. The location was right on the way to class, so I was able to just wake up 15 min early and be set with collecting my sample. I also chose this location because I thought there would be some interesting bacteria found there due to the activities that happen on and near the pyramid.

Do you expect a lot of isolates? Why or why not? Have you initial observations supported this?

I expected to get a fair amount of isolates due to the location and soil type. The soil was clay-like and as mentioned in class this tends to support more anaerobic microbes. However, since my sample was collected from the top layer of soil, I figured there would still be a good amount of aerobic microbes. I also thought due to the highly trafficked area (and activities that go on there), there would be a lot of different microbes. Also the sample was collected near the creek, and after hearing how there’s lots of stuff in the water during class, I again thought there would be plenty of microbes in my sample. Initial results have proven that my sample has a good amount of microbes in it, yet the diversity is lacking (the majority of colonies are off-white and round with very similar morphologies).

What media did you choose? What dilutions? Will you need to redo any? How did your sample differ on the different media?

I chose LB, R2A, and PDA media. Since I thought there would be lots of microbes in my sample I chose to do two of the less rich media and only the LB rich media. For similar reasons, I used the higher dilutions of 10^-1 through 10^-3 (numbering system in book) for each of the medias. Interestingly, the R2A had very rapid growth of both colonies and mycoides, and needed to be diluted to 10^-4 to obtain accurate counts. As for the different media, it mostly affected the diversity of the colonies rather than the number of colonies. For instance, the R2A tended to have mostly white colonies that pretty much looked the same and mycoides, whereas the PDA had many different morphologies and colors. LB samples tended to be somewhere in the middle regarding morphologies- there were many similar ones, but there were also some unusual/unique looking ones.

Fun with Soil – Minh

Where did you obtain your soil sample?
I obtained my soil sample from the plaza that is located in between Olin, Wold, and S&E (right outside the Starbuck’s exit). The exact coordinates are 42.8175459, -73.9278173.
I dug about 2 to 3 inches below the surface next to the shrubs that are situated outside of Olin.

Why did you choose this location?
I was working late at night in my lab in Wold, so I did not want to go too far to obtain the sample. The location did not seem like a “rich” site because only some shrubs are present there but across those plants was a closed-off ground due to the presence of asbestos, so that convinced me to pick the soil from that location.

Do you expect a lot of isolates? Why or why not?
Not necessarily. As I mentioned above, the site in that area does not have a lot of diverse plants as there are mostly shrubs and grass. However, the soil might be actually quite fertile as it is the property of Union College and the school probably uses rich soil for the plants.

Have you initial observations supported this?
On the first day, 24 hours after plating, there was a lot of growth for every different media that I used at the 10^-1 dilution. Other dilutions had some growth, but there were not as many colonies as on the 10^-1 plate. In addition, after 78 hours, I could start to see a diversity of different colonies being grown as there were plenty of different colored and shaped colonies present on the plates. This suggests that the soil was much richer than I had initially assumed.

What media did you choose? What dilutions?
For the media, I chose to use LB, 10% TSA and PDA plates. As for dilutions, I spread 100 µl of each 10^-1, 10^-2, and 10^-3 dilution for every different plate.

How did you sample differ on the different media?
Every plate had something particular that made it distinct from other plates which made the plates to be very interesting. LB had some different colonies, but the colonies that struck out were evenly spread across the plate; these colonies were brown in color and had a surrounding halo of similar color around them. 10% TSA plates had some diversity, but the colonies were rather small with less diverse pigments; there was a presence of mycoides on these plates as well. PDA plates were the most diverse, in terms of shape and color; some colonies were round and filamentous, and others were colored from light yellow to dark brown or even pink. However, most importantly, every plate contained some colonies that showed inhibition as they inhibited the growth of the neighboring colonies.

Will you need to redo any?
I did not redo any of the dilutions however I did additionally plate a new dilution,10^-4, for LB and PDA plates so that it would easier for me to count the number of colonies that grew on the plates.

 

Fun With Soil – Troy

Where did you obtain your soil sample?

I obtained my soil sample from outside the new S&E building next to the construction site.  Professor Salvo suggested this location, because she felt there would be interesting organisms there since the soil had not been turned over in many years.

Why did you choose this location?

Having stagnant soil allows for the growth of many different bacteria without disturbing any of them.  I chose this soil sample, because Professor Salvo and I knew there would be interesting organisms present that had not been disturbed in many years.

Did you expect a lot of isolates? Why or why not?

I expected some isolates, but I didn’t expect too many – the soil was sandy in texture and I thought that the organisms present would have a difficult time finding nutrients.  I did, however, think that this would make them more likely to produce antibiotics to fight for these nutrients.

Have your initial observations supported this?

My initial observations were that the bacteria grew out of control on my less dilute plates, but they grew beautifully on the more dilute plates.  I have also noticed a substantial amount of what appears to be AB production, but I will only know if this is the case after further analysis!  My observations that the less rich media (R2A) grew fewer bacteria was supported by the decrease in growth at the same dilution levels as the LB and AC plates.

What media did you choose?  How did your sample differ on the different media?

I chose the R2A (less rich), LB (rich), and AC (rich) medias.  I did this to support both bacteria that thrive in low nutrient environments as well as those that thrive in nutrient-rich environments.  I noticed that the bacteria grew at about the same rate in the R2A as the AC and LB when it was at a dilution 10 times less than the rich counterpart.  For example, when R2A was at 10^-1 and LB and AC were 10^-2 it seemed that they were closely related in growth.

What dilutions?

I ran my R2A at 10^0, 10^-1, and 10^-2 while I ran the LB and AC at dilutions of 10^-1, 10^-2, and 10^-3 dilution factors.

Will you need to redo any?

The dilutions worked beautifully.  The best example I can give of how well the dilutions worked was from the LB plates.   The 10^-1 plate had too many colonies to count, but the 10^-2 plate had 90 and the 10^-3 plate had 9 colonies.  This showed that the dilutions were accurate, and the plates were growing as expected.

2. Fun with Soil -Carly B

I collected my soil sample from the lawn in front of the Nott on campus. I dug down about an inch and then filled my test tube with soil and tried to avoid getting grass in it. The GPS coordinates were 42.8173 degrees N, 73.9300 degrees W.

I chose this location because I was interested in seeing what kind of bacteria was growing there since many students sit on the lawn in front of the Nott when it is nice out. I also wanted to see what was there because I know that lawn is constantly treated to keep up its appearance.
I do expect a lot of isolates because the lawn is treated so much that it makes it rich and good for sustaining the growth of the lawn and also bacteria.

So far this has been reflected on my culture plates. There has been a lot of growth and even a lot of overgrowth on most of my plates including the plates with less concentrated dilutions. I couldn’t count any of my plates from my first round of plating because they were so overgrown.

I chose to use LB, R2A, and AC for my media. I chose LB and AC because I figured the complex media would reflect their natural, rich environment of the lawn so I was confident I would get growth even with higher dilutions. I used R2A because I wanted to plate a minimal media since I figured the soil was so rich with bacteria that there might be almost too much bacteria to work with.

I plated a zero dilution, a 10^-1, and a 10^-2 dilution on R2A because this was the minimal media so I figured I should test out the more concentrated dilutions. I plated 10^-1, 10^-2, and 10^-3 dilutions for LB and Ac because they were the complex media so I figured the bacteria would grow more easily on this media and a less concentrated dilution would be the best to use.

Since pretty much all of my plates were overgrown and I couldn’t count cfu’s for any of them, I had to replate some dilutions. I replated a 10^-3 dilution on AC and R2A because I thought that if I left them in the incubator for a shorter amount of time before looking at them that I’d be able to count them and pick more isolated colonies and this was correct. I also replated a 10^-4 dilution on LB, AC, and R2A because there was overgrowth on all of my 10^-3 plates from the first round of plating so I thought doing a dilution with a lower concentration that it would be even better work with, however these plates barely had any growth after 2 days.

All three of my media had a lot of growth. I chose the fewest colonies from the R2A plates because those plates had some good colonies but there were a lot of extremely small colonies that were very close together which meant I couldn’t pick individual colonies up very easily. The LB and AC also had a lot of good colonies but they were very overgrown so it was hard to pick individual colonies. The colonies were overall larger on AC and LB and also more diverse.

Fun with Soil – Nikki

Where did you obtain your soil sample?

I decided to collect my soil sample from Union’s Octopus Community Garden on campus. I took the sample an inch or two down, just below the surface, so that I did not get the hard topsoil/mulch and it was near bulbs that were growing (I assumed they were onion bulbs). GPS coordinates- Latitude: 42.8 degrees Longitude: -73.9 degrees.

Why did you choose this location?

I chose this location because I thought it would be interesting to look at something available right on our campus that many members of the community use or partake in on a regular basis. I also expected the soil to be “rich” due to its use in the garden to grow vegetables and various plants.

Do you expect a lot of isolates? Why or why not? 

Yes! I expected there to be a lot of isolates due to the rich nature of the soil being used for gardening purposes. I also thought that maybe because various plants and vegetables grow there that there may be more diversity depending on what has been grown in that location now and previously. In addition, there are a lot of people that work in the garden there that could contribute to what is in the dirt.

Have your initial observations supported this?

Yes, I have a lot of growth on my plates. It seems like I have a lot of growth and a decent variety because many of them look different in their coloring or morphologies. The only countable plates I had were on the 10^-4 dilution plates.

What media did you choose?

I chose 10% TSA, LB, and AC for my three. Prof. Salvo suggested that everyone in the class should use LB for one of the choices. Then I chose 10% TSA and AC because they were for cultivating a wide variety of microorganisms, according to their descriptions in the handout. I thought I would have a wide variety for my soil sample and so I chose these two.

What dilutions?

I plated 10^-2, 10^-3, and 10^-4 dilutions on my plates for each of the three media. (However, going by the way the book does it, these need to be changed to 10^-1, 10^-2, and 10^-3).

Will you need to redo any?

I had growth for all of my plates at the various dilutions, but I decided to re-plate a few. My plates with the AC medium still had too many colonies to count and lots of growth making it difficult to distinguish, so I went one dilution further, 10^-5 (which is actually 10^-4 according to the book) and plated two of these. I am still waiting for these to determine the CFU, but after two days there is no growth yet. I also did one more plate with LB and 10%TSA at a 10^-4 (actually 10^-3) dilution because these were countable, but there were a few large growths and I wanted to compare to get a more accurate CFU. I am still waiting a few more days to get a count because after 2 days there were 2 colonies on the 10% TSA plate and no growth on the LB plate.

How did your sample differ on the different media?

All three had a decent amount and variety on all the different media. AC had the least “pickable” colonies and I was only able to pick 14 (hopefully the new plates will provide more) because mycoides were present as well as really large growths. The LB and a few from the 10% TSA had a very dark brownish pigment sort of radiating from the circular shape and no other growths around it.

Fun with Soil – Kara

“Where did you obtain your soil sample? Why did you choose this location?”
I obtained soil from under a tree that was located near my dorm. I chose this location because the day I collected soil it was very wet outside, so the soil under the tree was drier than most other soil. I also chose this location because it is near the dorm compost bin. I figured maybe because of the proximity to the compost there would be some interesting growth.

“Do you expect a lot of isolates? Why or why not? Have your initial observations supported this?”
I didn’t really know what to expect when I collected the soil. It was close to the compost, which likely has a lot of microbes. However, the soil under the tree is rather protected. My initial observations showed less robust growth than I expected. My CFU was only 4.5-1.2 10^6 colonies / gram of soil.
When I let the plates grow for several days there was more growth, but there appear to be only a few different types of colonies.

“What media did you choose? What dilutions? Will you need to redo any? How did you sample differ on the different media?”
I decided to use 2 “rich” medias-LB and AC, and 1 “less rich” media-PDA. I chose the 2 rich medias because I was unsure how rich my soil sample was in microbes. I chose the PDA because it was mentioned in class lecture that several microbes that produce antibiotics like to grow on PDA. I originally plated 10^0,1, and 2 dilutions of media in PBS. I had to redo a few because I waited 5 days (I was away over the weekend) to look at my plates, and they were all too dense to collect a CFU and patch colonies. I then plated more of the 10^2 and 10^3 dilutions on all 3 types of media, so individual colonies were more identifiable. My PDA plates were also covered in a thick slime, which was potentially hazardous so I threw it away. The AC and LB plates showed similar growth–mostly small, white, gray, and yellow, round colonies.

(P.S.) if I accidentally replied to people my apologies! it took me a few tries to get this is the right spot

Fun with soil- Nicole B

Where did you obtain your soil sample?
I got my soil sample in the manure pile at the barn my aunt rides at, Graystone Stables. I tried to go to the older and farther back part of the pile, and I took my sample from a layer about two inches below the surface of the pile.

Why did you choose this location?
I figured that not many other people have searched through a manure pile, and going to an actively decomposing mix of hay, wood shavings, and horse poop would reveal more than taking a sample from already spread dirt. I went to the back to try to get at a point where the feces was already decomposed to avoid fresh ones. I noticed three distinct layers in the manure pile: a top layer of dry but still presumably nutrient rich stall products, a middle layer of moist, dark, and slightly warm stall products that I assume was actively decomposing, and a bottom layer of dry and crumbly hay and soil. I took my sample from the middle layer.

Do you expect a lot of isolates? Why or why not? Have your initial observations supported this?
Yes, I did. Not only did I know that the results of a manure pile can support a lot of growth, the soil was warm to the touch due to the decomposers (I washed my hands afterwards). My observations have definitely supported this because I have an uncountable number of colonies even on my 10^-3 dilution plate.

What media did you choose? What dilutions?
I selected LB and AC media because they were nutrient rich and I figured the bacteria in my soil sample would like that, and I chose 10% TSA because it would make a good representation of bacteria that didn’t thrive in rich environments. I also didn’t have many others to choose from. Due to a misunderstanding of dilution, I made 10^-1, 10^-2, and 10^-3. I also made a 10^0 dilution just to see what that would look like, and threw it away after realizing it wouldn’t give me much data.

Will you need to redo any?
Over the weekend, I noticed that my 10^-3 dilution plates had a ton of colonies, making it uncountable (or really difficult to count). On Tuesday, I made 2 spread plates at a 10^-4 dilution for each media I used. The plates are in the incubator right now and are growing.

How did your sample differ on the different media?
So far, I’ve noticed that there are more green and blue tinted bacteria colonies on the 10% TSA plates than on the other plates, but the colors could simply be more noticeable due to the whiter color of the media. The 10% TSA plate also had white/grey colonies with rhizoid arms on the border. There were a couple of colonies on the AC plate that appeared to tower over the rest of the bacteria, rising about 0.5 cm above the plate. The LB plate had more fuzzy colonies on it, and I noticed more brighter yellow colonies on the plate compared to AC.

Fun With Soil- Kelsey

Where did you obtain your soil sample?
I collected my soil from my backyard here at school. I live at 22 Union Ave. If you walk into my back yard there is a parking lot that leads to two other houses– 20r and Carriage House. I collected the soil next to the cement wall that separates our houses from a house nearby. I have attached a picture below! I dug about 2.5 inches down to get a better soil, rather than a sandy, beer can infested selection. 

Why did you choose this location?

I chose this location because the two houses behind my own tend to have a lot of outdoor parties. I thought that I would get a lot of interesting bacteria due to the wastes and circumstances this environment is exposed to.

Do you expect a lot of isolates? Why or why not?

YES! I think that I will get tons of cool stuff from this dirt. I think that because this location is exposed to both human and animal waste that I will get a lot of interesting isolates. I also think that because there was some rusty old objects mixed in with the dirt, I am even more apt to get some interesting isolates.


Have you initial observations supported this?

Yes, I have had a lot of growth on my plates! The smallest CFU that I have is 2.16×10^6. I think this is a great number. I have had a lot of diversity with my plates as well. Lots of different shapes and colors of the colonies.

What media did you choose?
I chose three types of media– LB, R2A, and AC. I found that LB had the best growths, AC had a lot of overgrowth, and R2A provided the most diverse growths (but had mycoides at the lowest dilution).


What dilutions? 

I plated 3 different dilutions on 3 medias– totaling 9 plates. In terms of the books explanation the three dilutions were 10^-1, 10^-2, and 10^-3.

Will you need to redo any? 

I did not necessarily need to redo any, but I decided to plate 1 plate of R2A with a 10^-3 dilution, 1 plate of AC with a 10^-2 dilution, and 1 plate of LB on a 10^-3 dilution. I decided to do this in order to achieve even more diversity with my plates!

How did you sample differ on the different media? 

The sample differed across media in a few ways. AC with the sample caused a major overgrowth of one colony. The R2A and sample had mycoides growth across all dilutions except for 10^-3. The LB had the most variety of growth. I think that R2A provided the most diversity, with LB a close second. I would choose them to plate more if my new plates are unsuccessful.

How to get your post to the right place!

So this took me a while and I had help (thanks Joey and Nicole).

1. To post, go to the menu bar at the top and click on “new” and go down to “post”.
2. Please label your post with the title of the category and your name.
3. Write your post – you can expand the menu bar (using the last icon on the right called “toolbar toggle” to provide formatting options and ways to insert images, links, etc. I hate the auto double spacing, but if you hit “shift-return” instead of just “return”, it will single space.
You might notice that I included the questions posed in my post – I just highlighted and copied these from the first post – no need to be in edit mode.
4. BE SURE to go to the menus in the right sidebar and scroll to categories. Click the proper category so the post will end up there! This also allows you to see all of yous posts when you click on your name under the “author” list on the main page.
5. I will try to initiate a post with the directions included to get things started for each assignment.

Fun with Soil – Jill

Where did you obtain your soil sample?
My soil sample came from an old cedar sawmill site in the Adirondacks.  The mill was probably active in the 1920s and 30s, so while nothing remains of the mill itself, the deep pile of sawdust has settled and lacks any growth.
Why did you choose this location?
I was curious – I wouldn’t think was was a “rich” site, but might have some very selective types of microbes.
Do you expect a lot of isolates? Why or why not?
Not really. I figured the site was toxic, since after almost 100 years no trees or other plans have colonized the site.
Have you initial observations supported this?
Well – I was surprised how much grew, but I did plate the original suspension (the “no dilution” sample) as well as the 10 -1 and 10-2. But my cfu is relatively low – around 106 cfu/g.
What media did you choose? How did you sample differ on the different media?
Well – I did try all the medias to see what kind of differences I might see. I actually got more growth on the less nutrient media. Both LB, AC and R2A were very similar – low growth ( LB was 4.5 x 105) with mostly white plain looking colonies, very little diversity.  PDA definitely had the most diversity with a number of dark pigmented colonies – from dark brown to tan to reddish brown. I picked more form this plate as a result.  The 10% TSA had diversity, but less with pigment, some looked liked they might be filamentous. I saw no mycoides on the plates.
What dilutions?
(see above)
Will you need to redo any? I did plate a 10-3 dilution of each, but I don’t expect much more. As of 24 hours, nothing has grown.