Table 1

Identification of clinical isolates (n=158) by conventional methods compared to 16S rRNA gene sequence analysis
Conventional phenotyic methods 16S rRNA gene sequence analysis Final identification (supplemental conventional tests if required)
Identification (number of isolates) Level of identification and correctness of result Best reference species sequence % difference to reference species sequence GenBank accession numbers
Actinobacillus ureae (1) S 1; SI 2 Actinobacillus hominis Actinobacillus suis (low demarcation) 0.0, 0.4 KC866152 A. hominis (acidification of mannitol: A. hominis (positive), A. suis (negative) [1])
Aggregatibacter actinomycetemcomitans (2) S; SC Aggregatibacter actinomycetemcomitans 0.0, 0.3 KC866227; KC866228 A. actinomycetemcomitans
Aggregatibacter actinomycetemcomitans (1) S; SI Pasteurella bettyae 0.0 KC866143 P. bettyae
Aggregatibacter aphrophilus (11) S; SC Aggregatibacter aphrophilus 0.0-0.8 KC866144; KC866145; KC866146; KC866147; KC866148; KC866149; KC866150; KC866229; KC866230; KC866231; KC866272 A. aphrophilus
Aggregatibacter aphrophilus (2) S; SI Aggregatibacter aphrophilus 3.8, 2.9 KC866151; KC866153 Aggregatibacter sp.
Aggregatibacter aphrophilus (1) S; SI Neisseria sicca 0.8 KC866154 N. sicca (nitrate reduction: positive (N. mucosa), negative (N. sicca, N. subflava bv. flava); sucrose acidification: positive (N. sicca, N. mucosa), negative (N. subflava bv. flava) [18])
Neisseria subflava bv. flava 1.0
Neisseria mucosa (low demarcation) 1.1
Aggregatibacter sp. (1) G; GC Aggregatibacter aphrophilus 2.3 KC866155 Aggregatibacter sp.
Bergeyella zoohelcum (1) S; SI Myroides odoratimimus 5.9 KC866156 Flavobacteriaceae
Bergeyella zoohelcum (1) S; SI Neisseria zoodegmatis 0.3 KC866157 N. zoodegmatis
Capnocytophaga canimorsus (2) S; SC Capnocytophaga canimorsus 0.5, 0.4 KC866158; KC866159 C. canimorsus
Capnocytophaga ochracea (1) S; SI Capnocytophaga gingivalis 0.6 KC866160 C. gingivalis
Capnocytophaga ochracea (1) S; SI Capnocytophaga ochracea 2.5 KC866161 Capnocytophaga sp.
Capnocytophaga ochracea (5) S; SI Capnocytophaga sputigena 0.0-0.3 KC866162; KC866163; KC866164; KC866273; KC866274 C. sputigena3
Capnocytophaga ochracea (1) S; SI Dysgonomonas mossii 0.6 KC866165 D. mossii
Capnocytophaga ochracea (1) S; SI Leptotrichia trevisanii 0.2 KC866166 L. trevisanii
Capnocytophaga sp. (2) G; GC Capnocytophaga sputigena 0.0, 0.6 KC866167; KC866232 C. sputigena
Cardiobacterium hominis (4) S; SC Cardiobacterium hominis 0.0-0.5 KC866168; KC866233; KC866275; KC866299 C. hominis
CDC Group IIe (1) S; SI Chryseobacterium anthropi 0.2 KC866169 C. anthropi (acidification of fructose and sucrose: positive (C. haifense), negative (C. anthropi) [19])
Chryseobacterium haifense (low demarcation) 0.6
Comamonas sp. (1) G; GI Oligella urethralis 0.0 KC866170 O. urethralis
Dysgonomonas capnocytophagoides (1) S; SC Dysgonomonas capnocytophagoides 0.2 KC866171 D. capnocytophagoides
Eikenella corrodens (10) S; SC Eikenella corrodens 0.0-0.8 KC866172; KC866173; KC866174; KC866175; KC866176; KC866177; KC866178; KC866234; KC866235; KC866236 E. corrodens
Flavobacterium sp. (1) G; GC Flavobacterium lindanitolerans 0.4 KC866179 F. lindanitolerans
Gram-negative rods (1) N Actinobacillus hominis 0.3 KC866238 A. hominis
Gram-negative rods (1) N Actinobacillus hominis 0.0 KC866237 A. hominis (esculin hydrolysis: positive (A. suis), variable (A. hominis), negative (A. equuli); mannitol acidification: positive (A. equuli, A. hominis), negative (A. suis) [1])
Actinobacillus suis 0.0
Actinobacillus equuli (low demarcation) 0.5
Gram-negative rods (1) N Aggregatibacter actinomycetemcomitans 0.2 KC866239 A. actinomycetemcomitans
Gram-negative rods (2) N Aggregatibacter aphrophilus 0.3, 0.8 KC866240; KC866241 A. aphrophilus
Gram-negative rods (1) N Azospira oryzae 0.0 KC866276 A. oryzae
Gram-negative rods (1) N Brevundimonas terrae 0.6 KC866180 B. terrae
Gram-negative rods (3) N Capnocytophaga canimorsus 0.0-0.2 KC866277; KC866278; KC866279 C. canimorsus
Gram-negative rods (1) N Capnocytophaga sputigena 0.0 KC866280 C. sputigena
Gram-negative rods (2) N Cardiobacterium hominis 0.5, 0.6 KC866281; KC866282 C. hominis
Gram-negative rods (1) N Chryseobacterium haifense 0.2 KC866181 C. anthropi (acidification of fructose and sucrose: positive (C. haifense), negative (C. anthropi) [19])
Chryseobacterium anthropi (low demarcation) 0.5
Gram-negative rods (1) N Kingella denitrificans 0.0 KC866182 K. denitrificans
Gram-negative rods (1) N Moraxella atlantae 0.2 KC866242 M. atlantae
Gram-negative rods (2) N Moraxella lacunata 0.0 KC866283; KC866284 M. lacunata
Gram-negative rods (1) N Moraxella lincolnii 0.3 KC866243 M. lincolnii
Gram-negative rods (3) N Moraxella nonliquefaciens 0.0-0.7 KC866285; KC866286; KC866287 M. nonliquefaciens
Gram-negative rods (2) N Moraxella osloensis 0.0, 0.2 KC866288; KC866289 M. osloensis
Gram-negative rods (1) N Neisseria bacilliformis 0.0 KC866244 N. bacilliformis
Gram-negative rods (1) N Neisseria zoodegmatis 2.0 KC866245 Neisseria sp.
Gram-negative rods (4) N Neisseria elongata 0.0-0.3 KC866246; KC866247; KC866290; KC866291 N. elongata
Gram-negative rods (1) N Neisseria flavescens 0.5 KC866248 N. subflava (acidification of glucose and maltose: positive (N. subflava), negative (N. flavescens) [18])
Neisseria subflava (low demarcation) 0.7
Gram-negative rods (2) N Neisseria flavescens 0.3 KC866249; KC866250 N. subflava (acidification of glucose and maltose: positive (N. subflava), negative (N. flavescens) [18])
Neisseria subflava (low demarcation) 0.4
Gram-negative rods (4) N Neisseria weaveri 0.0-0.3 KC866251; KC866252; KC866253; KC866254 N. weaveri
Gram-negative rods (1) N Pasteurella bettyae 0.0 KC866292 P. bettyae
Gram-negative rods (1) N Pasteurella dagmatis 0.4 KC866255 P. stomatis (urease reaction: positive (P. dagmatis), negative (P. stomatis); acidification of maltose: positive (P. dagmatis), negative (P. stomatis) [1])
Pasteurella stomatis (low demarcation) 0.4
Kingella denitrificans (1) S; SC Kingella denitrificans 0.6 KC866183 K. denitrificans
Kingella denitrificans (1) S; SI Neisseria elongata 0.0 KC866184 N. elongata
Leptotrichia buccalis (1) S; SI Leptotrichia trevisanii 0.3 KC866293 L. trevisanii
Moraxella lacunata (1) S; SC Moraxella lacunata 0.5 KC866185 M. lacunata (gelatinase reaction: positive (M. lacunata), negative (M. nonliquefaciens) [20])
Moraxella nonliquefaciens (low demarcation) 0.7
Moraxella osloensis (1) S; SC Moraxella osloensis 0.0 KC866186 M. osloensis
Moraxella osloensis (1) S; SI Psychrobacter faecalis 0.0 KC866187 P. pulmonis (acidification of glucose and xylose: positive (P. faecalis), negative (P. pulmonis) [20])
Psychrobacter pulmonis (low demarcation) 0.2
Moraxella sp. (1) G; GC Moraxella canis 0.2 KC866188 M. canis
Neisseria sp. (1) G; GI Neisseria elongata 0.3 KC866256 N. elongata
Moraxella sp. (4) G; GC Moraxella nonliquefaciens 0.0-0.3 KC866189; KC866190; KC866257; KC866258 M. nonliquefaciens
Moraxella sp. (8) G; GC Moraxella osloensis 0.0-0.2 KC866191; KC866192; KC866193; KC866194; KC866259; KC866260; KC866261; KC866294 M. osloensis
Neisseria animaloris (EF4a) (1) S; SC Neisseria animaloris 0.0 KC866195 N. animaloris
Neisseria animaloris (EF4a) (1) S; SI Neisseria zoodegmatis 0.0 GU797849 N. zoodegmatis
Neisseria cinerea (2) S; SC Neisseria cinerea 0.0 KC866196; KC866197 N. cinerea (acidification of glucose and maltose: positive (N. meningitidis), negative (N. cinerea) [18])
Neisseria meningitidis (low demarcation) 0.3
Neisseria elongata (1) S; SI Aggregatibacter aphrophilus 2.4 KC866198 Aggregatibacter sp.
Neisseria elongata (3) S; SC Neisseria elongata 0.0-0.3 KC866203; KC866204; KC866205 N. elongata
Neisseria elongata (2) S; SI Neisseria bacilliformis 0.1, 0.4 KC866201; KC866202 N. bacilliformis
Neisseria elongata (1) S; SI Neisseria zoodegmatis 0.6 KC866206 N. zoodegmatis
Neisseria elongata (2) S; SI Eikenella corrodens 0.0 KC866199; KC866200 E. corrodens
Neisseria sp. (1) G; GC Neisseria shayeganii 0.3 KC866207 N. shayeganii
Neisseria sp. (1) G; GC Neisseria elongata 0.2 KC866270 N. elongata
Neisseria sp. (1) G; GC Neisseria oralis 0.0 KC866208 N. oralis
Neisseria weaveri (1) S; SC Neisseria weaveri 0.0 KC866211 N. weaveri
Neisseria weaveri (1) S; SC Neisseria shayeganii 0.2 KC866210 N. shayeganii
Neisseria weaveri (1) S; SI Azospira oryzae 0.0 KC866209 A. oryzae
Neisseria zoodegmatis (EF4b) (3) S; SC Neisseria zoodegmatis 0.0-0.5 KC866212; KC866213; KC866295 N. zoodegmatis
Oligella urethralis (2) S; SC Oligella urethralis 0.0 KC866214; KC866215 O. urethralis
Pasteurella aerogenes (1) S; SI Pasteurella aerogenes 2.7 KC866226 Pasteurella sp.
Pasteurella bettyae (2) S; SC Pasteurella bettyae 0.0 KC866216; KC866262 P. bettyae
Pasteurella canis (1) S; SC Pasteurella canis 0.0 KC866217 P. canis
Pasteurella canis (1) S; SI Pasteurella stomatis 1.6 KC866218 Pasteurella sp.
Pasteurella dagmatis (1) S; SC Pasteurella dagmatis 0.2 KC866271 P. dagmatis
Pasteurella multocida (14) S; SC Pasteurella multocida 0.0-0.2 KC866219; KC866220; KC866221; KC866222; KC866223; KC866263; KC866264; KC866265; KC866266; KC866267; KC866268; KC866296; KC866297; KC866298 P. multocida
Pasteurella pneumotropica (1) S; SI Bisgaard Taxon 22 1.7 KC866224 Pasteurella sp.
Pasteurella sp. (1) G; GI Necropsobacter rosorum 0.0 KC866269 N. rosorum
Roseomonas sp. (1) G; GC Roseomonas mucosa 0.0 KC866225 R. mucosa

1Assignment to taxonomic level: S = species, G = genus, N = not identified.

2Correctness of assignment: SC = correct at species level, SI = incorrect at species level, GC = correct at genus level, GI = incorrect at genus level, N = not identified.

3 Difficult differentiation of species in question by conventional tests.

de Melo Oliveira et al.

de Melo Oliveira et al. BMC Microbiology 2013 13:162   doi:10.1186/1471-2180-13-162

Open Data