End of the Semester!!

This is the end of the semester! This means that this graduate project is ending, and this will be my last post. I hope that you have enjoyed reading them, and learned something along the way! I have enjoyed this class and was able to use what I learned in the first Microbiology class to use now!

Virology

This week in lecture, we briefly discussed quality in the lab. This mostly consisted of correct temperatures, control organisms, and other regulations that maitain proper conditions in the lab. The other topic we discussed was virology. This testing is not routinely done in the hospital laboratory. Viruses are obligate intracellular parasites, and do not multiply by binary fission like bacteria. they can only be seen with an electron microscope. Viruses contain a nucleic acid core, envelope, and glycoprotein spikes. In order to replicate, the virus can attach, penetrate, uncoat, replicate, assembly, and release. There are patterns of viral disease. These include acute infections, persistent infections, and slow infection. The methods used to detect viruses vary significantly depending on the lab. One of the major viruses we think of is HIV. The link below is a short video that gives a good overview of how the virus attaches and the integration. Enjoy!

HIV

Antibiotic Resistance and Quality

This week in class we discussed antibiotic resistance. This is a very real and scary problem in our society today. The bacterial resistance can be several mechanisms including inate, acquired, or genetic recombination. Beta -lactams have an interesting mechanism of resistnace where the target or binding site is altered. S. aureus resistance to multiple drugs is a major problem we see frequently. The following article discusses this issue in meat and poultry in the United States. S. aureus contaminated 47% of the samples, and  multidrug resistance was common among isolates (52%). S. aureus genotypes and resistance profiles differed significantly among sample types, suggesting food animal–specific contamination. This is a problem that many people are begining to recognize and try to take action. The Washington Post published an article saying the American Medical Association and the Infectious Diseases Society of America have called on the FDA to ban feeding antibiotics to healthy animals. Testing for the extended spectrum beta-lactamases include both screenng and confirmatory tests. The most important things to remember is the physician will want to know what the bacteria is reststant and susceptile to, and treat the patiet quickly and effectively! Community acquired MRSA is more prevalent, and with football season approaching, athletes should remember to protect themselves!

http://cid.oxfordjournals.org/content/52/10/1227.full.pdf+html
http://www.washingtonpost.com/politics/groups-sue-fda-to-stop-addition-of-antibiotics-in-livestock-feed/2011/05/25/AGxfbVBH_story.html

Lab susceptability

This week in lab we were able to perform out own susceptibility tests. These tests included an agar disk diffusion on Staph epidermidis, an MIC combo plate, E test, CHROMagar, and Nitrocefin disk for beta-lactamase. For the agar diffusion, the plates were streaked and disks were placed and incubated overnight. The next day the zone was measured around each disk. Using given values, susceptibility was determined.

Then, a Microscan gram negative MIC panel was done. The pan is innoculated and incubated to be read the following day. Each well is read for growth or no growth, and each MIC is circled on the report sheet.

The CHROMAgar was streaked with the specimen swab and icubated. The plates were then read and interpreted. If mauve colonies were present, it is positive.

Lastly, the Nitrocefin disk test was performed. The red color seen below indicates a positive result and means the organism is resistant to penacillin and cephalosporin.

Susceptibility Testing Lecture

This week in class we discussed antimicrobial action and antimicrobial susceptibility tests. This is very important for both patients and physicians in order to effectively treat infections. The mechanism of activity varies among agents and some commons ones include Inhibition of cell wall synthesis, disruption of cell membrane, inhibition of nucleic acid synthesis (RNA or DNA), interference with essential , metabolites (ex. folic acid pathway), and Inhibition of protein synthesis (binds to 30S or 50S ribosomal subunit). Beta Lactams act on the cell wall, while glycopeptides inhibit cell call synthesis. Vancomycin is a popular example. Interfering with protein synthesis is also a mechanism, and this is done by tetracyclines, aminoglycosides, and macrolides. In order to detect susceptibility, several methods can be used. Some of these include broth dilutions, microdolutions, and agar dilutions. Additionally, there are automated systems that are available. In order to determine susceptibility, we can use an E test, MBC, MIC, and the Schlicter Test.

The following link is to an article containing a case history of a 79-year-old man with end-stage renal disease due to hypertension. The man had positive blood cultures for MRSA that was resistant to vancomycin. Read the article to learn more!

http://www.nejm.org/doi/full/10.1056/NEJM199902183400704

Skin, wounds, and Micobacterium lecture

Skin infections can be caused by many agents. Some of these are very serious including MRSA. These infections can be hospital or community acquired. Wounds and abscesses are also problems for many people that may be due to bites, burns, or injury. Some organisms involved may be S. aureus, S. pyogenes, Enterococcus, E. coli, Proteus, P. aeruginosa, and anaerobes. Eye infections are also common among some people. Some symptoms include swelling, exudates, and burning. The most common isolates are S. epidermidis, Lactobacillus, Corynebacterium, and P. acnes. Normal flora can vary in individuals, so each isolate can be identified. Ear infections can be seen in several forms including swimmer’s ear (P. aeruginosa), acute localized otitis externa (S. aerus), and chronic otitis externa (P. aeruginosa, anaerobes). Usually these are plated onto SBA, Choc, and MAC.

Mycobateria

http://www.msnbc.msn.com/id/42788111/ns/health-infectious_diseases/t/eating-armadillos-blamed-leprosy-south/

is a very serious disease that should be taken very seriously and when working with suspected cases, extreme caution should be taken. The main mode of transmission is inhalation, and as a result outbreaks are seen among people living in close quarters. There are 5 stages of infection, and most cases do not progress to the advanced stage. NTMs are non-tuberculosis mycobacterium, and these can be grouped into slow growers, and rapid growers. One very interesting noncultivable NTM is M. leprae, which causes leprosy. This has been seen recently in parts of the South acquired by people eating armadillos. Follow thw link below to the story.

Lecture GI and Genital

This week in lecture we discussed GI and genital tract infections. There are several diseases associated with the GI tract including gastroenteritis, enteritis, infectious diarrhea, and antibiotic associated diarrhea. An interesting fact that I learned from this lecture is that E. coli can be pathogenic or normal flora. The different pathogenic forms are ETEC, EPEC, EIEC, EAEC, and EHEC. Most isolates are the 0157: H7 strain. Salmonella, Shigella, and Camplobacter are all pathogens that are isolated in the lab. KIA, LIA, and Urea are used to ID and differentiate Shigella and Salmonella. When these are identifies, serotyping is done to identify the species. There are other pathogens and anaerobes that are identifies, but they follow procedures previously covered.

Genital Tract infections are commonly caused by sexually transmitted diseases. N. gonorrhoeae, C. trachomatis, HPV, HIV, Trichomonas, and C. albicans are among the most common. There are many diseases associated with the agents, and according ot symptoms a physician will order testing accordingly. A cervical swab should be put in transport media, charcoal cotton or rayon. Specimens for Chlamydia should be transported in 2 SP medium, on ice. Gram stains, wet preps, and direct antigen tests can all be done depending on what organism is suspected. The cell culture is still considered the gold standard. Selective media for a GC culture is MTM, Martin Lewis, and NYC.

Cervical and Fecal Cultures

This week in lab we performed GI and genital tract cultures. The cervical culture was plated onto SBA, Choc, and MTM. There were 2 colonies on SBA and choc, but only one on MTM. Because isolate 1 grew on MTM as pinpoint, small, translucent colonies Neisseria was suspected. The gram stain showed gram negative diplococci, oxidase positive, and a bacticard was pro positive confirming Neisseria gonorrhoeae. The other isolate was catalase positive and gram stained diptheroids and were identified as Corynebacterium.

On the feces culture, there was no growth on CVA while XLD, MAC, and SBA had 2 isolates. On XLD, the colonies were yellow (lactose positive), SLF on MAC, a large, white, mucoid beta hemolytic colonies on SBA. This was presumed to be E. coli ad normal flora. Isolate 2 had clear colonies on XLD and MAC, and large gray beat hemolytic mucoid colonies on SBA. Because there was no black seen in the center of the colonies, KIA was alk/a, LIA was purple/ yellow, and urea negative, Shigella was suspected. The serotyping identified it as Shigella flexneri. The case given with this specimen was a 4 year old who attended daycare who presented with vomiting, diarrhea, fever, lethargy, and irritability. His stool had bloody streaks and had numerous WBCs. Shigella is commonly acquired via the fecal oral route and is common in daycare settings.

The following link is a case history on Shigella flexneri. http://www.jpma.org.pk/PdfDownload/995.pdf

Throat and Sputum Lab

This week in lab we looked at throat cultures, a quick throat screen, sputum culture and sputum gram stains. We were given three throat swabs along with media that had already been plated out. There were two isolates on the SBA. The first was beta hemolytic translucent, white and glistened. The second was small, white, opaque and convex. The presumptive ID on number one was a beta hemolytic Streptococcus because the catalase test was negative. A PYR test was also done and was negative. From this I determined that a PathoDx should be done and was "C" positive indicating Streptococcus dysgalactiae subsp. Equisimilis. Notice from the picture below this looks like group A strep, and the PYR and PathoDx are what differentiate them. Isolate 2 was determined to be normal flora and was a coagulase negative Staph. The throat screens were very simple to do, and one of mine was positive for group A Streptococcal antigen, indicating the patient should be treated. The other was negative, so a culture should be done.

Streptococcus dysgalactiae subsp. Equisimilis (group G strep) beta hemolysis

The sputum cultures also had 2 isolates. On SBA, number 1 was mucoid, gray, and opaque while number 2 was small white and opaque. Number 1 grew on SBA, MAC, and Chocolate meaning it was a negative rod and was a SLF. An oxidase test was done and was negative so an API 20E gave results of Klebsiella pneumonia. The other isolate was coagulase negative Staphlococcus. This finding of K. pneumoniae was consistant with the case given that the patient had a cough producing thick bloody phlegm ("currant jelly"). He also had lower lobe infiltrate and a pulmonary abscess.

Lower Respiratory Infections

This week in class we finished discussing lower respiratory infections (LRI). The two most common infections seen and heard are bronchitis and pneumonia. Bronchitis can be either acute or chronic, each having a large impact on the individual invaded by the bacteria or virus. The most common bacteria see in bronchitis are S. pneomoniae, H. influenza, and M. catarrhalis. Pneumonia can be categorized into community-acquired and nosocomial (hospital) acquired. Many bacteria can be responsible for nosocomial  infections including Klebsiella, Enterobacteriacae, P. aeruginosa, S. aureus, S. pneumonia, Anaerbes, and Legionella. Another common infection is Mycoplasma. This is usually caused from M. pneumonia, which is often called walking pneumonia. Serology is most often used to confirm the infection and can be done by ELISA/IFA. The last bacterial agent I want to review is Chlamydophila. Chlamydophila psittaci is often referred to as atypical pneumonia, is transmitted to man via birds, and is classified as a category B biological warfare agent. Serology is the most commonly used method used to identify this agent. Chlamydophila pneumonia is asymptomatic and is major cause of community acquired pneumonia. This is also associated with coronary artery disease. I have had mycoplasma pneumonia and am interested in it, and as a result I have researched and attached a link to a journal article that looks at pneumonia in children with asthma.

http://ajrccm.atsjournals.org/cgi/reprint/172/9/1078

Lab- Urines and CSF

This week in lab we looked at urines and spinal fluids. The case I was given for CSF was a 13-month old child who was admitted a grand mal seizure, temperature, increased pulse and respiratory rate. He was lethargic, irritable, and a stiff neck. A lumbar puncture was performed and the WBC count of 4,650/ µL with 95% neutrophils, glucose of 48 mg/dL and protein of 107 mg/dL. I first gram stained the primary smear and quantitated the bacteria seen. There were more than 30 bacteria seen in each field observed (average), and they were described as some short rods, some pleomorphic rods, with some coccobacilli. The SBA media had pinpoint, grayish, translucent colonies satelliting with a quantitation of 4+. The chocolate agar also was quantitated at 4+ with smooth translucent gray colonies. We also gram stained a slide from the inoculated thioglycollate broth. This showed a possible contaminate because along with the long pleomorphic rods expected, there were gram positive cocci seen. With these findings, an API NH was done with a presumptive ID of Haemophilus. The API strip confirmed the child had an infection due to Haemophilus influenzae.

Gram stain negative pleomorphic rods with coccobacilli



Pseudomonas aeruginosa on SBA

Coagulase negative Staphlococcus

The urine specimen I had was plated on SBA, MAC, and Chromagar. On SBA, there were small white opaque colonies >100,000 CFU/mL, no growth on MAC, and >100,000 CFU/mL of white colonies on Chromagar. The presumptive ID was Staphlococcus. A catalase test was positive, Staphaurex negative, and Novobiocin sensitive. With these results, the final identification was Staphlococcus, coagulase negative. Then we plated/ streaked our urine specimen on to SBA, MAC, and Chromagar. I read the plates on Thursday and the SBA plate was very typical of Pseudomonas (grayish green, beta hemolysis, taco odor). The colonies were clear on MAC, and beige on Chromagar. The oxidase test was positive and spot indole negative and ID was Pseudomonas aeruginosa.

Week 2 UTI/ RTI

In class this week we discussed urinary tract infections along with upper and lower respiratory tract infections. Instead of traditional lecture for UTI, we were given parts of cases in groups and tried to determine what was causing infections in the hypothetical cases. There are five types of bacteriuria. One group was assigned to describe the types of collection of urine specimens, while another described testing done to test and confirm an infection.

On Thursday we discussed upper and lower respiratory infections. One thing that is important to remember about the URT is there is normal flora present. Group A strep (GAS) or S. pyogenes is the leading cause of pharyngitis. I have experienced a rash with a GAS infection and because some other people said so as well I was interested to learn more. I was unable to find a lot of information but I have included a link below to the emedicine website that describes an impetigo rash sometimes seen. One new thing I learned was a CAMP test was described for the detection of A. haemolyticum. I also remember that it is not necessary to do a gram stain on a throat swab or culture throat swabs for anaerobes. Some other pathogens seen are N. gonorrhoeae M. meningitidis B. pertussis C. diptheria, H. influenzae, S. aureus, and C. albicans. I will discuss more about the lower respiratory tract infections next week after we finish discussing it!

Streptococcus Group A Infections

Lab Week 2

In lab, we were able to use the material covered in lecture and actually have a case and 24-hour blood culture to plate onto specific agars and perform rapid and incubated tests. The first thing I did was a gram stain that showed gram positive cocci in pairs (clusters). I then plated the blood onto SBA with a P disk and incubated it in CO2 at 35C. From the P disk and a bile solubility test I determined it was sensitive and therefore Streptococcus pneumoniae. From the information I obtained in lab, I was able to consult several references and write a short statement about the clinical significance of the bacteria and how the patient in the case was likely infected. The picture below is a sheep blood agar with a P disk and positive sensitivity. This is also a review of alpha hemolysis!!

The most challenging part of the class and lab so far is using information I learned last semester. I feel that once I use it more often and become more comfortable with it I will enjoy the class but especially the lab more! Feel free to comment what your organism was and the reactions seen, and we can use it for review.

Bloodstream Infections

This week we discussed bloodstream infections and proper techniques used to isolate organisms from a blood culture bottle. The link below is an article published in the New York Times Health Guide from 2009. It is interesting that the newspaper would publish this, and suggests that there is an interest and need for public awareness. Also, notice the terminology and definitions used in the article, it will probably make you feel like a pro!

We also started discussing CSF and sterile fluids. Both blood and CSF are sterile fluids and therefore no bacteria should be found in them. It is important to remember not to refrigerate the specimen and to always use proper techniques to prevent contamination and the need for a recollect. It is imperative that the collection and storage of specimens be correct, as many of the patients these specimens are coming from are very ill. Meningitis is a situation where CSF would be collected and examined for bacteria or viruses. The causative agents associated with bacterial meningitis were discussed in more detail than viruses.


(The fire drill today was a first experience for me in a university setting!!)

http://health.nytimes.com/health/guides/test/blood-culture/overview.html

WELCOME

Welcome to Jennifer’s Infectious Disease blog created to comment on information covered in the course. I am a CLS student at UAB taking an infectious disease class. The content of the posts will be questions, comments, pictures, articles and anything else relevant to the class. This is designed to both reinforce topics covered in class and introduce new or further information that might be helpful in understanding. Please comment what you find interesting and helpful so we can make this semester a success. Please also feel free to ask questions that we could find answers to together! I will try to post things that I hope you find interesting and helpful!