Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia

Abstract

BackgroundThe nexus between resistance determinants, plasmid type, and clonality appears to play a crucial role in the dissemination and survival of carbapenem-resistant Klebsiella pneumoniae (CRKP). The incidence of infections involving CRKP in Saudi Arabia is increasing and there is a need for detailed molecular profiling of this pathogen for CRKP surveillance and control.MethodsThe resistance determinants of 71 non-redundant CRKP isolates were investigated by polymerase chain reaction (PCR) and sequencing. Plasmid typing was performed using PCR-based replicon typing and the clonality of isolates was determined by multilocus sequence typing. Capsular polysaccharide synthesis genes and other virulence factors were examined using multiplex PCR. Diversity was calculated using DIVEIN, clonal relationship was determined using eBURST, and phylogenetic analysis was performed using SplitsTree4.ResultsA polyclonal OXA-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by NDM-1 alone in 9/71 (12.7%) isolates. Coproduction of OXA-48 and NDM-1 was observed in 6/71 (8.5%) isolates. Both carbapenemase genes could be transferred into an Escherichia coli recipient. CTX-M-15 was the most abundant extended-spectrum β-lactamase gene detected in 47/71 (66.2%) isolates, whereas clone-specific CTX-M-14 (ST-199 and -709) was found in 15/71 (21%) isolates. Sixty-seven of 71 isolates were positive for one or more plasmid replicons. The replicons detected were: IncFII; IncFIIK; IncFIA; IncFIB; L/M; IncI1; and IncN. FIIK and L/M were predominant, with 69 and 67% positivity, respectively. All isolates were negative for the magA (K1), rmpA, and K2 genes and presented a non-hypermucoviscous phenotype.ConclusionA polyclonal CRKP reservoir of sequence types (STs)-37, − 199, and − 152 was observed and ST-152 appeared to be a “frequent carrier” of the NDM-1 gene. ST-199, a singleton not previously reported, showed a sequence diversity suggestive of positive selection. A significant association was evident between resistance determinants and the clonal types of K. pneumoniae: all ST-152 isolates were positive for NDM-1 but negative for OXA-48; ST-199 isolates were positive for OXA-48 but negative for NDM-1; and ST-709 and -199 isolates were positive for CTX-M-14. The incidence of certain clonal types in large numbers predicts an outbreak-like situation and warrants stringent surveillance and infection control.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3114-9) contains supplementary material, which is available to authorized users.

High contribution and impact of resistant gram negative pathogens causing surgical site infections at a multi-hospital healthcare system in Saudi Arabia, 2007–2016

“…On the other hand, the current rates were even lower than the extremely high rates of cephalosporin and carbapenem resistance among GNPs reported in some developing countries such as Egypt [13], India [29], and Iran [14]. The high rate of resistance in GNPs in the current study is probably reflecting a wide range of resistance mechanisms in GNPs observed in our hospitals, such as NDM, OXA 48 and MGrb and outer membrabe protein (OMP) resistance [30][31][32][33][34]. The high rate of resistance in GNPs in the current study is quite alarming as it already increased the mortality by 25%.…”

High Contribution and Impact of Resistant Gram Negative Pathogens Causing Surgical Site infections at a Multi-Hospital Healthcare System in Saudi Arabia, 2007-2016

“…On the other hand, the current rates was even lower than the extremely high rates of cephalosporin and carbapenem resistance among GNPs reported in some developing countries such as Egypt [20], India [36], and Iran [21]. The high rate of resistance in GNPs in the current study is probably reflecting a wide range of resistance mechanisms in GNPs observed in our hospitals, such as NDM, OXA 48 and MGrb and outer membrabe protein (OMP) resistance [37][38][39][40][41]. The high rate of resistance in GNPs in the current study is quite alarming as it already increased the mortality by 25%.…”

The Inc FII Plasmid and its Contribution in the Transmission of blaNDM-1 and blaKPC-2 in Klebsiella pneumoniae in Egypt

“…Another study done by Al-Marzooq et al [40] reported that the most common plasmid replicons were IncR and IncL/M. Moreover, a high incidence of conjugative FIIK (69%) and L/M plasmids (66%) found in CPKP isolates were reported in Saudi Arabia [41].…”