Table 2. Enzymes, efflux pumps, and mutations expected to confer resistance to antibiotics of clinical relevance^a.

Enzymeb	Gene location(s)	Coordinates	Resistance phenotype
NDM-1 (class B)	pNDM-US Tn125	122191–123003	Penicillins, cephalosporins, carbapenems, inhibitor-resistant
SHV-11 (class A)c	1. pKpn2146b	36313–37173	Penicillins, some cephalosporins, inhibitor-sensitive
	2. Chromosome	2612996–2613856
CTX-M-15 (class A)	1. pKpn2146b ISEcp1	47130–48005	Penicillins, some cephalosporins, aztreonam,
	2. Chromosome ISEcp1	5407530–5408405	inhibitor-sensitive
TEM-1 (class A)	pKpn2146b Tn2	50827–51687	Penicillins, some cephalosporins, inhibitor-sensitive
CMY-6 (class C)	pNDM-US ISEcp1	72203–73348	Penicillins, some cephalosporins, inhibitor-resistant
OXA-1 (class D)	pKpn2146b ΔIn37	38798–39673	Penicillins, inhibitor-resistant
AAC(3)-IIe	pKpn2146b	41116–41976	Gentamicin, tobramycin, netilmicin, sisomicin
AAC(6′)-Ib (43)	pNDM-US In46	115114–115737	Tobramycin, amikacin, netilmicin, sisomicin
AAC(6′)-Ib (1)	pKpn2146b ΔInTn1331	82745–83350	Tobramycin, amikacin, netilmicin, sisomicin
AAC(6′)-Ib-cr (29)	pKpn2146b ΔIn37	38113–38712	Tobramycin, amikacin, netilmicin, sisomicin, quinolones (low-level)
ANT(3″)-Ia	Kpn23SapB In127	2297711–2298502	Streptomycin, spectinomycin
APH(3″)-Ib (StrA)	pKpn2146b ISCR2	53244–54047	Streptomycin
APH(6)-Id (StrB)	pKpn2146b ISCR2	52408–53238	Streptomycin
Sul2	pKpn2146b ISCR2	54108–54923	Sulfonamides
RmtC	pNDM-US ISEcp1	120100–120945	Aminoglycosides (via rRNA modification)
Sul1	1. Kpn23SapB In127	2299007–2299846	Sulfonamides
	2. pNDM-US In46	116245–117084
DfrA14	pKpn2146b In191	8281–8754	Trimethoprim
QnrB9	pKpn2146b	26074–26742	Quinolones, fluoroquinolones
Mph(A)	pKpn2146c	16503–17408	Macrolides, Erythromycin
FosA	Chromosome	667960–668379	Fosfomycin
Efflux pump	Gene Location		Probable substrate(s)d
AcrAB-TolC	Chromosome	1249681–1254043	Aminoglycosides, β-lactams, tigecycline, macrolides
AcrEF-TolC	Chromosome	4936203–4940465	Minor role
EefABC	Chromosome	5354323–5329922	Chloramphenicol, tetracyclines, ciprofloxacin
MacAB-TolC	Chromosome	1857393–1860445	Macrolides
MdfA	Chromosome	1781588–1782820	Aminoglycosides, fluoroquinolones, chloramphenicol
MdtG,H,K,L,M,NOP	Chromosome	e	Many possible substrates (MFS superfamily pumps)
OqxAB	Chromosome	4169609–4173960	Chloramphenicol, fluoroquinolones, trimethoprim
EmrAB	Chromosome	4218886–4221612	Nalidixic acid, hydrophobic compounds
TetA(A)	pKpn2146c Tn1721	19168–20367	Tetracyclines
Gene	Mutation		Resistance phenotype
gyrA Gyrase	Ser83TTC → IleATC	3763583–3766216	Quinolone, fluoroquinolones
parC Topo IV	Ser80AGC → IleATC	4689294–4691552	Quinolone, fluoroquinolones
nfsA Nitroreductase	Frameshift	1826275–1826998	Nitrofurantoin

^aExcluding the resistance enzyme for bleomycin, an antibiotic used clinically only as an antitumor agent.

^bVariant number from Table 1 of Ramirez et al. [37] is used to distinguish the AAC(6′)-Ib variants.

^cTwo silent differences between the two copies.

^dProbable efflux substrates identified from literature sources including ARDB; the substrates list is not comprehensive and in many cases has been deduced from organisms other than K. pneumoniae.

^eMdt genes are scattered over the chromosome.