Dataset: Antibiotics

### Overview

These data are about the minimum inhibitory concentration (MIC) of three antibiotics for various bacteria.

### Observations

1. ↑ "Neomycin in skin infections: A new topical antibiotic with wide antibacterial range and rarely sensitizing" (1951) Scope

## Team Beta

* *Effect of Genus*:
	+ Certain genera have impractically high MCI for all antibiotics:
		- Aerobacter, Escherichia, Klebsiella, Mycobacterium, Pseudomonas (these all happen to be `gram = negative)`
* *Effect of Gram*:
	+ `gram = positive` – Data fall under the `MCI` threshold more often (`n_usable = 13`).
	+ `gram = negative` – Neomycin excels here, as few other antibiotics are effective in this regime.

1. ↑ Scatter plot of MCI values faceted by gram [1]

## Team Delta

- Neomycin appears to be effective by MIC against more bacteria than penicillin or streptomycin [2]

- Penicillin has some very high outlying MIC values.

- Certain bacteria (Staphylococcus aureus, Staphylococcus albus, Bacillus anthracis) can be treated by any of the 3 antibiotics effectively

 - Certain bacteria do not appear to be human-treatable by any of the 3 antibiotics (Pseudomonas aeruginosa, Mycobacterium tuberculosis, Klebsiella pneumoniae, Aerobacter aerogenes)

- Gram relates to the thickness of the membrane layer of the bacteria that can be attached to. Penicillin seems to show a correlation of MIC value about 1.0 and above for bacteria with negative gram, and mostly below 0.1 for positive gram. There does not appear to be much correlation between gram and MIC for the other antibiotics. [ref]

## Team Zeta

### The three antibiotics are much more effective against the gram-positive bacteria in this dataset

These antibiotics are more effective against the gram-positive bacteria in this dataset; and only neomycin is effective for use in humans against more than one of these gram-positive bacteria, while streptomycin can only effectively combat one of them in humans, and penicillin cannot effectively combat any of them in humans.

### Gram positive bacteria have evolved defenses other than a cell wall that make them drug-resistant

Gram negative bacterial strains in this dataset are more drug-resistant than Gram positive bacterial strains. Gram positive bacteria strains have a physical defensive layer (think peptidoglycan cell wall) against antibiotics that can be pierced by penicillin. Meanwhile, the Gram negative bacterial strains have developed/possess other defenses against antibiotics (efflux pumps, mutation, and lactamase production).

* Penicillin is effective for treating humans (MIC < 0.1 mug/ml) against the represented strains of Streptococcus, Staphylococcus, Diplococcus, and Bacillus.
* Neomycin is effective for treating humans (MIS < 0.1 mug/ml) against Staphylococcus, Salmonella, Escherichia, Bucella, and acillus.
* Streptomycin is effective for treating humans (MIS < 0.1 mug/ml) against Staphylococcus, Proteus, and Bacillus.
* None of the antibiotics are effective for treating Pseudomonas, Mycobacterium, Klebsiella, or Aerobacter. Of note, all of these strains are gram positive.

### For more than half the bacteria, the three antibiotics are not effective at a practical dosage

When looking at the MIC distribution across all bacteria (by antibiotic) and zooming into the sub-0.1 region, only neomycin has a median MIC (0.100)  within what’s considered a practical dosage. Zooming out, this is further confirmed by a point-plot where, visually, we can see a larger number of points above the 0.1 threshold for penicillin (10) and streptomycin (12).

### An antibiotic’s effectiveness against one strain of a bacterium does not guarantee its effectiveness against another strain

Aside from some clustering of bacteria under the Streptococcus genus (noting that there are only two data points, which isn’t a large sample size), the other genuses do not seem to cluster.

1. ↑ MIC of three antibiotics against various gram-negative and -positive bacteria[3]
2. ↑ Penicillin MIC < 0.1 Bacteria[4]
3. ↑ MIC of 3 antibiotics against various gram-negative and -positive bacteria[5]
4. ↑ Minimum inhibitory concentration for each genus vs different antibiotics[6]
5. ↑ Box-plot of MIC distribution across all bacteria when MIC is at most 0.1[7]
6. ↑ Point-plot of MIC distribution across all bacteria (per antibiotic)[8]
7. ↑ penicillin vs streptomycin MICS[9]