Supplementary Material

Table S1 Antibiotic resistance profile of K. pneumoniae strain KP58.

AntibioticsMIC(mg/

L)Interpretation

Ceftriaxonea ≥64 R

Cefepimea ≥64 R

Cefoxitina ≥64 R

Aztreonama ≥64 R

Piperacillin/tazobactama ≥128 R

Imipenemb >128 R

Meropenemb >128 R

Gentamicina ≥16 R

Tobramycina ≥16 R

Amikacina ≥64 R

Ciprofloxacina ≥4 R

Levofloxacina ≥8 R

Trimethoprim/Sulphamethoxazolea ≥16/304 R

Nitrofurantoina ≥512 R

Tigecyclineb 8 R

Colistinb ≥64 RaTested by AST-GN16.bTested by broth microdilution method.

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Table S2 Information of closely related strains to K. pneumoniae KP58.

StrainGenome size (Mb)

HostCollection

YearIsolation source

Accession number

L462 5.77521 Homo sapiens 2016 Feces NLEF01L451 5.71018 Homo sapiens 2016 Feces NLEE01L350 5.79568 Homo sapiens 2016 Feces NLDR01L400 5.7792 Homo sapiens 2016 Feces NLEA01L511 5.81278 Homo sapiens 2017 Feces NLEL01L513 5.81039 Homo sapiens 2017 Feces NLEM01L531 5.81895 Homo sapiens 2017 Feces NLEU01L256 5.81114 Homo sapiens 2016 Feces NLDM01K28 5.89302 Homo sapiens 2017 Sputum QOVH01L39 5.80805 Homo sapiens 2016 Feces NLDZ01L20 5.82712 Homo sapiens 2016 Feces NLDG01L30 5.81238 Homo sapiens 2016 Feces NLDP01L31 5.80468 Homo sapiens 2016 Feces NLDQ01

L39_2 5.91047 Homo sapiens 2018 Feces CP033954ZWH170 5.71482 Homo sapiens 2017 Feces QMKA01ZWH183 5.85121 Homo sapiens 2017 Feces QMKB01

K321 5.77889 Homo sapiens 2016 Blood QRCG01K293 5.77694 Homo sapiens 2017 Ascites QRCF01K287 5.77683 Homo sapiens 2016 Blood QRCE01K280 5.77437 Homo sapiens 2016 Blood QRCD01K410 5.7752 Homo sapiens 2016 Ascites QRCH01

BJCFK909 5.87181 Homo sapiens 2018 Sputum CP034123KP58 5.48386 Homo sapiens 2018 Urine CP041373QJJ36 5.80949 Homo sapiens 2016 Blood NOVA01QJJ51 5.83153 Homo sapiens 2016 Blood NOVC01

sklx33367 5.84045 Homo sapiens 2015 Blood NXEE01sklx33229 5.69537 Homo sapiens 2015 Blood NXED01

L388 5.94539 Homo sapiens 2016 Feces CP029220L182 5.77121 Homo sapiens 2016 Feces NLDE01

XPY207 5.80717 Homo sapiens 2016 Blood NXNH01XPY20 5.77634 Homo sapiens 2016 Blood PCFS01XPY166 5.8102 Homo sapiens 2016 Blood PCFR01

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Figure S1 Quality assessment and quality control (QC) metrics of the raw sequence data.

(A) Distribution of quality scores (Q value) for the Illumina HiSeq sequencing data. (B)

Distribution of read-over-read quality for Illumina HiSeq sequencing. (C) Histogram of read

lengths for Nanopore sequencing. (D) Read lengths vs average read quality plot for

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Nanopore sequencing.13

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Figure S2 Circular representation of the genome of K. pneumoniae KP58. (A) Chromosome.

(B) - (F) Plasmids. The two outermost blue circles (rings 1 and 2) represent the annotated

protein-coding sequence (CDS) features on the forward and reverse strands, respectively.

The black circle (ring 3) indicates the GC content (%), and the purple/green circle (ring 4)

represents the GC skew.

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