gram stains

Sink used for Acid Fast Bacilli Kinyoun stain. This is at the lab I’m currently doing my rotations at and I thought it was pretty.
Mycobacterium tuberculosis, the causative agent for Tuberculosis or TB, has a cell wall that’s high in lipid content. So, it doesn’t stain with regular gram stain; thus, they used acid fast staining techniques with carbolfuchsin.


Streptococcus pyogenes

Streptococcus pyogenes (also known as the flesh eating bacteria) is a gram-positive bacterium that usually grows in pairs or chains. It has been classified as a beta-hemolytic streptococcus because when cultured on a blood agar plate all the red blood cells are ruptured by the bacteria. Furthermore, it has been classified using Lancefield serotyping as group A, because it displays antigen A on its cell wall. Therefore, this bacterium is commonly called the beta-hemolytic group A streptococcus, or GAS.

This bacterium is responsible for a wide array of infections. It can cause streptococcal sore throat which is characterized by fever, enlarged tonsils, tonsillar exudate, sensitive cervical lymph nodes and malaise. If untreated, strep throat can last 7-10 days. Scarlet fever (pink-red rash and fever) as well as impetigo (infection of the superficial layers of skin) and pneumonia are also caused by this bacterium. Septicaemia, otitis media, mastitis, sepsis, cellulitis, erysipelas, myositis, osteomyelitis, septic arthritis, meningitis, endocarditis, pericarditis, and neonatal infections are all less common infections due to S. pyogenes

There are at least 517,000 deaths globally each year due to severe S. pyogenes infections and rheumatic fever disease alone causes 233,000 deaths. 

Key characteristics: Gram(+), beta-hemolytic, bacitracin(+), PYR(+), facultatively anaerobic.

anonymous asked:

Victor and Leo!

Victor Nikiforov: List 5 things you love (or) 5 things about your life.

five things i love, coming right up!!

  1.  summertime!!!!! i know i’m in the minority on this winter-loving heathen site but i fucking love summer and hot weather and sunshine and bright colors!!!!!!
  2. music!! i love my violin and piano lots, and even though they’re newer in my life i also love my viola and ukulele. and i think if i went back to it i’d love my clarinet more too!
  3. science!!!! i love biology and i’ve loved labwork ever since i first got introduced to it. one of my fondest memories of high school is hanging out in the lab with 3 of my classmates and our teacher, doing gram stains while singing to cheesy christmas music!
  4. tea. nothing else needs to be said here
  5. dancing!!!!!! i love love LOVE ballroom and it makes me so happy!! i’ve met a lot of great people through the club and learning to dance has made me just like, happier with myself in general?? :D

Leo de la Iglesia: Do you have a favorite genre of music?


im very bad at separating things by genre tbh, i guess if i had to pick i’d go with pop or indie pop maybe?? but also my taste is very broad i listen to cheesy 80s bollywood music and mozart too.

a good metric for whether i will like a song (though this is by no means an end-all-be-all) is “can i dance to it?” tbh, hahah

Urinary Tract Infections

Definition of UTI

  • Pathologic bacteria in urine
    • Asymptomatic patients: growth of > 10^5 (100,000) CFU/mL
    • Symptomatic patients: 10^2 (100) CFU/mL

Classification of UTI

  • Lower tract infections: urethritis, cystitis
  • Upper tract infections: pyelonephritis, prostatitis
  • Community-acquired
  • Nosocomial: catheter-related


  • E. coli - most common
  • Gram negative rods
  • Adenovirus - children


  • Colonization of external genetalia
  • Bacteria can ascend into the urinary tract 
  • Upper tract infection most common complication of lower tract infection
  • Hematogenous spread - S. aureus

Who gets UTIs?

  • Females > males
  • Increased incidence with sexual activity
  • Childhood: M > F

Female Patients

  • Vaginal introitus and distal urethra normally colonized by gram positive organisms
  • Female urethra more prone to gram negative infection 
    • Close to anus
    • Short length 
  • Risk factors
    • Hygiene issues
    • Sexual activity
      • Void after intercourse decreases this risk

Male Patients

  • Rare
  • > 50 years of age, BPH is main cause

Other Risk Factors

  • Pregnancy
  • Unsterile or prolonged catheterization
  • Obstruction
  • Vesicourethral reflux


  • Most common manifestation of UTI
  • Infection/inflammation of bladder
  • Most commonly E. coli, can be adenovirus
  • Clinical presentation
    • Irritative voiding 
    • Supraspubic discomfort
    • Other urinary complaints?
  • PE
    • Unremarkable
    • No CVA tenderness
  • Lab
    • Urinalysis
      • (+) LES
      • (+) Nitrites
    • Urine gram-staining
      • E. coli
      • Contamination possible
  • Acute urethral syndrome
    • “Painful voiding syndrome”
    • Dysuria with sterile culture
    • Irritants, trauma, etc.
  • Management
    • Antimicrobials
      • Short-term (< 7 days) for uncomplicated cases
      • Longer therapy (7-10 days) for DM, recurrent UTI, over 65, Men
    • Symptomatic treatment
  • Follow-up
    • Repeat urine C&S 3-5 days after antibiotics finished


  • Infection/inflammation of renal parenchyma and pelvis
  • Most commonly E. coli or Proteus sp. 
  • Presentation
    • Flank pain
    • Fever
    • Chills
    • Toxic appearance
    • CVA tenderness
  • Lab
    • Urinalysis
      • (+) LES
      • (+) Nitrites
      • WBC casts
    • Urine gram stain
      • E. coli
      • Contamination possible
    • CBC
      • Leukocytosis with left shift
  • Imaging
    • Only done in complicated cases
  • Complications
    • Sepsis/shock
    • Scarring/fibrosis
      • Chronic pyelonephritis
  • Management
    • Usually treated as outpatient
    • Empiric therapy
      • Broad-spectrum antibiotics
        • IV 
        • PO quinolone
        • No nitrofurantoin
        • Watch resistance for Augmentin and Bactrim 
      • 14+ days
        • Inpatient: 24 hours after fever resolves
        • Outpatient: 14 days
  • Follow-up
    • Repeat urine C&S 1-2 weeks after treatment completed
    • Treatment failure
      • Imaging or referral

UTIs in Pregnancy

  • Asymptomatic bacteriuria very common - treat due to risk of complications to fetus
  • Cystitis
    • No fluoroquinolones
    • Recheck urine C&S
  • Pyelonephritis
    • Hospitalization
    • Empiric IV therapy, then PO
    • No fluoroquinolones
    • Recheck urine C&S

Nosocomial UTIs

  • Foley catheters 
  • Care for UTIs not reimbursed by Medicare/Medicaid 

Recurrent Infections: more than 2-3 per year

Vesicoureteral reflux (VUR)

  • Reflux of urine from bladder into ureters/renal pelvis
  • Common cause of UTI in children
  • Renal scarring due to volume and duration of reflux
  • Presentation
    • Weight loss
    • Nocturnal enuresis
    • Failure to thrive
  • Labs
    • Urinalysis
      • (+) LES
      • (+) Nitrites
    • Urine gram stain
      • E. coli
    • Cast formation
  • Imaging
    • Voiding cystourethrogram (VCUG)
    • Management of VUR
      • Mild
        • Spontaneous resolution usually
        • Antibiotics until puberty
      • Severe
        • Surgical intervention
        • Antibiotics into condition corrected

Yersinia pestis

Yersinia pestis is the causative agent of the systemic invasive infectious disease often referred to as the plague. The Y. pestis is an extremely virulent pathogen that is likely to cause severe illness and death upon infection unless antibiotics are administered. In the past, Y. pestis has caused devastating epidemics during three periods of modern history; the Justinian Plague spread from the Middle East to the Mediterranean during the 6th-8th centuries AD and killed approximately 25% of the population below the Alps region. Perhaps the most famous incidence of any disease was the devastating Black Plague of 8th-14th century Europe that eradicated 25 million people (nearly 25% of the population) and marked the end of the Dark Ages. The third endemic began in 1855 in China and was responsible for millions of deaths.

Plague is a very serious illness, but is treatable with commonly available antibiotics. The earlier a patient seeks medical care and receives treatment that is appropriate for plague, the better their chances are of a full recovery.

Yersinia pestis is a Gram-negative bacillus member of the Enterobacteriaceae family, and is an obligate intracellular pathogen that must be contained within the blood to survive. It is also a fermentative, motile organism that produces a thick anti-phagocytic slime layer in its path. 

Key characteristics: Gram(-), catalase(+), oxidase(-), indole(-), urease(-)

Bacterial Taxonomy 1 - Classification Based on Morphology and the Gram Stain. 

Taxonomy, is literally the science of classification. Look at the picture above, and imagine that all those little divisions, like “firmicutes” are different phyla under the kingdom of bacteria. Then those phyla are further subdivided into different classes, then orders, then families, then genera, and then finally species! Take a look at how this works for one particular bacteria, called streptococcus mutans. 

Wow, there’s a lot to classify, probably why it’s taxonomy: it’s such a taxing job.

Ahem, right, so. As you’ve probably noticed, Streptococcus mutans is named using its Genera and its Species name. Similarly, all organisms have a scientific name comprising of two parts: The genus, followed by the species. It is very important to classify organisms in this way because: 

  1. It establishes criteria for identifying organisms. 
  2. Allows arrangement of related organisms into groups. 
  3. Provides important information on how organisms evolved.  

Bacteria are classified, usually, according to their morphological, metabolic and biochemical differences, although genetic and immunologic factors are also now being considered. 

One of the earliest, and most fundamental methods of classifying bacteria depended on the use of the Gram Stain. 

Gram Stain

Unlike large organisms like humans, parrots and dra-, erm, Komodo Dragons, which are easy to spot and have a distinct appearance to the eye, bacteria are colourless and invisible to light microscopy. Thus, gram staining had to be developed to give bacteria a colour, and visualize them. Since bacteria would either respond to the stain, or not, all bacteria were subsequently classified into gram-positive and gram-negative bacteria. 

There are 4 steps to the Gram Stain Procedure. 

  1. Pour crystal violet stain (a blue dye) and wait for 60 seconds. 
  2. Wash off with water and flood with iodine solution. Wait for 60 seconds. 
  3. Wash off with water and then “decolourize” with 95% alcohol solution. 
  4. Counter-stain with safranin (a red dye). Wait 30 seconds and then wash off with water. 

Basically, when viewed under the microscope, cells that absorb the crystal violet dye and hold on to it become blue: These are gram-positive. Alternatively, if the crystal violet is washed off by the 95% alcohol, the cells absorb the safranin and appear red. These are gram-negative. 

Gram Positive = Blue 

Imagine yourself sitting by the beach, opposite crystal blue waters, or kayaking across deep waters, or even river tubing across the bluest of rivers.. won’t you say yes to that? So, Blue = Positive. Note that Gram-Positive bacteria may also appear purple if the red safranin is not effectively washed off. This is because blue + red is purple. 

Gram Negative = Red

Now you’re sitting in sweltering red heat, sweat pouring down your body, the sun red in the sky. You don’t want that, do you? Or for comic book fans, you can picture Superman’s face when he sees a Red Sun in the sky. NOPE, thinks Superman. So Red = Negative. 

This difference occurs due to a difference in morphology of the bacteria. 

Gram Positive vs Gram Negative Bacteria 

Unlike eukaryotic animal cells which contain only one cell membrane composed of phospholipid separating the nucleus from the ECF, both gram-positive and gram negative bacteria contain more than 1 layer: the layer outside the bacterial cytoplasmic membrane is the peptidoglycan layer. 

Keep reading


Pseudomonas aeruginosa

Pseudomonas aeruginosa is a nonfermentative gram-negative bacillus. This bacterium is ubiquitous in soil and water, and on surfaces in contact with soil or water. Pseudomonas aeruginosa is an opportunistic pathogen, meaning that it exploits some break in the host defenses to initiate an infection. It causes urinary tract infections, respiratory system infections, dermatitis, soft tissue infections, bacteremia, bone and joint infections, gastrointestinal infections and a variety of systemic infections, particularly in patients with severe burns and in cancer and AIDS patients who are immunosuppressed.

Key characteristics: Gram(-), catalase(+), oxidase(+), motility(+), aerobic, produces pigments (green and blue), grows at 42°C.


Staphylococcus aureus

S. aureus is a type of bacteria. It stains Gram positive non-motile cocci. It is found in grape-like clusters. This is why it is called Staphylococcus.

Staphylococcus is one of the five most common causes of infections after injury or surgery. It affects around 500,000 patients in American hospitals annually. S. aureus may occur commonly in the environment. S. aureus is transmitted through air droplets or aerosol. Another common method of transmission is through direct contact with objects that are contaminated by the bacteria or by bites from infected persons or animals. Approximately 30% of healthy humans carry S. aureus in their nose, back of the throat and on their skin.

S. aureus has long been recognized as one of the most important bacteria that cause disease in humans. It is the leading cause of skin and soft tissue infections such as abscesses (boils), furuncles, and cellulitis. Although most staph infections are not serious, S. aureus can cause serious infections such as bloodstream infections, pneumonia, or bone and joint infections.

When S. aureus becomes resistant to many of the antibiotics used to treat ordinary infections we call it Methicillin-resistant Staphylococcus aureus (MRSA).

Key characteristics: catalase(+), oxidase(-), coagulase(+), mannitol(+), beta-hemolysis.


Escherichia coli

Probably the most famous bacterium in the world, E. coli is a Gram-negative, facultatively anaerobic, rod-shaped bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms.

Most E. coli are harmless and actually are an important part of a healthy human intestinal tract. However, some E. coli are pathogenic, meaning they can cause illness, either diarrhea or illness outside of the intestinal tract. The types of E. coli that can cause diarrhea can be transmitted through contaminated water or food, or through contact with animals or persons.

E. coli consists of a diverse group of bacteria. Pathogenic E. coli strains are categorized into pathotypes. Six pathotypes are associated with diarrhea and collectively are referred to as diarrheagenic E. coli.

  • Shiga toxin-producing E. coli (STEC)—STEC may also be referred to as Verocytotoxin-producing E. coli (VTEC) or enterohemorrhagic E. coli (EHEC). This pathotype is the one most commonly heard about in the news in association with foodborne outbreaks.
  • Enterotoxigenic E. coli (ETEC)
  • Enteropathogenic E. coli (EPEC)
  • Enteroaggregative E. coli (EAEC)
  • Enteroinvasive E. coli (EIEC)
  • Diffusely adherent E. coli (DAEC)
Science Event

I volunteered in January to be a part of this “Science Event” development team to work on the Microbiology part. Two of my peers and I were the helpers. I had a lot of fun. Don’t get me wrong, it was incredibly stressful and I think I scared both of my collaborators when my finely hidden enthusiasm for microbiology emerged. I get much too excited over these things. I mean, I think about it a lot. I can’t lie. I’ve wanted to work with diseases and causative agents since I was in middle school and this desire has not waned. It grew. Lovely. But I hide my excitement…by being very sedate and trying not to look at things too long. 

But anyway, I did a lot of work for this. I guess it was a mixed blessing/curse not having my regular micro job last week…for one, I got rather depressed not having any micro to do, but I found out rather quickly that I had more to do than I had originally thought. So, more time ftw! 

The three of us actually pieced everything together. I mean everything! We didn’t steal any questions. We read everything that the teams were supposed to know. We went around getting the samples we’d need. We rewrote questions to fit what we could obtain. We fixed questions last minute to make way for plans that had fallen through. 

I personally, proofread our questions, made an answer key and an answer sheet. 

Fun story! We needed a slide of Gram + bacteria (Gram stained purple). We asked the head of the event at our school, but she doesn’t deal with bacteria, so she told us to ask our Microbiology teacher. However, he was out of town. So, one of us (not me) emailed him to check if he may have any prepared slides we could use. But then we got word that our specific adviser for the micro event had prepared slides, so we were relieved. But the day of, we discovered that her prepared slides were really old and fading and all the Gram + Micrococcus luteus looked red. (how confusing). And then we heard from the head that she had talked to our Micro teacher who was going to make us Gram stains. But was told we already had them. Damn it! *Note: I thought that the gesture to make us the Gram stains was very kind.

So, we got into the Micro lab and I made the Gram stain with old M. luteus which turned out a lot better than I expected. The adviser said it was perfectly fine. When we took it to another microscope, I liked it better. 

Anyway, I think we made the test too hard even by following the guidelines for what they should have known. I can’t say anything specific and I won’t. Other than the Gram stain part. 


There’s Pepper getting weighed. He’s lost weight it would seem. They examined him, did a crop swab, and a gram stain.

The verdict? Well, Pepper has a bacterial infection. There was a lot of gram negative bacteria in his crop. They took blood and are doing a CBC to look for underlying causes. The results of that will likely be told to me Monday.

In the meantime, Pepper needs to be given Baytril, an antibiotic, every 12 hours, followed by Benebac Plus. Depending on the results of the blood test, and if the antibiotics help him recover, he may need to go back in.

Thank you so much again for your generosity! I was able to cover the entire vet bill, and should be able to cover the next visit if he needs to return. Any leftover money is going in a savings account to be used in the event of another bird emergency.

We Know When You're Lying (Most of the Time)

Recently admitted a young person with horrific orbital cellulitis- like dripping pus down their face, can’t even see the pupil when we pried open their eyelids level horrible.

And the gram stain from their eye came back gram negative diplococci… And their STI test came back positive for gonorrhea. So we think they have gonorrhea in their eye too.

However, (after kicking parents out of the room) they furiously denied having ever come in contact with any person’s genitals, boy or girl. They told three different doctors the same story.

The next day they shyly admitting to kissing their partner.

Then today we sat down with them and said, “So, our tests show that you have a sexually transmitted disease.” Finally they fessed up to having unprotected sex a few times. Luckily we were already treating them with an antibiotic that covered gonorrhea because we didn’t believe the never-had-sex story.

So! If a doctor asks you a question, tell the truth the first time, because it just makes things easier for everyone. We’re not going to judge you or tattle on you, we have to know the truth so we can provide proper care.

Also use a condom!!

johnlock au where john and sherlock are microbes. johns a gram negative bacterial cell bc he has lots of layers like an ogre, while sherlock is a gram positive cell bc he has one big thick dfp barrier between his literally microscopic smoll self and the world (also he stains purple during a gram stain, so like his purple shirt 💜). john tries to touch sherlock w his big long monster sex pilus to ~exchange genetic information~ sherlock does a happy wiggle when it touches his cell butt

anyway, theyre in love bye