Table 2.
List of mutations identified by WGS in ciprofloxacin-resistant S. pneumoniae
| Gene IDa | Gene function | Mutationb,c,d |
||
|---|---|---|---|---|
| R6M2B | T5-R6M2B | T1-60827e | ||
| spr0084 | Conserved hypothetical protein | RSS1 | ||
| spr0085 | Hypothetical protein | RSS1 | ||
| spr0086 | Hypothetical protein | RSS1 | ||
| spr0129 | Hypothetical protein | G-3T | ||
| spr0291 | Phosphotransferase system (PTS system) IIA component | RSS2 | ||
| spr0309 | Hypothetical protein | RSS3 | ||
| spr0310 | Alpha-1-6-glucosidase | RSS3 | ||
| spr0335 | 6-Phosphogluconate dehydrogenase | G1246C | ||
| V416L | ||||
| spr0757 | DNA topoisomerase IV subunit A | C245T | C245T | |
| S79F | S79F | |||
| spr0931 | Conserved hypothetical protein | RSS4 | ||
| spr0952 | Hypothetical protein | 12-nucleotide deletion downstream | ||
| spr0974 | Phosphoenolpyruvate carboxylase | RSS5 | ||
| spr0981 | Glycosyltransferase | RSS6 | ||
| spr1039 | Second subunit of major exonuclease | RSS7 | ||
| spr1099 | DNA gyrase subunit A | G247A | G247A | |
| E85K | E85K | |||
| spr1248 | Conserved hypothetical protein | RSS8 | ||
| spr1249 | Alpha-acetolactate decarboxylase | RSS8 | ||
| spr1250 | Conserved hypothetical protein | RSS8 | ||
| spr1251 | ABC transporter substrate-binding protein; glutamine-binding protein | RSS8 | ||
| spr1544 | Preprotein translocase subunit SecA | A-28G | ||
| spr1545 | Hypothetical protein | RSS9 | ||
| spr1885 | ABC transporter ATP-binding/membrane-spanning protein—unknown substrate | RSS10 | ||
| spr1886 | Degenerate transposase | RSS10 | ||
| spr1887 | ABC transporter ATP-binding/membrane-spanning protein—unknown substrate | RSS10 | ||
| spr1902 | NAD(P)H-dependent glycerol-3-phosphate dehydrogenase | C248T | RSS11 | |
| T83I | ||||
| spr1919 | ABC transporter membrane-spanning permease—maltose/maltodextrin | RSS12 | ||
| spr1945 | Choline-binding protein | RSS13 | ||
| spr1946 | Degenerate transposase (orf1) | RSS13 | ||
| spr1979 | d-Alanine transfer from undecaprenol-phosphate to the poly(glycerophosphate) chain | RSS14 | ||
| spr1981 | d-Alanine transfer from Dcp to undecaprenol-phosphate | RSS14 | ||
| spr1982 | d-Alanine-d-alanyl carrier protein ligase | RSS14 | ||
| spr1983 | Hypothetical protein | RSS14 | ||
| spr1988 | Glycerol uptake facilitator protein | RSS15 | ||
| spr1989 | Glycerol-3-phosphate dehydrogenase, truncation | RSS15 | ||
| spr1990 | Glycerol-3-phosphate dehydrogenase, truncation | RSS15 | ||
a
ID, identity. Nomenclature according to the genome annotation of S. pneumoniae R6.
b
When mutations are within coding regions, the change in amino acids is also indicated in italics.
c
In noncoding sequence, the number preceded by a hyphen indicates the position upstream of the ATG.
d
Mutations in bold were further studied to determine their potential role in CIP resistance.
e
Mutations in bold RSSs have been confirmed in the parental isolate 60827.