1 | Introduction
Klebsiella variicola
( K. variicola), a
Gram-negative and facultative anaerobic bacillus, belongs to theKlebsiella genus of the Enterobacteriaceae family [1].
Such bacteria have been found in human, animals, insects, plants, and
environments [2-4]. K. variicola infections can cause a
series of human diseases, such as bloodstream infections, respiratory
tract infections, and neonatal sepsis [5-7]. Moreover, bloodstream
infections due to K. variicola harbored a higher 30-day mortality
rate than its notorious relative,Klebsiella
pneumoniae (K.
pneumoniae ) [8]. Notably, most cases caused by K.
variicola infections were often misidentified as being infected withK. pneumoniae because of their high similarities in biochemical
and phenotypic features, which leads to the underestimation of the real
prevalence of K. variicola infections in clinical practice
[9]. Additionally, K. variicola could cause bovine mastitis
and affect the milk production and quality [10].
With the misuse and abuse of
antibiotics in clinical and agriculture environments, the last few years
has witnessed the rapid increase of
multidrug-resistant
(MDR) K. variicola strains
[11-13]. Accumulating evidence has reported that MDR K.
variicola strains were detected in several countries, such as USA,
Australia, Tanzania, Germany and China [3,
14].
Horizontal
gene transfer (HGT) is deemed as
the main mechanism for the transmission of
antibiotic resistance genes
(ARGs), in which plasmid serves a
vector role. It has been documented that K. variicola harbored an
open genome and shared similar plasmid types with other members of theKlebsiella genus, especially K. pneumoniae, thereby
indicating frequent plasmid-mediated HGT among these species [1,
15]. In particular, ARGs-related IncFIBk,
IncFIIk and IncFII replicons were often shared betweenK. variicola and K. pneumoniae [16, 17].
The clustered regularly
interspersed short palindromic repeats
(CRISPR) and
CRISPR-associated genes
constitute an RNA-guided adaptive immunity system
(CRISPR/Cas system), which
protects bacteria against HGT of
mobile
genetic elements (MGEs), such as
plasmids and phages [18]. CRISPR/Cas system is composed of three
main parts: i) CRISPR loci that consist of several non-contiguous
direct repeats
(DRs) separated by stretches of
variable sequences called as spacers; ii) a group of cas genes
essential for adaptive immunity; iii) the leader sequence that acts as
the promoter [19]. Generally, the CRISPR/Cas system operates in
three stages: adaptation, expression, and interference [20]. During
adaptation, a fragment of foreign DNA is captured and integrated into
CRISPR array in an ordinal manner, thus forming a new R-S unit.
Subsequently, the R-S unit is transcribed into
precursor CRISPR RNA
(pre-crRNA), which is then
processed to produce a mature
CRISPR RNA
(crRNA). Upon subsequent
infection, the crRNA targets and recognizes complementary DNA sequence
to degrade exogenous genes with the guide of Cas protein. According to
the content of cas genes, two classes, six types, and over 45
subtypes of CRISPR/Cas systems have been identified [21]. Class I
CRISPR/Cas systems (type I, III, and IV) rely on heteromeric
multi-protein effector complexes, whereas class 2 systems (type II, V,
and VI) depend on single multi-domain effector proteins, such as Cas9,
Cpf1, and C2c2 [22]. In addition to the adaptive immunity,
CRISPR/Cas system performs several other biological roles, including
regulating gene expression, and participating in DNA repair and genomic
evolution [23-25]. Several studies have explored the diversity of
CRISPR/Cas systems in multiple species, including Bifidobacterium[26], Escherichia coli [27], and even the relatives toK. variicola, K. pneumoniae [28]. It has been demonstrated
that K. pneumoniae mainly carried type I-E, I-E* and IV-A
CRISPR/Cas systems, which played different roles in the dissemination of
antibiotic resistance in K. pneumoniae [29]. AlthoughK. variicola is becoming another species of concern afterK. pneumoniae in Klebsiella genus due to its ability to
acquire and spread ARGs, little is known about the role of CRISPR/Cas
system in this species.
Here, we employed a genome mining approach to analyze the
characterization of the CRISPR/Cas system in K. variicolastrains, explore the association between CRISPR evolution and MLST
(multiple locus sequence typing), and discussed the potential role of
CRISPR/Cas system in ARGs spread.