Klebsiella oxytoca is an anaerobic gram-negative bacterium living in the human nasopharynx and intestines, animal intestines, water, and soil [1]. As an important opportunistic pathogen of hospital infection [2], it can cause sepsis [3], urinary tract infections [4], respiratory diseases [5], meningitis [6], etc. Its pathogenicity is assigned to the production of cytotoxin, which mainly induces apoptosis by inhibiting DNA synthesis [2]. K. oxytoca is now the clinically prevalent pathogen, ranging from 2 to 24% [7]. Similarly to other populations of bacteria, K. oxytoca has also developed resistance to various antibiotics through several mechanisms, for example, enzyme degradation and effective removal by efflux pump [8]. Additionally, it can exchange the resistance genes carried by plasmids with other bacteria, leading to the outbreak of hospital infections and community-acquired human infections [2]. Four hundred ninety-two sequence types of K. oxytoca have been described (https://pubmlst.org/organisms/klebsiella-oxytoca; accessed 9 Sep 2022), and the pandemic of K. oxytoca is mainly associated with the clonal complex 2, which includes ST2, -9, -18, -19, -57, -58, -61, -63, -141, -154, -155, and − 176 [9]. According to the Institute of Clinical and Laboratory Standards (CLSI) guidelines, K. oxytoca strains are generally resistant to ampicillin and ticarcillin. In recent decades, the extensive use of antibiotics, immunosuppressants, and invasive surgery significantly increased the clinical isolation of multidrug-resistant K. oxytoca [7]. The emergence of drug-resistant strains has made clinical treatment extremely difficult, dramatically increasing mortality among infected patients [10]. World Health Organization (WHO) has suggested the carbapenem-resistant Klebsiella app. as one of the bacteria to develop new drugs. Various virulence factors, minimum nutritional requirements, and a high anti-microbial resistance rate have made this organism an extremely dangerous pathogen [2]. Due to the bacterium's high drug resistance level, the infection's treatment has become a considerable challenge, and the situation will worsen when the infected patients have immune hypofunction complications.
β-lactamases production is one of the effective mechanisms for gram-negative bacteria to resist β-lactams antibiotics drugs [11–13]. KPC-type β-lactamases belong to class A β-lactamases which have been extensively spread in Klebsiella app [14]. KPC-2, first described in 2003 in K. pneumonia isolates, has 99% identity with enzyme KPC-1 [15, 16]. KPC-producing bacteria are epidemic in several countries and are considered a significant cause of hospital-acquired infection [17–19]. So far, more than 20 different KPC variants have been distinguished, even though KPC-2 and − 3 are still the most common variants [20]. Generally, β-Lactamases hydrolyzed β-Lactam antibiotics by forming covalent acylase intermediates and deacidifying activated water molecules [21]. However, carbapenems are difficult to hydrolyze by most β-Lactamase owing to the slow hydrolysis speed of the acyl-enzyme intermediate [22]. KPC-2 β-lactamase, however, enables its carbapenem antibiotic resistance through rapid deacylation of covalent intermediates. This makes it unique among class A β-lactamases to resist clavulanic acid, sulbactam, and tazobactam, resulting in ineffective commercially available β-lactamase inhibitors [23, 24]. Resistance to extended-spectrum β-lactamases (ESBLs) is a significant clinical problem[12, 17, 25, 26].
Vietnam Extended Spectrum Beta-lactamase (VEB) enzyme, which belongs to minor ESBLs, first emerged in Southeast Asia in 1999, named VEB-1, produced by a Pseudomonas aeruginosa strain [27]. Since then, VEB-1 enzyme-producing isolates have been detected to be widely distributed throughout Asia and Europe [28]. BlaVEB−3 was first identified in China, encoded by an Enterobacter cloacae strain chromosome with ESBL activity. Compared to the VEB-1, amino acid changes in VEB-3 occurred at position 56 with 'Leu' replaced by 'Phe', located in the N-terminal sequence of the mature protein, and position 18 with the 'Ile' replaced by 'Val', located in the putative leader peptide sequence[29]. The VEB-type ESBLs promote resistance to cefepime, aztreonam, and ceftazidime but can be inhibited by clavulanate and avibactam [29]. Although many gene sequences contain blaVEB−3 in the gene database according to NCBI databases, its appearance was mentioned in a few articles.
Antibiotic resistance (AR) in bacteria is one of humanity's biggest threats, and plasmid plays a crucial role in disseminating antibiotic resistance among clinical pathogens[30]. IncF plasmid is a narrow-host-range plasmid limited by the host range of Enterobacteriaceae. This plasmid relies on both host-encoded and self-encoded factors for duplication[31]. It typically carries an additional replication subtype to facilitate replication initiation, aiming to help a wide range of host-wide replication. [32]. IncF plasmid pKpQIL in Klebsiella pneumoniae ST258 was first described by Villa and his colleagues [33]. After its initial description, IncF plasmids have been identified in countries where they mediate the transmission of blaKPC [34, 35]. A recent study by Zhou Ying et al. prompted that the pandemic of KPC-producing K. pneumoniae (CG258) is closely related to the absence of an I-E type CRISPR-Cas system[36]. This immune system can effectively hinder the invasion and existence of blaKPC-IncF plasmid in K. pneumoniae[37, 38]. IncC plasmid is a broad-host-range plasmid that exists in various strains, including Escherichia coli, Yersinia pestis, Salmonella enterica, etc.[39], and involved in the transmission of ESBLs and carbapenemases genes and mercuric ion resistance among Gram-negative bacteria [40]. Early studies suggested that the IncC group should be classified into type 1a, type 1b, and type 2 based on differences in the orf1832/orf1847 and rhs1/rhs2, i1, and i2 fragments and a short patch in the genome[41].
Here, we characterized a K. oxytoca strain YL6, which contains a complete I-E type CRISPR-Cas system, harboring two plasmids, the blaVEB−3 bearing IncC plasmid pYL6-1 and blaKPC−2 bearing IncFII plasmid pYL6-2.