Introduction
Methods
Clinical isolates and clinical data
DNA extraction and whole genome sequencing
Assembly and annotation
emm typing and multilocus sequence typing
Core genomes alignment and mapping — whole genome alignments
Virulence factors
Hyaluronic acid assay
Resistome and antibiotic susceptibility testing
Results
Isolates and clinical presentations
Identifier | Gender | Age (years) | Sample | Primary diagnosis | Secondary diagnosis | Outcome |
---|---|---|---|---|---|---|
ISR1 | F | 1 | Blood culture | Complicated pneumonia with bilateral empyemas and TSS | RSV Bronchiolitis | Good |
ISR2 | M | 1 | Pleural fluid | Complicated pneumonia with parapneumonic effusion | RSV infection | Good |
ISR3 | M | 4 | Blood culture | Complicated pneumonia with parapneumonic effusion and TSS | Influenza A infection | Good |
ISR4 | M | 6 | Pharyngeal swab | Oto-mastoiditis with subsequent meningitis and TSS | Influenza B infection | Good |
ISR5 | F | 47 | Blood culture | Pneumonia complicated by ARDS | – | Good |
ISR6 | F | 1 | Post-mortem, pleural fluid | Complicated pneumonia with parapneumonic effusion and TSS | – | Death |
ISR7 | M | 49 | Blood culture | Skin and soft tissues infection (cellulitis) | – | Good |
ISR8 | M | 79 | Blood culture | Skin and soft tissues infection (cellulitis) complicated by deep venous thrombosis and acute renal failure | – | Good |
ISR9 | F | 58 | Blood culture | Septic arthritis | – | Good |
ISR10 | F | 76 | Blood culture | Skin and soft tissues infection complicated by TSS | – | Good |
ISR11 | F | 15 | Blood culture | Complicated pneumonia with parapneumonic effusion | – | Good |
emm-type and MLST
Isolates |
emm-type (.subtype) |
emm-cluster | ST |
gki
|
gtr
|
murI
|
mutS
|
recP
|
xpt
|
yqiL
|
---|---|---|---|---|---|---|---|---|---|---|
ISR3 |
emm1.0 | A-C3 | 28 | 4 | 3 | 4 | 4 | 4 | 2 | 4 |
ISR4 |
emm1.0 | A-C3 | 28 | 4 | 3 | 4 | 4 | 4 | 2 | 4 |
ISR7 |
emm22 | E4 | 46 | 9 | 8 | 1 | 1 | 1 | 3 | 4 |
ISR8 |
emm22 | E4 | 46 | 9 | 8 | 1 | 1 | 1 | 3 | 4 |
ISR9 |
emm28.0 | E4 | 458 | 11 | 77 | 14 | 5 | 9 | 17 | 19 |
ISR11 |
emm28.0 | E4 | 52 | 11 | 6 | 14 | 5 | 9 | 17 | 19 |
ISR1 |
emm3.1 | A-C5 | 15 | 2 | 6 | 8 | 5 | 2 | 3 | 2 |
ISR2 |
emm75.0 | E6 | 880 | 11 | 2 | 110 | 3 | 50 | 8 | 7 |
ISR5 |
emm73.0 | E4 | 331 | 43 | 2 | 2 | 47 | 1 | 3 | 4 |
ISR6 |
emm5.23 | Ya
| 99 | 33 | 30 | 7 | 5 | 5 | 26 | 3 |
ISR10 |
emm89.0 | E4 | 101 | 16 | 2 | 8 | 3 | 1 | 13 | 3 |
Core-genome alignment and mapping
Virulence factors and regulation of virulence
emm1
|
emm22
|
emm28
|
emm3
|
emm75
|
emm73
|
emm5
|
emm89
| |||
---|---|---|---|---|---|---|---|---|---|---|
ISR3 | ISR4 | ISR7 | ISR8 | ISR9 | ISR11 | ISR1 | ISR2 | ISR5 | ISR6 | ISR10 |
cpa
|
cpa
|
fbaA
|
fbaA
|
fbaA
|
fbaA
|
cpa
|
cpa
|
fbaA
|
fbaB
|
fbaA
|
emm
|
emm
|
fbp54
|
fbp54
|
fbp54
|
fbp54
|
emm
|
emm
|
fbp54
|
fbp54
|
fbaB
|
fbaA
|
fbaA
|
grab
|
grab
|
hasA
|
hasA
|
fbaB
|
fbaB
|
hasA
|
hasA
|
fbp54
|
fbp54
|
fbp54
|
hasC
|
hasC
|
hasB
|
hasB
|
fbp54
|
fbp54
|
hasB
|
hasB
|
hasC
|
fctA
|
fctA
|
hylP
|
hylP
|
hasC
|
hasC
|
grab
|
grab
|
hasC
|
hasC
|
lmb
|
fctB
|
fctB
|
ideS/mac
|
ideS/mac
|
lmb
|
lmb
|
hasA
|
hasA
|
lmb
|
lmb
|
mf/spd
|
grab
|
grab
|
lmb
|
lmb
|
mf/spd
|
mf/spd
|
hasB
|
hasB
|
mf/spd
|
mf/spd
|
scpA
|
hasA
|
hasA
|
mf/spd
|
mf/spd
|
mf2
|
mf2
|
hasC
|
hasC
|
mf2
|
mf2
|
scpB
|
hasB
|
hasB
|
mf2
|
mf2
|
scpA
|
scpA
|
hylP
|
hylP
|
scpA
|
mf3
|
slo
|
hasC
|
hasC
|
scpA
|
scpA
|
scpB
|
scpB
|
ideS/mac
|
ideS/mac
|
slo
|
scpA
|
smeZ
|
ideS/mac
|
ideS/mac
|
scpB
|
scpB
|
slo
|
slo
|
lmb
|
lmb
|
smeZ
|
scpB
|
speB
|
lepA
|
lepA
|
slo
|
slo
|
smeZ
|
smeZ
|
mf/spd
|
mf/spd
|
speB
|
slo
|
speG
|
lmb
|
lmb
|
smeZ
|
smeZ
|
speB
|
speB
|
scpA
|
scpA
|
speC
|
smeZ
| |
mf/spd
|
mf/spd
|
speB
|
speB
|
speC
|
speC
|
ska
|
ska
|
speG
|
speB
| |
mf3
|
mf3
|
speC
|
speC
|
speG
|
speG
|
slo
|
slo
|
speH
|
speC
| |
scpA
|
scpA
|
speG
|
speG
|
speJ
|
speJ
|
smeZ
|
smeZ
|
speI
|
speG
| |
ska
|
ska
|
ssa
|
speK
|
speB
|
speA
| |||||
slo
|
slo
|
ssa
|
speG
|
speB
| ||||||
smeZ
|
smeZ
|
speK
|
speG
| |||||||
speA
|
speA
|
ssa
|
speK
| |||||||
speB
|
speB
|
ssa
| ||||||||
speG
|
speG
| |||||||||
speJ
|
speJ
| |||||||||
srtC1
|
srtC1
|