Characterization of an IMP-4-Producing Klebsiella pneumoniae ST1873 Strain Recovered from an Infant with a Bloodstream Infection in China

Purpose Imipenemase (IMP), an Ambler class B metallo-β-lactamase, is an important carbapenemase that confers resistance to almost all β-lactams. In this study, we characterized the genomic feature of an IMP-4-producing Klebsiella pneumoniae ST1873 strain, a rare sequence type (ST) isolated from an infant with a bloodstream infection in China. Patients and Methods K. pneumoniae strain, BKP19, was collected from a bloodstream infection in an infant who was hospitalized at the department of paediatrics. The whole genome sequence of the strain was sequenced using the Illumina NovaSeq 6000 platform and long-read MinION sequencer. Multilocus sequence typing, antimicrobial resistance gene identification, plasmid and phylogenetic relationship analysis of the strain were analysed by various bioinformatics approaches. Results K. pneumoniae BKP19 was resistant to multiple antimicrobials, including carbapenems. Eleven antimicrobial resistance genes corresponding to beta-lactam resistance, quinolone resistance, phenicol resistance and fosfomycin resistance could be identified in the genome. The carbapenem resistance gene blaIMP-4 was located in an IS26-associated class 1 integron of an IncN-type plasmid with 39,033 bp (pIMP-4-BKP19). Sequence alignment revealed that pIMP-4-BKP19 is closely related to the common plasmid carrying IMP-4 in K. pneumoniae (pIMP-HZ1-like plasmid) but is smaller, lacking the quinolone resistance gene qnrS1 and multiple tra gene orthologs. Conjugation experiment revealed that pIMP-4-BKP19 is a non-conjugative plasmid. According to in silico MLST analysis, K. pneumoniae strain BKP19 belongs to a sporadic clone ST1873. Conclusion In summary, our study reports the first genome sequence of a K. pneumoniae ST1873 strain harbouring the class B β-lactamase blaIMP-4 in an IncN-type plasmid recovered from an infant with a bloodstream infection in China. Considering the global emergence of IMP-4 carbapenemase, more attention must be paid to prevent its future prevalence.


Introduction
Klebsiella pneumoniae is an important pathogen of the Enterobacteriaceae family that causes a variety of infectious diseases, including pneumonia, liver abscesses, urinary tract infections and bacteraemia. The emergence of carbapenem-resistant K. pneumoniae (CRKP) leaving few therapeutic options available. Imipenemase (IMP), an Ambler class B metallo-β-lactamase, is an important carbapenemase that confers resistance to almost all β-lactams. One of the most commonly observed IMP variants is IMP-4, which was firstly detected in Acinetobacter spp. in Hong Kong in 2001. 1 Since then, IMP-4-type carbapenemases have spread globally. [2][3][4][5] The bla IMP-4 gene is often integrated in broad-host-range conjugative plasmids and is transferred between different Gram-negative bacilli (eg, Enterobacteriaceae, Acinetobacter spp., Pseudomonas aeruginosa). 1,[5][6][7][8] The horizontal transfer of bla IMP-4 in these plasmids is frequently associated with class 1 integrons. 9,10 Plasmid-borne bla IMP-4 has been sporadically reported in different Gram-negative bacilli in China. 6,[11][12][13] However, only a few studies have reported the complete sequence of bla IMP-4 -harbouring plasmids, 6,10,14 which limits our understanding of the transmission mechanism of bla IMP-4 between different Gram-negative bacilli.
Klebsiella pneumoniae carbapenemase (KPC) has emerged as the predominant carbapenemase in K. pneumoniae in China, while there are relatively few IMP-4 producing strains. 15 Carbapenemase IMP is often distributed among multiple STs in K. pneumoniae, especially some rare STs.
In this study, the IMP-4-producing K. pneumoniae strain BKP19 was collected from a bloodstream infection in an infant who was hospitalized at the department of paediatrics. The isolate was preliminarily identified using the VITEK MS system (bioMérieux, France) and was further confirmed by 16S rRNA gene sequencing. The whole genome of the strain was sequenced. The bla IMP-4 -harbouring plasmid and genetic characteristics of the strain were analysed to gain a better understanding of the transmission mechanism of bla IMP-4 .

Patient and Isolate
A female neonate with a birth weight of 1.13 kg was hospitalized at the department of paediatrics half an hour after preterm delivery at a tertiary hospital in Hangzhou, Zhejiang Province, China. During her hospitalization, the neonate received multiple antimicrobial treatments, including cefotaxime, erythromycin, vancomycin and meropenem. Carbapenem-resistant K. pneumoniae was isolated from a blood sample from the patient one month later after her hospitalization. The isolate was preliminarily identified using the VITEK MS system (bioMérieux, France) and was further confirmed by 16S rRNA gene sequencing.

Antimicrobial Susceptibility Test
Antimicrobial susceptibility testing was conducted using the VITEK 2 system (bioMérieux, France) with Gram-negative antimicrobial susceptibility testing cards (AST-GN16) and the Etest method following the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Antimicrobial susceptibility was determined using the breakpoints approved by the CLSI. 16

Whole-Genome Sequencing
The genomic DNA of the isolate was extracted using a QIAamp DNA Mini Kit (Qiagen, USA). The Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA) and a long-read MinION sequencer (Nanopore, Oxford, UK) were used for whole-genome sequencing. The de novo hybrid assembly of both short Illumina reads and long MinION reads were performed using Unicycler. 17 The wholegenome sequence was automatically annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server.

Multilocus Sequence Typing and Antimicrobial Resistance Gene Identification
Multilocus sequence typing (MLST) and the identification of antimicrobial resistance genes and plasmid replicons were performed using the BacWGSTdb server. 18

Plasmid Analysis
The graphical circular map of the bla IMP-4 -carrying plasmid was converted by the CGView Server. 19 The comparisons between the bla IMP-4 -carrying plasmid and similar plasmids were conducted by using the BLAST Ring Image Generator (BRIG) in concentric rings. 20 The comparison of the bla IMP-4 -carrying plasmid with the most closely related plasmid was performed by EasyFig 2.2.3. 21

Conjugation Experiment
The transfer capacity of the bla IMP-4 -harbouring plasmid was investigated in a conjugation experiment. 22 Rifampicinresistant E. coli EC600 was used as the recipient, and strain BKP19 was used as the donor. The donor and recipient bacteria were cultured in MH broth for 4 hrs. Aliquots of 100 μL of each cultured donor and recipient bacterium were mixed together. A 40 μL aliquot of the mixture was spotted on a sterile filter membrane, which was placed on a Muller-Hinton (MH) agar plate, followed by incubation at 35°C for 18 h. The bacteria were washed from the filter membrane, and bla IMP-4 -positive E. coli transconjugants were selected on MH agar plates supplemented with rifampicin (800 mg/L) and imipenem (8 mg/L).

Phylogenetic Analysis
The phylogenetic relationship between BKP19 and other K. pneumoniae strains retrieved from the NCBI GenBank database was analysed using the BacWGSTdb server. 18,23 The BacWGSTdb server offers core genome Multilocus Sequence Typing (cgMLST) and single nucleotide polymorphism (SNP) approaches to investigate the phylogenetic relationship of the uploaded genome sequence with sequences deposited in the database. The database currently contains 7480 K. pneumoniae strains.

Nucleotide Sequence Accession Numbers
The results of this whole-genome shotgun project have been deposited at DDBJ/EMBL/GenBank under accession number VWRO00000000. The version described in this paper is the first version.

Ethical Approval
This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of Zhejiang Provincial People's Hospital. Written informed consent from the patient was exempted by the Ethics Committee of Zhejiang Provincial People's Hospital because the present study only focused on bacteria. The clinical isolate K. pneumoniae BKP19 was part of the routine hospital laboratory procedure.

Results and Discussion
The MICs of the antibiotics tested are presented in Table 1. K. pneumoniae BKP19 was resistant to multiple antimicrobials, including cefazolin, ceftriaxone, cefepime, cefoxitin, imipenem, meropenem, ciprofloxacin and levofloxacin. This strain was susceptible to aminoglycosides, aztreonam, tigecycline and colistin.
pIMP-4-BKP19 is an IncN-type plasmid that comprises 39,033 bp. The circular map of pIMP-4-BKP19 is presented in Figure 1. It contains conserved IncN-type backbone regions that contain a replication gene and its accessory structure for plasmid replication. The tra genes (traB, traK and traM) for conjugal transfer, the stbABC operon for plasmid maintenance, the ardA, ardK and ardR genes with an antirestriction function and the mucAB operon for UV protection were identified in the plasmid backbone. The  gene was located in an IS26-associated class 1 integron, preceded by IS26-intI1 in the upstream region and followed by another IS26 sequence in the downstream region. The similarity of pIMP-4-BKP19 to other bla IMP-4 -carrying plasmids was analysed with the Basic Local Alignment Search Tool (BLASTN). Several similar bla IMP-4 -carrying plasmids were found in the NCBI GenBank database (Figure 2). The most common type of plasmid carrying IMP-4 in K. pneumoniae that has been reported to date is a pIMP-HZ1-like IncN-type plasmid with a size of approximately 50 kb (eg, K. pneumoniae strain Kp1 plasmid pIMP-HZ1, accession no KU886034, 51,599 bp; K. pneumoniae strain 24,854 plasmid p24854-IMP, accession no. MH909341, 51,393bp), 14 these plasmids also carry the quinolone resistance gene qnrS1. The structural characteristics of pIMP-4-BKP19 compared to pIMP-HZ1 and p24854-IMP are presented in Figure 3. The structure of the pIMP-4-BKP19 plasmid is very similar to these two plasmids, with >99% query coverage and >99% nucleotide identity, but pIMP-4-BKP19 is smaller than the other plasmids (only 39,033 bp). There are three major genetic differences between the backbones of pIMP-4-BKP19 and the pIMP-4-BKP19 39,033 bp pIMP-HZ1-like plasmids. First, a segment downstream of bla IMP-4 is shortened and reversed, with an IS26 mobile element occurring on each side of the segment. The reduced sequence mainly includes genes encoding the tra gene orthologs (traC, traE, traF and traG). Second, the quinolone resistance gene qnrS1 is absent. There are insertion elements on both sides of the qnrS1 gene in the pIMP-HZ1-like plasmid. It is likely that the qnrS1 gene was introduced into the IncN plasmid through these insertion elements. Third, some nucleotide sequences downstream of ISKpn19 are absent. Conjugation experiment revealed that pIMP-4-BKP19 is a non-conjugative plasmid. According to the in silico MLST analysis, K. pneumoniae strain BKP19 belongs to sequence type (ST) 1873, which is a very rare ST. IMP often appears in some rare STs (eg, ST476, ST2270, ST37, ST107, ST133, ST323, ST686, ST1114) in K. pneumoniae. 6,10,12,24 We analysed the genome data in the NCBI GenBank database (accessed on 10 December 2019) and found that no ST1873 K. pneumoniae sequences are currently available in the database. We then further analysed the similar isolates with the threshold of 2000 (based on the cgMLST strategy) in BacWGSTdb. Fifteen phylogenetically related K. pneumoniae strains could be found in the database (Table S1). The strain closest to BKP19 was K. pneumoniae PN089E1 (ST2958) isolated from Cameroon in 2016 with 1610 different alleles.
Here, we report the first genome sequence of a K. pneumoniae ST1873 strain harbouring the class B β-lactamase bla IMP-4 recovered from an infant with a bloodstream infection in China. Comprehensive analysis of the bla IMP-4 -carrying plasmid revealed that it was an IncN-type plasmid that has variant region within the integron mediated by IS26. Plasmids belonging to the IncN type commonly exhibit a broad host range and high transmission efficiency. 6 It seems that the IS26-associated class 1 integron contributes to the dissemination of IMP-4 in different plasmids and that the IS26 mobile element plays an important role in the recombination of plasmid backbones. Our data may help to understand the genomic features of this bacterial pathogen. The genome sequence of K. pneumoniae BKP19 can be used as a reference sequence for comparative genomic analysis to obtain a better understanding on the transmission mechanism of bla IMP-4 .

Conclusion
Our study reports the first genome sequence of a K. pneumoniae ST1873 strain harbouring the class B β-lactamase bla IMP-4 in a IncN-type plasmid recovered from an infant with a bloodstream infection in China. Considering the global emergence of IMP-4 carbapenemase, more attention must be paid to prevent its future prevalence.

Acknowledgments
This study was supported by grants from the National Natural Science Foundation of China (81702042), Natural  Figure 3 Comparative analysis of the homologous regions shared by three IncN-type plasmids (pIMP-4-BKP19, p24854-IMP and pIMP-HZ1). The plasmids were annotated by Rapid Annotation using Subsystem Technology (RAST) server. The figure was produced using EasyFig v. 2.2.3, and BLASTN was used to compare sequence homology with the following threshold parameters: minimum length of 100 bp accompanied by 90% identity. Antimicrobial resistance genes are indicated in red, IS elements are indicated in purple, and all other genes are indicated in blue.
Science Foundation of Zhejiang Province (LQ19H200003) and the Zhejiang Provincial Medical and Health Science and Technology plan (2018KY344 and 2019KY311).