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Table 1 Results of MetaMLST applied to the 1614 samples of the MetaSUB dataset. MetaMLST was applied on the full panel of 113 species, detecting in total 121 known and 510 previously unobserved profiles. The table reports the number of samples and STs found for both known and novel STs of the 15 species profiled in the MetaSUB dataset. The prevalence values are normalized over the total number of samples (1614)

From: Profiling microbial strains in urban environments using metagenomic sequencing data

Species

Known

Novel

  
 

Number of samples

Number of STs

Number of samples

Number of STs

Prevalence across dataset

Most prevalent ST (samples)

Acinetobacter baumannii

69

22

123

117

11.90%

ST71 (20)

Enterobacter cloacae

63

39

89

85

9.42%

ST50 (7)

Stenotrophomonas maltophilia

15

12

98

90

7.00%

ST100009 (3)

Cronobacter spp.

2

2

66

56

4.21%

 

Klebsiella pneumoniae

13

12

38

38

3.16%

 

Bacillus cereus

15

11

17

17

1.98%

 

Klebsiella oxytoca

12

5

18

18

1.86%

ST44 (8)

Achromobacter spp.

2

2

27

27

1.80%

 

Enrerococcus faecalis

6

5

18

18

1.49%

 

Propionibacterium acnes

4

2

18

18

1.36%

 

Escherihia coli

3

2

16

15

1.18%

 

Pseudomonas fluorescens

1

1

7

6

0.50%

 

Pseudomonas aeruginosa

5

1

1

4

0.37%

 

Clostridium botulinum

1

5

5

1

0.37%

 

Total

211

121

541

510

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