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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