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Table 1 Genetic mechanisms of antibiotic resistance in bacteria isolated from the patient throughout hospital course

From: Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report

Specimen/Organism/Date of collectionAntibiotic resistance phenotype by ASTGenotype/Resistance
Sequence typeΒ-lactam antibioticsAminoglycosidesQuinolonesMacrolidesGlycopeptidesOther drugs
MDRO screen
Enterococcus faecium
29/08/2018
AMP, LZD, GENS, VANC16; E. faecium
ST unknown
 aac(6′)-aph(2″)
ant(6)-Ia
parC 80I
gyrA 83Y
Erm (B), erm (T)VanHaxaph(3′)-III
Tet(L)
MDRO screen
Escherichia coli
29/08/2018
AMP, AMC, TZP, AZT, CXM, FEP, FOX, CAZ, CRO, CIP, LVX, GEN, ETP, IPM, MEM, SXTCP18; E coli ST410CMY-2
CTX-M-15
NDM-5
OXA-1
TEM-1B
aac(3)-IId, aac(6′)-Ib-cr
aadA5, aph(3″)-Ib
aph(6)-Id
aac(6′)-Ib-cr
gyrA 83 L
gyrA 87 N
parC 80I
  dfrA17
sul1, sul2
MDRO screen
Klebsiella pneumoniae
29/08/2018
AMK, AMP, AMC, TZP, AZT, CXM, FEP, FOX, CAZ, CRO, CIP, LVX, GEN, ETP, IPM, MEM, SXTCP19; K. pneumoniae ST2096CTX-M-15
OXA-1
OXA-232
SHV-28
TEM-1A
aac(6′)-Ib-cr
aadA2
armA
aac(6′)-Ib-cr
oqxAB
gyrA 83Y
gyrA 87G
parC 80I
  dfrA1, dfrA12, dfrA14
sul1
tet(L)
Urine
Enterococcus faecium
09/09/2018
AMP, LZD, GENS, VAN, CIP, NIT, TETC17; E. faeceum ST80 aac(6′)-aph(2″)
aph(3′)-III
gyrA 83I
parC 80I
erm(A), erm(B), erm(T)VanHAXtet(L)
Blood (PICC line)
Escherichia coli
26/03/2019
AMK, AMP, AMC, TZP, AZT, CFZ, CFL, CXM, FEP, FOX, CAZ, CRO, CIP, LVX, GEN, ETP, IPM, MEM, SXT, CZA, C/T, FOFCP48; E. coli ST405blaNDM-5
blaTEM-1B
aadA2gyrA 83 L
gyrA 87 N
parC 80I
erm(B) dfrA12
sul1
Blood
(peripheral)
Klebsiella pneumonaie
06/04/2019
AMK, AMP, AMC, TZP, AZT, CXM, FEP, FOX, CAZ, CRO, CIP, LVX, GEN, ETP, IPM, MEM, SXT, FOF, TGC, CSTC12; K pneumoniae ST395CTX-M-15
NDM-5
OXA-1
OXA-232
SHV-11
TEM-1B
aac(6′)-Ib-cr
aadA2
aph(6)-Id
rmtB
strA
aac(6′)-Ib-cr
oqxAB
gyrA 83I
parC 80I
erm(B) dfrA12
dfrA7
sul1
Blood
(port a cath)
Elizabethkingia meningoseptica
06/04/2019
AMK, AZT, FEP, CAZ, CRO, GEN, IPM, MEMC11R; E. meningosepticaB-14
GOB-1
    CME-2
  1. AMK amikacin, AMC amoxicillin-clavulanic acid, AMP ampicillin, SAM ampicillin-sulbactam, AZM azithromycin, ATM aztreonam, CFZ cefazolin, CFL cephalexin, FEP cefepime, CTX cefotaxime, FOX cefoxitin, CAZ ceftazidime, CZA ceftazidime-avibactam, C/T ceftolozane-tazobactam, CRO ceftriaxone, CXM cefuroxime, LEX cephalexin, CEF cephalothin, CHL chloramphenicol, CIP ciprofloxacin, CLR clarithromycin, CLI clindamycin, CST colistin, DOX doxycycline, ETP ertapenem, ERY erythromycin, FOF fosfomycin, GEN gentamicin, GENS gentamicin synergy, IPM imipenem, KAN kanamycin, LVX levofloxacin, LZD linezolid, MEM meropenem, NIT nitrofurantoin, OXA oxacillin, PEN penicillin, PIP piperacillin, TZP piperacillin-tazobactam, STR streptomycin, TET tetracycline, TGC tigecycline, TMP trimethoprim, SXT trimethoprim-sulfamethoxazole, VAN vancomycin
  2. *Bacterial whole genome sequencing (WGS) was performed as described in the supplemental methods and data were analyzed as described previously [4]