Table 1.
Characteristics of 63 misID streptococci analysed in the study
| Isolate | Isolation year | Centre | Optochin susceptibility (mm) | Deoxycholate solubility | Aprox. genome size (Mb) | Penicillin | Antimicrobial resistance determinants | S. pneumoniae MLST genes | rST | C203 in 16S rRNA | ply | 9808 | 9828 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S. pseudopneumoniae clade* | |||||||||||||
| k_378 | 1995 | GRA | S (22) | DS | 2.22 | S | erm(B), tet(M) | gdh, gki, recP | 106388 | – | + | + | + |
| 00_79 | 2000 | LUB | S (19) | DS | 2.24 | S | tet(M) | aroE, gki, spi | 106402 | – | + | + | + |
| 00_3613 | 2000 | SAN | S (27) | DS | 2.28 | S | – | aroE, gdh, gki, spi | 106403 | A/C | + | + | + |
| 01_1343 | 2001 | SUW | S (20) | DS | 2.28 | S | tet(M) | aroE, recP, spi, ddl | 106405 | – | + | + | + |
| 01_2106^ | 2001 | KOL | S (22) | DNS | 2.18 | I | tet(M) | aroE, gdh | 106393 | – | + | + | + |
| 02_339 | 2002 | SCH | S (18) | DNS | 2.26 | S | – | aroE, gdh, spi, ddl | 106406 | – | + | + | + |
| 02_477 | 2002 | GDA | S (19) | DS | 2.12 | S | – | aroE, xpt | 106407 | – | + | + | – |
| 02_1013 | 2002 | GDA | S (18) | DS | 2.20 | S | – | aroE, gdh, spi, ddl | 106391 | – | + | + | – |
| 03_3167 | 2003 | WRO | S (20) | DNS | 2.22 | S | – | spi, xpt, ddl | 106409 | – | + | + | + |
| 04_2154| | 2004 | GDA | S (26) | DS | 2.24 | S | – | aroE, gdh | 106394 | – | + | + | + |
| 06_812 | 2006 | SUW | S (20) | DS | 2.24 | S | mef(A) | aroE, gki, xpt, ddl | 106410 | – | + | + | – |
| 06_2877 | 2006 | BYD | S (20) | DS | 2.15 | I | erm(B), tet(M) | aroE, gdh, gki, spi, ddl | 106396 | – | + | + | + |
| 08_646 | 2008 | SUW | S (18) | DS | 2.14 | S | – | aroE, gdh, gki, spi | 106390 | A/C | + | + | + |
| 09_716 | 2009 | POZ | S (20) | DS | 2.19 | I | erm(B), tet(M) | aroE, gdh, gki, spi, ddl | 106415 | – | + | + | + |
| 09_1055^ | 2009 | SUW | S (18) | DS | 2.24 | S | – | aroE, gdh, gki, ddl | 106424 | – | + | + | – |
| 09_1449 | 2009 | SUW | S (18) | DS | 2.20 | S | – | aroE, gdh, xpt, ddl | 106392 | – | + | + | + |
| 10_1559 | 2010 | BYD | S (15) | DNS | 2.19 | S | erm(B), tet(M) | aroE, gdh, gki, spi, xpt | 106416 | – | + | + | – |
| 10_3764 | 2010 | KSZ | S (17) | DNS | 2.17 | I | erm(B), tet(M) | aroE, gdh, gki, spi, xpt, ddl | 106397 | – | + | + | + |
| 10_4155 | 2010 | SUW | S (18) | DS | 2.21 | S | – | aroE, gdh, gki, recP, spi, ddl | 106417 | – | + | + | – |
| 10_4272 | 2010 | SUW | S (15) | DS | 2.18 | S | mef(A), tet(M) | aroE, gki, spi, xpt, ddl | 106398 | – | + | + | + |
| 11_10824 | 2011 | SUW | S (27) | DNS | 2.22 | I | erm(B), cat, tet(M) | aroE | 23944 | – | + | + | + |
| 12_636 | 2012 | SUW | S (14) | DS | 2.17 | S | mef(A), tet(M) | aroE, gki, spi, xpt, ddl | 106421 | – | + | + | + |
| 12_3506 | 2012 | GRM | S (19) | DNS | 2.12 | I | – | ST11884 (7 loci) | 106415 | – | + | + | + |
| 12_6178 | 2012 | SUW | S (19) | DS | 2.19 | S | – | aroE, gdh, gki, xpt, ddl | 106423 | – | + | + | + |
| 13_3874^ | 2013 | WRO | S (18) | DS | 2.20 | ND | – | aroE, gki, spi, ddl | 106427 | – | + | + | + |
| 14_4477 | 2014 | OTW | S (25) | DS | 2.17 | S | ParC[S79I] | aroE, gdh, xpt | 106428 | – | + | + | – |
| 15_1290 | 2015 | SUW | S (21) | DS | 2.22 | S | – | aroE, gdh, gki, ddl | 106429 | – | + | + | + |
| 15_1969 | 2015 | PLO | S (21) | DS | 2.18 | S | – | aroE, gdh, gki, xpt | 106426 | – | + | + | – |
| 15_2001 | 2015 | SUW | S (23) | DS | 2.22 | S | erm(B), tet(M) | aroE, gki, recP, spi, ddl | 106430 | – | + | + | + |
| 15_2100 | 2015 | SUW | S (20) | DS | 2.14 | I | erm(B), tet(M) | ST11884 (7 loci) | 106431 | – | + | + | + |
| 15_2741 | 2015 | RUS | S (22) | DS | 2.19 | I | erm(B), tet(M) | aroE, gki, recP, spi, ddl | 106432 | – | + | + | + |
| 596553-like* | |||||||||||||
| k_402 | 1995 | MKM | S (19) | DS | 2.08 | S | – | – | 106389 | – | + | – | – |
| k_432 | 1995 | SUW | S (25) | DS | 2.10 | I | – | – | 106389 | – | + | – | – |
| k_628 | 1997 | RAB | S (26) | DS | 2.19 | R | tet(M) | spi | 23934 | – | + | – | – |
| 00_68 | 2000 | WAW3 | S (22) | DNS | 2.11 | S | [erm(B), tet(M)] | spi | 106401 | – | + | – | – |
| 01_544 | 2001 | SCH | S (26) | DNS | 2.17 | I | – | gdh | 106404 | – | – | – | – |
| 03_202 | 2003 | GDA | S (25) | DS | 2.19 | S | – | gdh | 23926 | – | + | – | – |
| 03_563 | 2003 | WAW2 | S (23) | DS | 2.22 | S | erm(B), tet(M) | gdh, recP, ddl | 23929 | – | + | – | – |
| 03_2579 | 2003 | BYD | S (26) | DS | 2.15 | I | erm(B), tet(M) | gdh, ddl | 106408 | – | + | – | – |
| 04_3705 | 2004 | GDA | S (26) | DNS | 2.03 | S | ParC[S79R] | – | 23930 | – | + | – | – |
| 04_4094 | 2004 | GDA | S (28) | DS | 2.23 | I | [erm(B)], tet(M) | gdh, ddl | 23924 | – | + | – | – |
| 07_1032 | 2007 | TOR | S (24) | DS | 2.23 | S | erm(B), tet(M) | gdh, recP, ddl | 106411 | – | + | – | – |
| 07_1449 | 2007 | BYD | S (24) | DS | 2.20 | I | mef(A) | ddl | 106413 | – | + | – | – |
| 07_3473 | 2007 | BYD | S (21) | DS | 2.00 | I | – | – | 106414 | – | – | – | – |
| 08_3109 | 2008 | POZ | S (27) | DS | 2.14 | R | erm(B), tet(M) | – | 106395 | – | – | – | – |
| 08_3851 | 2008 | WAW1 | S (25) | DS | 2.14 | I | erm(B), tet(M) | – | 106395 | – | – | – | – |
| 08_3894 | 2008 | POZ | S (27) | DS | 2.11 | I | erm(B), tet(M) | – | 106395 | – | – | – | – |
| 09_428 | 2009 | POZ | S (26) | DS | 2.13 | I | erm(B), tet(M) | – | 106395 | – | – | – | – |
| 09_2342 | 2009 | KSZ | S (21) | DNS | 2.00 | I | – | – | 23930 | – | + | – | – |
| 09_2785 | 2009 | POZ | S (25) | DS | 2.11 | R | erm(B), tet(M) | – | 106395 | – | – | – | – |
| 09_5004 | 2009 | SUW | S (15) | DS | 2.04 | I | – | – | 106399 | – | + | – | – |
| 10_8854 | 2010 | KSZ | S (27) | DS | 2.11 | I | erm(B), mef(A), tet(M) | – | 106425 | – | + | – | – |
| 11_1621 | 2011 | SUW | S (22) | DNS | 2.13 | I | – | recP | 106418 | – | – | – | – |
| 11_9903 | 2011 | SOS | S (20) | DS | 2.14 | R | – | ddl | 106419 | – | + | – | – |
| 12_53 | 2012 | KSZ | S (23) | DNS | 2.14 | I | erm(B), tet(M) | ddl | 106420 | – | + | – | – |
| 12_4886 | 2012 | KSZ | S (21) | DS | 2.25 | S | [erm(B)], tet(M) | – | 23948 | – | + | – | – |
| Other S. mitis-like* | |||||||||||||
| k_90 | before 1995 | NK | S (15) | DNS | 1.99 | S | – | gdh, recP, ddl | 106387 | – | – | – | – |
| k_163 | NK | S (14) | DNS | 1.98 | S | – | gdh, recP, ddl | 106387 | – | – | – | – | |
| 99_5346 | 1999 | BYD | S (25) | DS | 2.03 | R | mef(A), cat, tet(M) | gki | 106400 | – | + | – | – |
| 06_714 | 2006 | SOS | S (17) | DNS | 1.98 | S | mef(A) | – | 23956 | – | – | – | – |
| 06_959 | 2006 | WAW1 | S (18) | DNS | 2.08 | S | tet(M) | recP, spi | 106412 | – | – | – | – |
| 08_1453 | 2008 | KSZ | R (11) | DS | 2.18 | R | erm(B), mef(A), tet(M) | – | 23925 | – | + | – | – |
| S. oralis-like# | |||||||||||||
| 12_5905 | 2012 | SUW | S (18) | DNS | 1.85 | S | – | – | 44151 | – | – | – | – |
S, susceptible; I, intermediate; R, resistant; DS, deoxycholate-soluble; DNS, deoxycholate-nonsoluble; presumably silent erm(B) and tet(M) genes within square brackets; +, positive; −, none detected; ND, not determined due to the lack of growth under test conditions; invasive isolate 15_1969 from blood marked with grey background. BYD, Bydgoszcz; GDA, Gdańsk; GRA, Grajewo; GRM, Grodzisk Mazowiecki; KOL, Kołobrzeg; KSZ, Koszalin; LUB, Lublin; MKM, Maków Mazowiecki; OTW, Otwock; PLO, Płock; POZ, Poznań; RAB, Rabka; RUS, Ruda Śląska; SAN, Sanok; SCH, Sochaczew; SOS, Sosnowiec; SUW, Suwałki; TOR, Toruń; WAW, Warszawa; WRO, Wrocław; NK, not known
*Based on the core-genome analysis results (see also Fig. 2)
#Based on the rMLST and MLSA analyses (see also Fig. 1)
^Identified as S. mitis in MLSA (see also Fig. 1a)
|Identified as S. mitis in rMLST (see also Fig. 1b)