#62 terms for phenotypes related to resistance to antimicrobial agents

[Jonathan Herrera]

The following is only a partial list, the rest of the terms not found here are on the tracker already (ex. rifampins).

For Nicer looking version of this Please see the google doc here: https://docs.google.com/document/d/1KhEducmHePja1F56pZtCVfbaqkW_KgR0RX14WLqvPQs/edit#

[NOTE FROM ADMIN Marcus Chibucos: Links like the one above, while helpful for internal project personnel, might not be accessible by most people reading this thread. Consider adding such information to a wiki (either the OMPwiki or this development site wiki?), where everyone can read it.]
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ANTIMICROBIAL Compound Increase/Decrease RESISTANCE
Synonyms: Antibiotics, Antifungals, Antivirals, Antimetabolite

Definition: Any compounds that kills (microbiocidal) or inhibit growth (microbiostatic) of bacteria. This is different from bacteriocins with the same function but are proteins.

We should also do a redirect for increase/decrease sensitivity.

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Increase/Decrease Macrolides Resistance (Antibiotic)

-- Increase/decrease resistance to macrolides

Definitions:

Structure characterized by 14-, 15- or 16-membered lactone ring, substituted with several neutral or amino sugars. (1)

Macrolide antibiotics are effective inhibitors of bacterial protein biosynthesis. They bind to the large 50S ribosomal subunit at or near the peptidyl transferase center and block the elongation of the peptide chain. (2)

Terms that should redirect to Macrolides
Erythromycin, Clarithromycin, Azithromycin, Dirithromycin, Roxithromycin, Telithromycin, Carvomycin A, Josamycin, Troleandomycin, Spectinomycin, Spiramycin
Other:
*There are several more (see: http://en.wikipedia.org/wiki/Category:Macrolide_antibiotics\) but these listed I have verified through pubmed as macrolides. .

Sources:
* http://en.wikipedia.org/wiki/Macrolide#cite_ref-pharmamotion_1-0
(2) http://ecocyc.org/ECOLI/NEW-IMAGE?type=COMPOUND&object=Macrolide-Antibiotics

Erythromycin is on another term request (OMP term request-3513407) as with a newer Kasugamycin term request (Kasugamycin Dependent Growth - ID: 3538256). These should be ignored in the meantime.

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Increase/Decrease resistance to Diaminopyrimidine Compound (several)

Definition:
Is an organic chemical compound that includes many dihydrofolate inhibitors, but not all dihydrofolate inhibitors are Diaminopyrimidine.
Structure:
Are compounds with a pyrimidine ring with 2 attached amine groups.

Redirects from searches to here:
* Trimethoprim, Iclaprim(1) - Antibiotics
* pyrimethamine, trimetrexate, and piritrexim(2) diaveridine(1)- Non-Antibiotics compounds that act as inhibitors.

Sources:
(1) PMID: 22161732
TMP and DVD (diaveridine) are diaminopyimidine anti-microbial agents

(2) PMCID: PMC90829

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Beta Lactams (Antibiotics)
*This needs more info - ecocyc has none*

Definition: A broad class cyclic amide where most work by proteins synthesis inhibition.

Structure: It is a 4 membered cyclic amide with the amide attached to the beta position to the carbonyl group.
--increase/decrease resistance to b-lactams

Searched terms that should redirect here:
Subclass antibiotics - penicillin, ampicillin, cephaloxporins, cefoxitin, monobactams, carbapenams.

Beta Lactams are divided further into subclasses. Not sure if we want to divide to that level.
see: http://www.aafp.org/afp/2000/0801/p611.html

Link to resources
Antibiotic list http://en.wikipedia.org/wiki/List_of_antibiotics
Beta-lactam info http://en.wikipedia.org/wiki/Beta-lactam_antibiotic#cite_note-pmid10950216-0

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Sideromycins (Antibiotics)
Synonyms (1967): Sideramines & siderochromes.

--Incease/decrease resistance to sideromycins

Sideromycins Are iron carriers (Fe3+ siderophores) that are covalently linked to the antibiotic Moiety.

Searches that should redirect here:
Antibiotics - Albomycin, salmycin

References:
PMID:19130258

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Azole Class (An Antifungal)

-Increase/Decrease Resistance to Triazole

Definition: Inhibits enzyme (lanosterol 14 α-demethylase) necessary to convert lanosterol to ergosterol which is important for fungal membrane structure and function.

Structure: Azoles are nitrogen heterocyclic rings with one other non-carbon atom (sulfure, oxygen or nitrogen).

Searched terms that should redirect to Azole:
Triazole- acts against bacteria

There are several other classes of azole antifungal but we do not know if they act as anti bacterial agents. Should we add these as well? A more complete list can be found on Wikipedia.

* In paper (PMID:3025879) they use 1,2,4-triazolyl-3-Alanine.

Sources:

http://en.wikipedia.org/wiki/Triazole

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC172087/

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Chloramphenicol or Nitrobeneze (antibiotic-unclassifiable)
Synonyms: chlornitromycin, Chloromycetin (Other brand names on wikipedia),

*Chloramphenicol, in bacteria, inhibits protein synthesis by binding to 50s subunit, thus preventing peptide bond formation, chain elongation, by peptidyl transferase.

nitrobenzene moiety in its structure. Nitrobenzene is a very broad classification so I am not sure if we should group chloramphenicol as a nitrobenzene antimicrobial agent. Before this is incorporated I want to figure this out.

http://en.wikipedia.org/wiki/List_of_antibiotics - lists it as others

http://www.merckmanuals.com/professional/infectious_diseases/bacteria_and_antibacterial_drugs/chloramphenicol.html?qt=&sc=&alt=

http://www.scribd.com/doc/2024490/Tetracyclines-Chloramphenicol-and-Mis

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Quinolones (Antibiotic)

Searches that should redirect to quinolones:
Antibiotics: Nalidixic Acid,Ciproflixacin, Levofloxacin, Trovafloxacin, 2-Quinolones, 4-Quinolones

* There is a longer and more complete list on http://en.wikipedia.org/wiki/Quinolones#Generations

-Increase/Decrease resistance to Quinolones

Definitions: A broad class of antibiotics which inhibit DNA replication and transcription.

PMID:12702699

[Jonathan Herrera]

Difference between state and relative

Relative phenotypes are comparative in nature. Like if we knock out this gene, then the cell swims SLOWER than if we did not do the knockout. Slower as compared to what? Compared to a non-knockout. So it is relative.

State phenotypes are not comparative in nature, i.e. they are what they are. For example, a MOTILE organism has the inherent capacity to swim in any situation, whether or not it does.

So for an E. coli cell with some reduced swimming capacity, we'd say it is:
1. MOTILE (the state phenotype)
2. DECREASED MOTILITY (the relative phenotype)

I will try to get those defs in there soon. But FYI, those are just large grouping terms, and the terms "relative phenotype" and "state phenotype" will not be used for annotation, per se.

[Jonathan Herrera]

Need to ad response to Metals.
This should be right under Antimicrobial Resistance node.

-Antimicrobial Compound Resistance
--Resistance to Metal
---Resistance to Ion (should we instead have cat/anion?)

Assesion numbers from ChebI will Let us know for example that it is Cu+2

Need to also modify Definition for Antimicrobial compound since technically a compound does not encompass metal elements. Possibly replace with the word agent? or if anyone has term that is relavent.

Definitions for Metal resistance should be very similar to what GO nuts has here:
http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010038

[Debby Siegele]

We decided to organize the antimicrobial agent resistance phenotypes based on chemical classes, such as beta-lactams, macrocodes, etc. The individual compounds agent(s) tested will be indicated in a separate field using their CHEBI ids. There may be some exceptions, for example, chloramphenicol, seems to be in a class by itself, but the general policy will be to make not make terms for individual antimicrobial agents. The ontology released in October 2014 reflects this decision.