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Table 3 The Streptococcus and Enterococcus species alignment of 16S–23S rRNA region to GenBanka, b

From: Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S–23S rRNA region

Species NGS of 16S -23S rRNA region BLAST GenBank 1st ID Score NGS of 16S - 23S rRNA region BLAST GenBank 2nd ID Score Difference between 1st and 2nd ID
Streptococcus anginosus Streptococcus anginosus 4410/4411 (99.9%) Streptococcus intermedius 4287/4419 (97.0%) 2.9%
Streptococcus australis Streptococcus australis 4159/4270 (97.4%) Streptococcus oralis 4204/4255 (98.8%) 1.4%
Streptococcus canis Streptococcus canis 4296/4301 (99.9%) Streptococcus dysgalactiae 4206/4303 (97.8%) 2.%
Streptococcus constellatus Streptococcus constellatus 4324/4340 (99.6%) – – –
Streptococcus cremoris Streptococcus cremoris 4317/4317 (100%) Lactococcus garvieae 4043/4391 (92.1%) 7.9%
Streptococcus criceti Streptococcus criceti 4649/4649 (100%) – – –
Streptococcus durans Streptococcus durans 4359/4366 (99.8%) Enterococcus hirae 4330/4368 (99.1%) 0.7%
Streptococcus dysgalactiae Streptococcus dysgalactiae 4300/4301 (99.9%) Streptococcus canis 4201/4303 (97.6%) 2.3%
Streptococcus equi Streptococcus equi 4429/4429 (100%) – – –
Streptococcus gallolyticus Streptococcus gallolyticus 4278/4284 (99.9%) Streptococcus pasteurianus 4259/4286 (99.4%) 0.5%
Streptococcus gordonii Streptococcus gordonii 4265/4267 (99.9%) Streptococcus sanguinis 4161/4291 (97.0%) 2.9%
Streptococcus infantarius Streptococcus infantarius 4282/4284 (99.9%) Streptococcus equinus 4284/4284 (100%) 0.1%
Streptococcus intermedius Streptococcus intermedius 4284/4291 (99.8%) Streptococcus gordonii 4138/4302 (96.2%) 3.6%
Streptococcus mitis Streptococcus mitis 4247/4259 (99.7%) Streptococcus pneumoniae 4238/4259 (99.5%) 0.2%
Streptococcus mutans Streptococcus mutans 4408/4408 (100%) – – –
Streptococcus oligofermentans Streptococcus oligofermentans 4263/4263 (100%) Streptococcus sanguinis 4145/4285 (96.7%) 3.3%
Streptococcus oralis Streptococcus oralis 4251/4259 (99.8%) Streptococcus pneumoniae 4237/4257 (99.5%) 0.3%
Streptococcus parasanguinis Streptococcus parasanguinis 4227/4261 (99.2%) Streptococcus sanguinis 4137/4273 (97.6%) 1.6%
Streptococcus pasteurianus Streptococcus pasteurianus 4283/4284 (99.9%) Streptococcus gallolyticus 4258/4286 (99.4%) 0.5%
Streptococcus pluranimalium Streptococcus pluranimalium 4295/4304 (99.8%) Streptococcus halotolerans 4163/4316 (96.5%) 3.3%
Streptococcus pneumoniae Streptococcus pneumoniae 4255/4258 (99.9%) Streptococcus pseudopneumoniae 4238/4259 (99.5%) 0.4%
Streptococcus porcinus Streptococcus porcinus 4558/4558 (100%) – – –
Streptococcus pseudopneumoniae Streptococcus pseudopneumoniae 4245/4261 (99.6%) Streptococcus pneumoniae 4243/4260 (99.6%) 0.0%
Streptococcus pseudoporcinus Streptococcus pseudoporcinus 4498/4498 (100%) – – –
Streptococcus pyogenes Streptococcus pyogenes 4435/4436 (99.9%) Streptococcus suis 4199/4457 (94.2%) 5.7%
Streptococcus salivarius Streptococcus salivarius 4283/4283 (100%) Streptococcus vestibularis 4270/4283 (99.7%) 0.3%
Streptococcus sanguinis Streptococcus sanguinis 4254/4275 (99.5%) Streptococcus gordonii 4162/4292 (97.0%) 2.5%
Streptococcus sobrinus Streptococcus sobrinus 4412/4424 (99.7%) – – –
Streptococcus suis Streptococcus suis 4420/4420 (100%) – – –
Streptococcus tigurinus Streptococcus oralis subsp. tigurinus 4223/4261 (99.1%) Streptococcus oralis 4221/4261 (99.1%) 0.0%
Streptococcus uberis Streptococcus uberis 4352/4352 (100%) Streptococcus iniae 4197/4358 (96.3%) 3.7%
Streptococcus urinalis Streptococcus urinalis 4291/4292 (99.9%) Streptococcus agalactiae 4136/4305 (96.1%) 3.8%
Enterococcus casseliflavus Enterococcus casseliflavus 4263/4266 (99.9%) Enterococcus gallinarum 4256/4266 (99.8%) 0.1%
Enterococcus cecorum Enterococcus cecorum 4214/4224 (99.8%) Lactobacillus plantarum 3754/4277 (88.0%) 11.8%
Enterococcus durans Enterococcus durans 4311/4313 (99.9%) Enterococcus silesiacus 4083/4342 (94.0%) 5.9%
Enterococcus faecium Enterococcus faecium 4377/4381 (99.9%) Enterococcus hirae 4321/4387 (98.5%) 1.4%
Enterococcus faecalis Enterococcus faecalis 4258/4262 (99.9%) Enterococcus wangshanyuanii 4122/4270 (96.5%) 3.4%
Enterococcus hirae Enterococcus hirae 4359/4367 (99.8%) Enterococcus durans 4330/4368 (99.1%) 0.7%
  1. aFor species not included in a Table (Streptococcus acidominimus, Streptococcus adjacens, Streptococcus cristatus, Streptococcus difficilis, Streptococcus downei, Streptococcus equinus, Streptococcus infantis, Streptococcus ovis, Streptococcus saccharolyticus, Streptococcus sinensis, Enterococcus avium, Enterococcus porcinus, Enterococcus raffinosus), there are no reference genomes available. bSpecies for which the NGS-based approach did not allow the proper identification based on previously described criteria are indicated in bold
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Antimicrobial Resistance & Infection Control

ISSN: 2047-2994

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