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Table 1 Bacterial species tested on the ASPv5.3 to date

From: Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux

Bacterial

species

Genome

available?1

Rumsfeld

Category

Ribosomal

predictions7

No. strains tested

on ASP microarray

Correct ID

p-value2

Best

mis-ID3

mis-

ID3

p-value

    

v1

v2

v3

v4.3

v5.3

   

Acinetobacter baumannii (γ-proteobacteria)

No

UU

no ribosomals

 

1

1

 

1

N/A (0+12)4

None5

-

Bacillus anthracis (firmicutes)

Yes

KK

n/a

1

1

 

3

3

4.43e-170 (0+122)

B. cereus

1.31e-133

Burkholderia mallei (β-proteobacteria)

Yes

KK

n/a

   

3

3

1.55e-179 (5+136)

B. pseudomallei

1.34e-163

Burkholderia pseudomallei (β-proteobacteria)

Yes

KK

n/a

   

3

3

6.61e-171 (2+159)

B. mallei

3.43e-110

Clostridium difficile (firmicutes)

Yes

KK

n/a

1

1

9

12

4

1.11e-4 (0+3)

None

-

Clostridium sordellii (firmicutes)

No

UU

no ribosomals

  

1

 

1

N/A (0+2)

None

-

Clostridium tetani (firmicutes)

No

UU

no ribosomals

  

1

 

1

N/A (0+1)

None

-

Coxiella burnetii (γ-proteobacteria)

Yes

KK

n/a

   

2

3

3.32e-19 (0+11)

None

-

Enterobacter sakazakii (enterobacteriaeae)

No

UU

γ-proteobacteria (10/14 enterobacteriaceae)

  

14

11

14

N/A (10+13)

E. coli

1.35e-11

Enterobacter cloacae (enterobacteriaeae)

No

UU

γ-proteobacteria (10/11 enterobacteriaceae)

 

1

1

 

1

N/A (3+19)

E. coli

3.47e-7

Entrococcus faecium (firmicutes)

No

UU

Firmicutes

 

2

2

2

 

N/A (1+11)

S. aureus

7.77e-4

Escherichia coli (γ-proteobacteria)

Yes

KU

n/a

1

1

1

 

1

8.82e-9 (8+23)

S. flexneri

1.35e-4

Francisella tularensis (γ-proteobacteria)

Yes

KK

n/a

   

3

3

7.33e-65 (3+24)

None

-

Klebsiella pneumoniae (γ-proteobacteria)

No

UU

n/a

 

1

1

 

1

N/A (0+8)

E. coli

3.19e-4

Legionella pneumophilia (γ-proteobacteria)

Yes

KK

n/a

   

3

3

7.08e-102 (0+58)

None

-

Staphylococcus aureus (firmicutes)

Yes

KK/KU

n/a

2

1

1

 

3

8.18e-168 (KK) (4+98) 5.87e-129 (KU) (10+102)

None

-

Stenotrophomonas maltophilia (γ-proteobacteria)

No

KU6

proteobacteria (γ- or β-)

 

1

1

 

1

N/A6 (1+6)

None

-

Yersinia pestis (γ-proteobacteria)

Yes

KK

n/a

3

2

  

2

1.35e-219 (11+188)

Y. pseudoTB

5.32e-202

Yersinia pseudotuberculosis (γ-proteobacteria)

Yes

KK

n/a

  

3

 

3

8.65e-199 (10+129)

Y. pestis

3.44e-188

  1. 1 = Indicates availability of at least one sequenced strain at time of analysis. 2 = example p-value for correct prediction (on ASPv5.3), 3 = example of best incorrect prediction and p-value (on ASPv5.3), 4 = number of positive reporters from example hybridisation (ribosomals + 'virulence' genes), reporters from these genus/species underrepresented on ASPv5.3 due to lack of completed genome sequences however positive genes give information of bacteria (e.g. antibiotic resistance) and any positive ribosomal genes can be used to predict to the level of family/genus, 5 = None indicates no significant match with any BLAST predictions within current database, 6 = S. maltophilia sequence not available at time of analysis, 7 = identification of UU's using ribosomal genes (n/a = not appropriate if species can be elucidated), if present, based on the number of genera which the ribosome is present in at least 1 species (number of predicted genera including duplicates).
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BMC Microbiology

ISSN: 1471-2180

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