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. 2017 Apr 11;111(4):166–175. doi: 10.1080/20477724.2017.1314069

Genome sequencing and comparative analysis of an NDM-1-producing Klebsiella pneumoniae ST15 isolated from a refugee patient

Tamara Salloum a, Harout Arabaghian a, Sahar Alousi a, Edmond Abboud b, Sima Tokajian a,✉
PMCID: PMC5498761  PMID: 28395597

Abstract

The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum β-lacatamase (ESBL) producing K. pneumoniae strains, is directly correlated with increased patient morbidity and mortality and prolonged hospitalization and costs. In this study, a comprehensive genomic analysis encompassing the resistomics, virulence repertoire and mobile genetic elements of an NDM-1 positive ESBL-producing K. pneumoniae EA-MEH ST15 isolated from a urine sample collected from a Syrian refugee was conducted. Illumina paired-end libraries were prepared and sequenced resulting in 892,300 high-quality reads. The initial assembly produced 329 contigs with a combined 5,954,825 bp and a 56.5% G+C content. Resistome analysis revealed the presence of several β-lactamases including NDM-1, SHV-28, CTX-M-15 and OXA-1 in addition to 18 other genes encoding for resistance, among which are aph(3′)-Ia, aac(6′)Ib-cr, armA, strB, strA and aadA2 genes. Additionally, five plasmids IncFIB(Mar), IncHI1B, IncFIB(pKPHS1), IncFIB(K) and IncFII(K) and four integrated phages were detected. In silico MLST analysis revealed that the isolate was of sequence type ST15. To our knowledge this is the first in-depth genomic analysis of a NDM-1 positive K. pneumoniae ST15 in Lebanon associated with the recent population migration. The potential dissemination of such MDR strains is an important public health concern.

Keywords: ESBL, MDR, Klebsiella pneumoniae, draft-genome sequencing, ST15, NDM-1, SHV-28, Middle East

Introduction

Klebsiella pneumoniae are non-motile, encapsulated, lactose-fermenting, Gram-negative, facultative anaerobic rods of the Enterobacteriacae family [1]. They have been linked to both community-acquired and nosocomial infections worldwide, especially in patients with diabetes mellitus, alcoholism [2], immunocompromised patients [3], and in intensive care units [4]. The escalating burden of antibiotic resistance and specifically the dissemination of extended-spectrum β-lactamases (ESBLs) producing K. pneumoniae strains are directly correlated with increased patient morbidity and mortality [5], prolonged hospitalization time and costs [6]. ESBLs confer antimicrobial resistance against a wide range of β-lactams such as penicillins, aztreonam, and second and third generation cephalosporins [7].

Carbapenemases-producing K. pneumoniae is a major worldwide health concern [8,9]. Two particularly alarming carbapenemases are class B New Delhi Metallo-β lactamase-1 (NDM-1) [10] and class A K. pneumoniae carbapenemase (KPC) [11]. NDM-1 is capable of hydrolyzing all β-lactams, including carbapenems, with the exception of monobactams [12]. It is transmitted through mobile genetic elements and has been observed in several Enterobacteriacae species, in at least 40 countries particularly in poor resource settings [13]. KPC-producing K. pneumoniae are associated with mortality rates as high as 50%, due to limited treatment choices [14].

Some K. pneumoniae sequence types (STs) such as ST11, 15, 101, 147, 336 and ST258 have been implicated in worldwide epidemics/endemics. Particularly, ST258 is linked to the global dissemination of K. pneumoniae KPCs [14,15].

With the availability of six complete K. pneumoniae genomes [16–20] and several ongoing sequencing projects [21], the whole-genome sequencing (WGS) of K. pneumoniae has given insights into its pathogenicity, resistomics and genome plasticity [16]. Yet, little evidence exists on the complex relationship between ESBL production and pathogenesis in K. pneumoniae [22].

In this study we report the first comprehensive comparative genome analysis of an NDM-1-producing K. pneumoniae ST15 isolated from a urine sample collected from a Syrian refugee in Lebanon.

Materials and methods

Ethical approval

Ethical approval was not required as the clinical isolate was collected and stored as part of routine clinical care. Clinical isolate and patient record/information were anonymized and de-identified prior to analysis.

Sample collection

The isolate was recovered from the urine sample of an 84-year old Syrian male patient suffering from pneumonia admitted to the Middle East Institute of Health (MEIH) in Lebanon in October 2015. The patient arrived in Lebanon in 2014 when he was hospitalized for having hypertension, atrial fibrillation, moderate chronic pericardial effusion, chronic obstructive pulmonary disease and morbid obesity. He has previously undergone craniotomy and was treated for inguinal hernia.

Antimicrobial testing

Antimicrobial susceptibility test by the disk diffusion method was performed to determine the resistance patterns of the isolate to 27 different antibiotics: Penicillins (Amoxicillin, ticarcillin, amoxicillin + clavulanic acid and piperacillin + tazobactam), cephalosporins (Cefalotin, cefoxitin, cefuroxime, cefixime, cefotaxime, ceftriaxone, ceftazidime and cefepime), monobactams (Aztreonam), carbapenems (Imipenem, meropenem and ertapenem), aminoglycosides (Amikacin, gentamycin and tobramycin), quinolones (Norfloxacin, ciprofloxacin, levofloxacin and ofloxacin), tetracyclines (Tetracycline and tigecycline), sulfamides (sulfamethoxazole + trimethoprim) and nitrofurans (Nitrofurantoïn) (Oxoid, England). All antimicrobial testing was performed on Mueller-Hinton agar by the flooding technique and data interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guidelines [23].

DNA isolation and sequencing

DNA extraction was performed using the Nucleospin DNA extraction Kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions.

Genome sequencing

Genomic DNA (gDNA) was used as input for library preparation using the Illumina Nextera XT DNA library preparation kit (Illumina). 1 μg of sample DNA was used as input for library preparation. The gDNA was subjected to end-repair, A-tailing, ligation of adaptors including sample-specific barcodes as recommended in the manufacturer’s protocol. The resulting library was quantified using Qubit. The library was sequenced on an Illumina MiSeq with paired-end 500 cycles protocol to read a length of 250 bp.

Genome assembly and annotation

Genome assembly was performed de novo using Spades Genome Assembler Version 3.6.0 [24]. Quality control checks of raw sequence data was performed using FastQC version 1.0.0 [25]. For comparison purposes, the assembled genome was annotated using two different tools: the RAST server (http://rast.nmpdr.org) [26] using the Glimmer default option for open reading frame (ORF) calling and the Prokka Genome Annotation software v1.0.0 [27]. The number of tRNAs and rRNAs were identified using ARAGORN v1.2.36 [28], and the RNAmmer Prediction Server 1.2 [29], respectively. The classification of predicted genes was performed using the Clusters of Orthologous Groups of proteins database [30]. The obtained ORFs were subjected to BLAST analysis against the Antibiotic Resistance Database [31] and the Comprehensive Antibiotic Resistance Database [32]. Resfinder was also used to identify resistant determinants, using a 98% identity threshold (ID) [33]. Virulence factors (VFs) were identified through BLAST search against VFDB [34]. The multilocus sequence type (MLST) was determined using the MLST 1.8 server [35] available on www.genomicepidemiology.org. The MLST profiles were determined based on PubMLST.org. The clonal group cgMLST was determined using the publically available cgMLST database [36]. The presence of plasmids was determined using PlasmidFinder 1.3 [37]. Plasmid contigs were identified using BLASTn against the nucleotide sequence database. PHAST was used to determine putative phage sequences in the genome [38]. The function linked to annotated genes was inferred by UniProtKB [39] and QuickGO [40]. IslandViewer 3 was used to identify putative genomic islands (GIs) using three independent methods for island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM [41]. Insertion sequences (ISs) were identified using IS-finder [42].

Comparative genome analysis

For comparative analysis, the following genomes were included: K. pneumoniae EA-MEH, K. pneumoniae Ecl8 (accession # HF536482.1), a streptomycin-resistant reference strain for targeted gene manipulations [43], LAU-KP1 (accession # AYQE00000000.1) producing OXA-1 and SHV-11 isolated previously from a patient in Lebanon [44], K. pneumoniae KGM-IMP216, positive for OXA-1, NDM-1, SHV-28 among other resistance genes and isolated from a urine sample collected from a patient in Lebanon (accession # LJOI01000001.1) [45], and six of the closest matches to K. pneumoniae EA-MEH obtained through BLASTn: K. pneumoniae NTUH-K2044 (accession # AP006725.1), K. pneumoniae strain XH209 (accession # CP009461.1), K. pneumoniae strain U25 (accession # CP012043.1), K. pneumoniae strain NUHL24835 (accession # CP014004.1), K. pneumoniae strain BR (CP015990.1) and K. pneumoniae strain KP36 (accession # CP017385.1). K. pneumoniae PMK-1 (accession # CP008929), a ST15 NDM-1 producing isolate linked to a nosocomial outbreak in Nepal in 2012, was used as a reference for genome comparisons [46].

K. pneumoniae EA-MEH contigs were reordered in ProgressiveMauve [47] using reference strain K. pneumoniae PMK-1 (accession # CP008929) [46]. Phylogenetic analysis based on 37 marker genes was generated using Phylosift [48].

For the visualization of sequence feature information based on the sequence analysis results, circular genome representations of K. pneumoniae EA-MEH was obtained using CGview Server V 1.0 [49] through comparison with K. pneumoniae Ecl8, LAU-KP1 and PMK-1 (Figures 1 and 2).

Figure 1.

Figure 1.

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Circular genome representation of K. pneumoniae EA-MEH compared with K. pneumoniae Ecl8 (HF536482.1) [43], PMK-1 (CP008929), [46] and LAU-KP1 (AYQE00000000.1) (Tokajian et al., 2015). Starting from the outermost ring the feature rings depict: K. pneumoniae Ecl8 Blast results (red), PMK-1 Blast results (green) and LAU-KP1 Blast results (blue) representing the positions covered by the BLASTN alignment, G+C content (black), G+C positive skew (green) and G+C negative skew (purple). Image created using CGview Server V 1.0 [49].

Figure 2.

Figure 2.

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K. pneumoniae EA-MEH circular genome. Starting from the outermost rings the tracks represent: Open reading frames (ORF) (red), G+C skew (black), G+C plot (green positive skew and purple negative skew). The image was generated using CGview Server V 1.0 [49].

Capsule typing

The capsular type wzi was determined by a PCR assay followed by sequencing using the primers and PCR conditions described in Table 1. Briefly, the obtained PCR products were purified using ExoSAP-IT (Thermo Fisher Scientific, USA). The amplicons were sequenced using the ABI Prism BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystem, USA). PCR products were sequenced on the Genetic Analyzer 3500 (Life Technologies, USA) using the BigDye XTerminator purification kit (Applied Biosystems, USA). The capsular genotype was determined by uploading the wzi gene sequence to the Institut Pasteur K. pneumoniae database (http://bigsdb.web.pasteur.fr/).

Table 1.

Primers sequences and PCR conditions used for the amplification of blaSHV, blaNDM and wzi genes.

Gene Primers Sequence 5′-3′ Ta °C Product size (bp) References
wzi wzi-F GTG CCG CGA GCG CTT TCT ATC TTG GTA TTC C 55 587 bp [50]
wzi-R GAG AGC CAC TGG TTC CAG AA[C or T] TT[C or G] ACC GC
NDM NDM-1-F GAC CGC CCA GAT CCT CAA 55 700 bp [51]
NDM-1-R CGC GAC CGG CAG GTT
SHV SHV-F GCC CGG GTT ATT CTT ATT TGT CGC 62 792 bp [52]
SHV-R TCT TTC CGA TGC CGC CGC CAG TCA
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Resistance genes typing

The presence of blaSHV and blaNDM genes was confirmed by individual PCR assays followed by sequencing, as previously described (Table 1). Sequences were identified using BLASTn.

Nucleotide sequence accession number

This draft genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number: LSBZ00000000.1.

Results

Genomic features

The draft genome sequence of K. pneumoniae EA-MEH was 5,954,825 bp in size with a G+C content of 56.5% in 329 contigs. Annotation of this assembly using RAST identified 5615 coding sequences (CDS), 84 tRNAs and 15 rRNAs. Prokka identified 85 tRNAs, 12 rRNAs, three CRISPRs and 5530 CDS. Genes linked to carbohydrates (873), amino acid derivatives (558), cofactors, vitamins, prosthetic groups and pigments (377) were the most abundant among the SEED subsystem categories. Comparison of K. pneumoniae EA-MEH to the reference strain PMK-1 based on sequence similarity (percent identity ≥ 80) showed that 546 genes are unique for EA-MEH and that most of the functional genes including metal transport are also conserved in the reference strain.

Isolates typing

MLST

In silico MLST analysis based on seven house-keeping genes (gapA, infB, mdh, pgi, phoE, rpoB and tonB) classified the K. pneumoniae EA-MEH as sequence type ST15 belonging to CG15. In silico pMLST based on FII, FIA and FIB loci typed the isolate as [FII+:A−:B−].

Capsular genotyping

The capsular genotype of the clone was determined to be wzi93 associated with serotype K60.

Resistance profile

Antimicrobial susceptibility testing revealed that K. pneumoniae EA-MEH was resistant to all tested antibiotics and had intermediate resistant for two carbapenems: imipenem and meropenem. The minimal inhibitory concentration (MIC) was also determined for the following major antimicrobial agents: 16 mg/l for amoxicillin, 16 mg/l for amoxicillin-clavulanic acid, 32 mg/l for tazobactam, 8 mg/l for imipenem, 6 mg/l for cefotaxime, 16 mg/l for amikacin, 2 mg/l for ciprofloxacin, and 0.125 mg/l for colistin (S). The ResFinder confirmed the observed resistance patterns and identified the presence of six distinct genes conferring resistance to aminoglycosides (aph(3′)-Ia, aac(6′)Ib-cr, armA, strB, strA and aadA2), a number of β-lactamases (blaSHV-28, blaCTX-M-15, blaNDM-1 and blaOXA-1) and genes encoding for fluoroquinolone, macrolide, lincosamide and streptogramin (MLS), phenicol, sulphonamide and trimethoprim resistance. The isolate was susceptible to colistin, fosfomycin, fusidic acid, nitroimidazole, oxazolidinone, rifampicin and glycopeptide (Table 2). Despite the presence of the tetracycline resistance gene tet(D), antimicrobial susceptibility testing showed that K. pneumoniae EA-MEH was sensitive to tetracycline and tigecycline. The Resistance Gene Identifier based on BlastP Hist in the Comprehensive Antibiotic Resistance Database further elucidated the presence of various CTX-M types, OXA types and NDM types and the streptomycin resistance protein B encoded by aph(6′)-Id (Table 2).

Table 2.

Resistance genes, plasmids and phages identified in K. pneumoniae EA-MEH.

Predicted phenotype Resistance gene Position in contig
Aminoglycoside resistance aph(3′)-Ia 143..956
aac(6′)Ib-cr 1878..2477
armA 3442..4215
strB 3710..4546
strA 4546..5349
aadA2 634..1425
Beta-lactam resistance blaSHV-28 12372..13232
blaCTX-M-15 176..1051
blaNDM-1 4496..5308
blaOXA-1 917..1747
Quinolone resistance QnrB66 13226..13870
aac(6′)Ib-cr 1878..2477
oqxB 77466..79915
oqxA 79939..81114
MLS - Macrolide, Lincosamide and Streptogramin B resistance msr(E) 6514..7989
mph(E) 8045..8929
Phenicol resistance catB3 338..779
catA1 750..1409
Sulphonamide resistance sul1 25..861
Tetracycline resistance tet(D) 1979..3163
Trimethoprim resistance dfrA12 1833..2330
dfrA14 5978..6460
Others Elongation factor G 2687…4789
Fluoroquinolone resistant (gyrA) (Ser83 → Phe & Asp87 → Ala) 46525…44111
Fosfomycin resistance protein (FosA) 15585…16004
Plasmids IncFIB(Mar) 1579..2017
IncHI1B 2932..3501
IncFIB(pKPHS1) 32186..32745
IncFIB(K) 4153..4712
IncFII(K) 8938..9085
Phages Vibrio phage henriette 12B8 (NC_021073) 111576-120734
Sphingomonas phage PAU (NC_019521) 57324-63593
Bacillus phage G (NC_023719) 94476-106610
Salisaeta icosahedral phage 1 (NC_017983) 73831-84962
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Mobile genetic elements and phage-associated regions

Five plasmids of the IncF family were identified: IncFIB(Mar), IncHI1B, IncFIB(pKPHS1), IncFIB(K) and IncFII(K) (Table 2).

PHAST identified four phage-associated regions in K. pneumoniae EA-MEH genome: Vibrio phage henriette 12B8 (NC_021073), Sphingomonas phage PAU (NC_019521), Bacillus phage G (NC_023719) and Salisaeta icosahedral phage 1 (NC_017983) (Table 2), with many phage-related proteins unique to EA-MEH compared to the reference; Only two phage-associated regions were identified in PMK1 (Entero P1 (NC_005856); Entero P88 (NC_026014)).

A total of 38 GIs were also detected ranging in size from 4,095 bp to 186,289 bp (Average: 19,274 ± 31,298 bp) with at least three, seven and nine islands conferring resistance to mercury, antimicrobial agents and heavy metals, respectively. Two GIs were related to defective phages, one to cell division and one to sugar transport and metabolism. GIs encoded ABC-type multidrug transport system, bleomycin resistance protein (ble), streptomycin resistance, aminoglycosides resistance and β-lactamases (Table S1).

A total of 105 ISs were identified in K. pneumoniae EA-MEH using IS-finder with 120 open-reading frames (ORFs) related to ISs. Some of the detected ISs included: IS1 (IS1B, IS1D, IS1G, IS1R, IS1SD, IS1X2, IS1X3, IS1X4), IS3 (ISEc36, ISKpn8, ISSen4, ISYen3), ISKpn21, ISKpn25, IS6 and others. Tn3 was detected downstream of ISAba125, which in turn was downstream of blaNDM-1. Another Tn3 resided further upstream of blaNDM-1. The downstream Tn3 was not detected in PMK-1. This order was interrupted in other isolates as well (Figure 3).

Figure 3.

Figure 3.

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Structure of the blaNDM-1 locus in K. pneumoniae EA-MEH compared to PMK1, KGM-IMP216 and LAU-KP1 reference strains as inferred from RAST. Transposases were identified and labeled using the IS Finder database.

Virulence factors

A BLAST search revealed 173 VFs in K. pneumoniae EA-MEH, classified into 18 different categories. Among the identified VFs, two were related to capsular polysaccharide (wcbF; siaD/synD) (Table S2).

Phylogenetic tree

Phylogenetic analysis indicated a close association between K. pneumoniae EA-MEH and PMK-1 (Figure 4). LAU-KP1 clustered with XH209, Ecl8 and TUH-K2044 forming a single clade. KGM-IMP216 clustered more closely to U25 and UHL24835. K. pneumoniae strain BR and KP36 formed two branches distinct from the other isolates.

Figure 4.

Figure 4.

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Phylogenetic tree of K. pneumoniae EA-MEH compared to the reference strains.

Discussion

To the best of our knowledge, this is the first in-depth comparative genomic analysis of ST15 NDM-1 and ESBL-producing K. pneumoniae in Lebanon. ST15 is part of the epidemic CG15 within the MLST clonal complex 14 (CC14) [53]. ST15 has been previously implicated in numerous hospital outbreaks worldwide [13, 46]. Its success is partly attributed to the accumulation of various resistance genes with no fitness cost, including several β-lactamases [54]. Additionally, K. pneumoniae harbors all three drug resistance mechanisms found in Gram-negative bacteria [55], which are the acquisition of antibiotic catalytic genes, mutations in antibiotic targets and membrane proteins and the differential expression of efflux systems and pumps [56], and all were detected in K. pneumoniae EA-MEH.

K. pneumoniae EA-MEH was found to harbor several plasmid-borne resistance genes including four conferring β-lactam resistance (blaSHV-28, blaCTX-M-15, blaNDM-1, blaOXA-1) that were previously identified in Enterobacteriacae disseminating in Europe [57,58]. Additionally, 18 other enzymes conferring resistance to aminoglycosides, quinolone, MLS, phenicol, sulfonamide, tetracycline and trimethoprim were detected. K. pneumoniae is intrinsically resistant to ampicillin with the blaSHV being part of its core genome [59]. Despite the presence of the tetracycline resistance gene tet(D), antimicrobial susceptibility testing showed that the isolate was sensitive to tetracycline and tigecycline. Previous studies showed no correlation between the presence of tetracycline resistance determinants tet(A) or tet(E) and the MIC of tigecycline in Enterobacteriaceae [60]. The transcription repressor of the multidrug efflux pump acrAB operon, acrR, and which was found in EA-MEH, could be accounted for this genotype/phenotype discrepancy [61]. Although nitroimidazole, oxazolidinone and glycopeptides have poor activity against Gram-negative bacteria [62], these antimicrobials are not commonly used in Lebanon. Susceptibility to glycopeptides was also previously described Escherichia coli isolated from Lebanon [63].

blaNDM-1 is frequently coupled with several antibiotic resistance genes located on the same conjugative plasmids [13], narrowing and sometimes excluding all therapeutic options [14]. Concomitant detection of blaCTX-M-15 and blaSHV in MDR K. pneumoniae was linked to nosocomial outbreaks involving ST15, ST147 and ST336 [15]. K. pneumoniae EA-MEH also carried oqxA and oqxB genes as part of its core genome, encoding for quinolone/fluoroquinone resistance and armA encoding for aminoglycoside resistance [59]. All are among the major resistance determinants in MDR K. pneumoniae causing severe infections in hospitals and communities worldwide [13].

Plasmids of the IncF family are known to acquire novel virulence traits through replicon diversification and horizontal gene transfer [64], which contributes to the adaptability of K. pneumoniae to different health care setting [65]. IncFIB(K) plasmid was detected with high homology to plasmid pKPN3, conferring copper and silver resistance [66], additionally IncFIB(K) and IncFII(K) were previously linked with the global dissemination of CTX-M-15 [64].

The numerous Tn3 ISs detected upstream and/or downstream of blaNDM-1 in K. pneumoniae EA-MEH, LAU-KP1 and PMK1 mediate genomic plasticity and the acquisition of resistance genes through homologous recombination [67]. blaNDM-1 detected in this study has a chimeric structure forming one blaNDM-bleMBL operon with the bleomycin resistance gene bleMBL [68]. The blaNDM-bleMBL operon along with few neighboring genes, were preassembled in Acinetobacter spp. before transmission to Enterobacteriaceae. The blaNDM-bleMBL operon was previously detected on transposon Tn125 having two ISs (ISAba125) [65]. The absence of the upstream ISAba125 in K. pneumoniae EA-MEH could suggest deletion linked to Tn3 insertion, which is common in Enterobacteriaceae and is in contrast to A. baumannii [69].

Prophages contribute to genome plasticity and favor the transfer of antimicrobial resistance genes and VFs [70]. They were additionally used as potential therapeutic agents and as markers for diagnosis and epidemiological typing in K. pneumoniae [71]. Although K. pneumoniae PMK1 was the closest to EA-MEH on BLASTn showing the highest sequence similarity (Figures 1 and 4), their prophage DNA profile did not match.

Among the 173 VFs identified in K. pneumoniae EA-MEH, 40 genes were related to metal uptake. Siderophores and iron-metabolism are critical for virulence in K. pneumoniae [72], playing an important role in modulating the immune response and protecting against reactive oxygen species [73]. Moreover, the capsule is an essential virulence determinant in K. pneumoniae. The polysaccharide capsule helps the pathogen to evade phagocytosis [74] and complement-mediated killing [75], and to suppress β-defensin expression [76]. Different capsular serotypes were linked to biofilm formation in carbapenem-resistant K. pneumoniae [72]. The capsular genotype of K. pneumoniae EA-MEH was wzi93 related to serotype K60, and was recently connected to the transmission of a CTX-M-15-producing ST15K. pneumoniae between patients treated in a single center in the Netherlands followed by inter-institutional spread [58]. The role of the capsular serotypes in the pathogenesis of K. pneumoniae requires further attention and could be considered as a novel therapy target [58].

Phylogenetic analysis revealed the clustering of related STs into three major clades. K. pneumoniae EA-MEH ST15 formed a separate clade with PMK1 ST15. K. pneumoniae LAU-KP1 ST336 clustered with XH209 ST17, an MDR strain isolated from the blood of a patient in China [57]. The latter two STs are closely associated, since ST336 is a single-locus variant (SLV) of ST17 with both belonging to the same clonal group (CG) 17 [77]. Similarly, K. pneumoniae KGM-IMP216 ST14 clustered with U25 ST14, an MDR strain isolated from a tertiary care hospital in India [77], and with NUHL24835, NDM-5-producing K. pneumoniae ST14 strain from China [78]. The observed phylogenetic heterogeneity among the three isolates recovered from Lebanon (K. pneumoniae EA-MEH ST15, LAU-KP1 ST336 and KGM-IMP216 ST14) underlined the diversity in their molecular features.

The identification of NDM-1 producing ST15 K. pneumoniae in a hospital setting in Lebanon is alarming and poses a public health concern. It is compulsory to expand our current understanding of the genome plasticity in K. pneumoniae spp. through in-depth functional genomic analysis. This requires the effective cooperation between clinicians and public health practitioners in the region for adequate monitoring coupled with the implementation of effective control measure. Understanding the dynamics of transmission and shifting disease control away from policies focused on geopolitical borders would help in better understanding and controlling communicable diseases especially the ones associated with population displacement.

Supplemental data

Supplemental data for this article can be accessed at http://dx.doi.org/10.1080/20477724.2017.1314069.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary Material

YPGH_1314069_Supplementary_Material.zip
Click here for additional data file. (35.8KB, zip)

Acknowledgements

We thank the staff of the Middle East Institute of Health (MIEH) for their cooperation in sample collection.

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