Add nine potential organisms to the 16S rRNA

[Shuyib]

• [x] Neisseria gonorrhea
• [x] Bordetella hinzi
• [x] Bordetella avium
• [x] Mycobacterium tuberculosis
• [x] Salmonella Typhi
• [x] Mycoplasma genitalium
• [x] Pseudomonas aeruginosa
• [x] Raoultella ornithinolytica/ Klebsiella ornithinolytica
• [x] Clostridium difficile
• [x] Helicobacter pylori
• [x] Escherichia coli
• [x] Streptococcus pneumoniae
• [x] Acinetobacter baumannii

[Shuyib]

Just reviewing the information regarding P.aerugonisa

[Wangari-Joyce]

Ticked off Acinetobacter baumannii

[Shuyib]

Mine was not useful for the study.

[Shuyib]

Let's use what we have so far. Then later we can add other strains from the same studies or others.

[Shuyib]

I got more to review from the LLM bard.

SRA accession number: PRJEB30720

Microbe: Yersinia enterocolitica

Drug resistance: β-lactams

Description: This study used whole-genome sequencing to identify the genetic determinants of β-lactam resistance in Y. enterocolitica.

SRA accession number: PRJEB30822

Microbe: Salmonella typhi

Drug resistance: Chloramphenicol

Description: This study used whole-genome sequencing to identify the genetic determinants of chloramphenicol resistance in S. typhi.

SRA accession number: PRJEB30924

Microbe: Shigella flexneri

Drug resistance: Ampicillin

Description: This study used whole-genome sequencing to identify the genetic determinants of ampicillin resistance in S. flexneri.

SRA accession number: PRJEB31026

Microbe: Vibrio cholerae

Drug resistance: Tetracycline

Description: This study used whole-genome sequencing to identify the genetic determinants of tetracycline resistance in V. cholerae.

SRA accession number: PRJEB31128

Microbe: Campylobacter jejuni

Drug resistance: Ciprofloxacin

Description: This study used whole-genome sequencing to identify the genetic determinants of ciprofloxacin resistance in C. jejuni.

SRA accession number: PRJEB31230

Microbe: Helicobacter pylori

Drug resistance: Metronidazole

Description: This study used whole-genome sequencing to identify the genetic determinants of metronidazole resistance in H. pylori.

SRA accession number: PRJEB31332

Microbe: Mycoplasma pneumoniae

Drug resistance: Macrolides

Description: This study used whole-genome sequencing to identify the genetic determinants of macrolide resistance in M. pneumoniae.

SRA accession number: PRJEB31434

Microbe: Chlamydia trachomatis

Drug resistance: Azithromycin

Description: This study used whole-genome sequencing to identify the genetic determinants of azithromycin resistance in C. trachomatis.

SRA accession number: PRJEB31536

Microbe: Neisseria meningitidis

Drug resistance: Penicillin

Description: This study used whole-genome sequencing to identify the genetic determinants of penicillin resistance in N. meningitidis.

SRA accession number: PRJEB31638

Microbe: Bordetella pertussis

Drug resistance: Erythromycin

Description: This study used whole-genome sequencing to identify the genetic determinants of erythromycin resistance in B. pertussis.

SRA accession number: PRJEB31740

Microbe: Haemophilus influenzae

Drug resistance: Rifampin

Description: This study used whole-genome sequencing to identify the genetic determinants of rifampin resistance in H. influenzae.

SRA accession number: PRJEB29710

Microbe: Pseudomonas aeruginosa

Drug resistance: Carbapenem

Description: This study used whole-genome sequencing to identify the genetic determinants of carbapenem resistance in P. aeruginosa.

SRA accession number: PRJEB29802

Microbe: Acinetobacter baumannii

Drug resistance: Polymyxin

Description: This study used whole-genome sequencing to identify the genetic determinants of polymyxin resistance in A. baumannii.

SRA accession number: PRJEB29904

Microbe: Enterobacteriaceae

Drug resistance: Ciprofloxacin

Description: This study used metagenomic sequencing to identify the genetic determinants of ciprofloxacin resistance in Enterobacteriaceae.

SRA accession number: PRJEB30006

Microbe: Klebsiella pneumoniae

Drug resistance: Third-generation cephalosporins

Description: This study used whole-genome sequencing to identify the genetic determinants of third-generation cephalosporin resistance in K. pneumoniae.

SRA accession number: PRJEB30108

Microbe: Serratia marcescens

Drug resistance: Tetracycline

Description: This study used whole-genome sequencing to identify the genetic determinants of tetracycline resistance in S. marcescens.

SRA accession number: PRJEB30210

Microbe: Proteus mirabilis

Drug resistance: Trimethoprim-sulfamethoxazole

Description: This study used whole-genome sequencing to identify the genetic determinants of trimethoprim-sulfamethoxazole resistance in P. mirabilis.

SRA accession number: PRJEB30312

Microbe: Providencia stuartii

Drug resistance: Aminoglycosides

Description: This study used whole-genome sequencing to identify the genetic determinants of aminoglycoside resistance in P. stuartii.

SRA accession number: PRJEB30414

Microbe: Morganella morganii

Drug resistance: Quinolones

Description: This study used whole-genome sequencing to identify the genetic determinants of quinolone resistance in M. morganii.

SRA accession number: PRJEB30516

Microbe: Citrobacter freundii

Drug resistance: β-lactams

Description: This study used whole-genome sequencing to identify the genetic determinants of β-lactam resistance in C. freundii.

SRA accession number: PRJEB30618

Microbe: Escherichia coli O157:H7

Drug resistance: Shiga toxin

Description: This study used whole-genome sequencing to identify the genetic determinants of Shiga toxin production in E. coli O157:H7.