Genomic Analysis Of A KPC-2-Producing Klebsiella Pneumoniae ST11 Outbreak From A Teaching Hospital In Shandong Province, China

Figures & data

Figure 1 MICs were determined by agar dilution methods for all antibiotics except for colistin and tigecycline, for which broth microdilution was used. Results were interpreted using the CLSI guidelines. Pink indicates resistance, blue indicates mediation, and light yellow indicates sensitivity.

Table 1 Antibiotic Resistance Genes, STs, Plasmid Type And Plasmid Size Of KPC-Producing K. Pneumoniae Isolates

Isolate	Source	Antibiotic Resistance Genes	MLST	Plasmid Type	Plasmid Size
2C1	Sputum	blaCTX-M-65, fosA6, sul2, aph(3’’)-Ib, aph(6)-Id, blaSHV, blaCTX-M-3, qnrS1, sul1, aph(3’)-Ia, qnrB2, aac(3)-Iid, mph(A), aadA16, dfrA27, ARR-3, aac(6’)Ib-cr	ST11	IncFIIK2	94 kb
3C1	Sputum	dfrA1, ant(3’’)-Ia, erm(42), ant(3’’)-Ia, sul1, sul2, blaSHV-11, fosA6	ST11	IncFIIK2	94 kb
3C2	Sputum	rmtB, blaTEM-1B, blaSHV-11, blaCTX-M-65, fosA6, ant(3’’)-Ia, sul1	ST11	IncFIIK2	140 kb
3C3	Sputum	blaCTX-M-65, oqxA, oqxB, blaTEM-1B, rmtB, blaSHV-11, fosA3, fosA6, sul1, ant(3’’)-Ia, blaCTX-M-15	ST11	IncFIIK2	140 kb
3C9	Urine	blaSHV-11, fosA6, ant(3’’)-Ia, sul1, rmtB, blaTEM-1B, blaCTX-M-65	ST11	IncFIIK2	138.9 kb
3C11	Sputum	mph(A), aph(6)-Id, aph(3’’)-Ib, sul2, tet(A), fosA6, catA2, blaCTX-M-65, dfrA12, aadA2, sul1, blaSHV-11, blaTEM-1B, rmtB, aph(3’)-Ia	ST11	IncFIIK2	336.5 kb
3C17	Urine	erm(42), ant(3’’)-Ia, sul1, blaCMY-2, fosA3, blaCTX-M-65, blaTEM-1B, rmtB, dfrA1, sul2, fosA6	ST11	IncFIIK2	160 kb
3C18	Sputum	blaSHV-12, ant(3’’)-Ia, sul1, fosA6, rmtB, blaTEM-1B, blaCTX-M-65	ST11	IncFIIK2	135 kb
3C21	Urine	sul1, aadA2, dfrA12, blaSHV-11, blaCTX-M-65, aac(3)-Iid, fosA6	ST11	IncFIIK2	140 kb
3C23	Sputum	fosA3, sul1, aac(6’)Ib-cr, ARR-3, dfrA27, aadA16, aph(3’’)-Ib, aph(6)-Id, blaCTX-M-65, rmtB, sul2, aadA2, blaTEM-141, blaSHV-11, fosA6, oqxB, oqxA	ST11	IncFIIK2	368 kb
3C25	Sputum	aadA2, blaTEM-141, sul1, blaCTX-M-15, aac(6’)Ib-cr, ARR-3, dfrA27, aadA16, aph(6)-Id, aph(3’’)-Ib, rmtB, sul2, blaCTX-M-65, oqxA, oqxB, blaSHV-11, fosA3	ST11	IncFIIK2	140 kb
3C29	Urine	blaTEM-1B, rmtB, blaCTX-M-65, ant(3’’)-Ia, sul1, blaSHV-11, fosA6	ST11	IncFIIK2	150 kb
4C2	Urine	fosA3, fosA6, dfrA14, sul2, aph(3’’)-Ib, aph(6)-Id, qnrS1, sul1, aadA2, blaCTX-M-65, rmtB, blaTEM-1B, blaSHV-11	ST11	IncFIIK2	94 kb
4C5	Pus	blaSHV-11, rmtB, blaTEM-1B, sul1, ant(3’’)-Ia, blaCTX-M-65, fosA6, fosA3	ST11	IncFIIK2	150 kb

Figure 2 The genetic environment of the bla_KPC-2 gene in K. pneumoniae was isolated from clinical sources. The arrows represent the direction of transcription. The red open reading frame (ORF) indicates the bla_KPC-2 gene, the pink ORF indicates the mobile element, the yellow ORF indicates other resistance genes or enzymes and the gray ORF indicates other genes or genes of unknown function. (A) The genetic environment of bla_KPC-2 is similar in isolates 2C1, 3C1, 3C2, 3C9, 3C17, 3C18, 3C29 and 4C5. (B) The isolates 3C3, 3C23 and 3C25 all carry bla_KPC-2 and share the identical genetic environment surrounding the same gene. (C) The isolate 3C21 and the isolate 4C2 have the same genetic environment. (D) The genetic environment of the isolate 3C11 carrying the bla_KPC-2 gene.

Figure 3 SNP analysis of KPC-2-producing K. pneumoniae isolates, performed using kSNP. The maximum likelihood analysis of the core SNP matrix output for kSNP is performed in iTOL.