Add new airway pathogens to organism-strain mapping file

[jaclyn-taroni]

Issue Number

Closes #3365

Purpose/Implementation Notes

I am adding the following organisms to config/organism_strain_mapping.csv:

Staphylococcus aureus Streptococcus pneumoniae Stenotrophomonas maltophilia Aspergillus fumigatus Klebsiella pneumoniae

Methods

Tom Hampton noted the following as common laboratory strains in an email communication:

Staphylococcus aureus subsp. aureus USA300 Streptococcus pneumoniae TIGR4 Aspergillus fumigatus Af293

• Klebsiella pneumonia MGH 78578 was listed several times in the request list.
• K279a is documented as the strain to use for comparative genome analysis Stenotrophomonas maltophilia (ref)

I've assembled the following table to help with review (specifically, checking that the assembly information looks good):

Organism	Strain	Assembly	URL
Staphylococcus aureus	USA300	ASM1346v1	https://bacteria.ensembl.org/Staphylococcus_aureus_subsp_aureus_usa300_fpr3757_gca_000013465/Info/Index/
Streptococcus pneumoniae	TIGR4	ASM688v1	https://bacteria.ensembl.org/Streptococcus_pneumoniae_tigr4_gca_000006885/Info/Index/
Stenotrophomonas maltophilia	K279a	ASM7248v1	https://bacteria.ensembl.org/Stenotrophomonas_maltophilia_k279a_gca_000072485/Info/Index/
Aspergillus fumigatus	Af293	ASM265v1	https://fungi.ensembl.org/Aspergillus_fumigatus/Info/Index
Klebsiella pneumoniae	MGH 78578	ASM1630v1	https://bacteria.ensembl.org/Klebsiella_pneumoniae_subsp_pneumoniae_mgh_78578_gca_000016305/Info/Index/

Tom has reviewed this list.

Types of changes

What types of changes does your code introduce?

• New feature (non-breaking change which adds functionality)

Functional tests

List out the functional tests you've completed to verify your changes work locally.

N/A

Checklist

Put an x in the boxes that apply.

• [ ] Lint and unit tests pass locally with my changes
• [ ] I have added tests that prove my fix is effective or that my feature works
• [ ] I have added necessary documentation (if appropriate)
• [ ] Any dependent changes have been merged and published in downstream modules

Screenshots

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