Table 3 List of genes encoding for supposed virulence factors and affected by single nucleotide polymorphisms

ctpA

Cation transporting P-type ATPase

Reduced CFUs

NS

100895

A/S

ctpI

Cation transporting P-type ATPase

Reduced CFUs

S

130449

A/A

mce1F

Mce protein

Reduced tissue pathology and increased survival

NS

206453

G/A

Rv0176

Mce protein

Reduced CFUs, reduced tissue pathology, and increased survival

NS

208299

P/R

pckA

Iron-regulated phosphoenolpyruvate carboxykinase

Reduced CFUs

NS

252105

M/I

pcaA

Mycolic acid cyclopropane synthase

Reduced CFUs in lung

NS

561021

H/Y

pstS1

phosphate-binding lipoprotein component of inorganic phosphate transport system

Reduced multiplication

NS

1042991

P/A

mprB

Two component sensor kinase

Reduced CFUs in lung latent stage

S

1098698

G/G

oppA

Oligopeptide-binding lipoprotein component of peptide transport system

Reduced CFUs in organs in the chronic infection, increased survival

S

1433114

G/G

oppD

Oligopeptide-transport ATP binding protein

Reduced CFUs in organs in the chronic infection, increased survival

S

1434648

V/V

irtA

Iron-regulated transporter

Reduced CFUs in macrophages and lung

S

1514732

R/R

irtB

Iron-regulated transporter

Reduced CFUs in macrophages and lung

S

1515922

V/V

Rv1410c

Aminoglycoside/tetracycline-transport integral membrane protein

Reduced CFUs

S

1586360

A/A

pks5

Polyketide synthase

Reduced CFUs in organs

S

1726541

Y/Y

eccB5

EsX-5 type VII secretion system protein

Reduced CFUs

S

2017898

T/T

eccD5

EsX-5 type VII secretion system protein

Reduced CFUs

S

2032701

A/A

mycP5

Pro-rich membrane-anchored serine protease (mycosin)

Reduced CFUs

NS

2033748

G/A

katG

Catalase peroxidase peroxynitritase T

Reduced CFUs, resistance to INH

S

2155389

P/P

Rv1931c

Probable transcriptional regulatory protein

Reduced CFUs

S

2183054

G/G

fadE18

Acyl-CoA dehydrogenase

Reduced CFUs

S

2184781

G/G

mce3A

Mce protein, ? virulence factor

Reduced tissue pathology and increased survival

S

2210055

T/T

dosT

Histidine kinase response regulator

Moderate reduction CFUs

S

2273627

G/G

pks12

Polyketide synthase

Reduced CFUs

S

2294876

R/R

pafA

Proteasome accessory factor A

Reduced CFUs in organs and less tissue pathology

S

2355511

V/V

mpa

Proteasone ATPase

Reduced CFUs in organs and less tissue pathology

S

2375883

K/K

Rv3083

Probable monooxygenase

Reduced CFUs

NS

3448567

H/D

nuoG

NADH dehydrogenase

Increased animal survival and reduced CFUs in organs

S

3518089

G/G

Rv3236c

Probable conserved integral membrane transport protein

Reduced phagosome ROS production

S

3612571

V/V

ponA2

Penicillin-binding protein

Moderate reduction in CFUs

NS

4122882

R/S

mmpL8

Predicted drug exporter of the RND superfamily

Reduced CFUs in organs

S

4291134

R/R

esxA

Early secretory antigenic target

Reduced CFUs

S

4352875

N/N

eccE2

Type VII secretion system protein

Reduced CFUs

NS

4367659

V/A

eccE2

Type VII secretion system protein

Reduced CFUs

NS

4367911

I/T