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Open Access

Peer-reviewed

Research Article

Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014

  • Ørjan Samuelsen ,

    Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Project administration, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

    orjan.samuelsen@unn.no

    Affiliations Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway, Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway

    ⨯
  • Søren Overballe-Petersen,

    Roles Conceptualization, Data curation, Investigation, Validation, Writing – review & editing

    Affiliation Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway

    ⨯
  • Jørgen Vildershøj Bjørnholt,

    Roles Data curation, Investigation, Resources, Validation, Writing – review & editing

    Current address: Institute of Clinical Medicine, University of Oslo, Norway and Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway.

    Affiliation Department of Infectious Disease Epidemiology, Norwegian Institute of Public Health, Oslo, Norway

    ⨯
  • Sylvain Brisse,

    Roles Data curation, Funding acquisition, Methodology, Resources, Software, Supervision, Validation, Writing – review & editing

    Affiliation Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France

    ⨯
  • Michel Doumith,

    Roles Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Writing – review & editing

    Affiliation Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom

    ⨯
  • Neil Woodford,

    Roles Funding acquisition, Resources, Supervision, Validation, Writing – review & editing

    Affiliation Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom

    ⨯
  • Katie L. Hopkins,

    Roles Data curation, Investigation, Resources, Validation, Writing – review & editing

    Affiliation Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom

    ⨯
  • Bettina Aasnæs,

    Roles Data curation, Investigation, Validation, Writing – review & editing

    Affiliation Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway

    ⨯
  • Bjørg Haldorsen,

    Roles Data curation, Investigation, Validation, Writing – review & editing

    Affiliation Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway

    ⨯
  • Arnfinn Sundsfjord,

    Roles Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Validation, Writing – review & editing

    Affiliations Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway, Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway

    ⨯
  • on behalf of The Norwegian Study Group on CPE

    Representatives of the Norwegian Study Group on CPE are listed in the acknowledgements

    ⨯

Abstract

The prevalence of carbapenemase-producing Enterobacteriaceae (CPE) is increasing worldwide. Here we present associated patient data and molecular, epidemiological and phenotypic characteristics of all CPE isolates in Norway from 2007 to 2014 confirmed at the Norwegian National Advisory Unit on Detection of Antimicrobial Resistance. All confirmed CPE isolates were characterized pheno- and genotypically, including by whole genome sequencing (WGS). Patient data were reviewed retrospectively. In total 59 CPE isolates were identified from 53 patients. Urine was the dominant clinical sample source (37%) and only 15% of the isolates were obtained from faecal screening. The majority of cases (62%) were directly associated with travel or hospitalization abroad, but both intra-hospital transmission and one inter-hospital outbreak were observed. The number of CPE cases/year was low (2–14 cases/year), but an increasing trend was observed. Klebsiella spp. (n = 38) and E. coli (n = 14) were the dominant species and blaKPC (n = 20), blaNDM (n = 19), blaOXA-48-like (n = 12) and blaVIM (n = 7) were the dominant carbapenemase gene families. The CPE isolates were genetically diverse except for K. pneumoniae where clonal group 258 associated with blaKPC dominated. All isolates were multidrug-resistant and a significant proportion (21%) were resistant to colistin. Interestingly, all blaOXA-48-like, and a large proportion of blaNDM-positive Klebsiella spp. (89%) and E. coli (83%) isolates were susceptible in vitro to mecillinam. Thus, mecillinam could have a role in the treatment of uncomplicated urinary tract infections caused by OXA-48- or NDM-producing E. coli or K. pneumoniae. In conclusion, the impact of CPE in Norway is still limited and mainly associated with travel abroad, reflected in the diversity of clones and carbapenemase genes.

Citation: Samuelsen Ø, Overballe-Petersen S, Bjørnholt JV, Brisse S, Doumith M, Woodford N, et al. (2017) Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014. PLoS ONE 12(11): e0187832. https://doi.org/10.1371/journal.pone.0187832

Editor: Patrick Butaye, Ross University School of Veterinary Medicine, SAINT KITTS AND NEVIS

Received: June 14, 2017; Accepted: October 26, 2017; Published: November 15, 2017

Copyright: © 2017 Samuelsen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: Whole genome sequence data have been deposited at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA295003. Original data regarding patient details have been aggregated to secure anonymity as approved by the Regional Ethical Committee and the Data Protection Officer at the University Hospital of North Norway. Complete data are available after consideration by the Regional Ethical Committee (rek-nord@asp.uit.no)/Data Protection Officer (personvernombudet@unn.no) for researchers who meet the criteria for access to confidential data. All other data contained within the paper and Supporting Information.

Funding: The study was performed as part of our routine work and the authors received no specific funding for this study. There was no additional external funding received for this study.

Competing interests: PHE's AMRHAI Reference Unit has received financial support for conference attendance, lectures, research projects or contracted evaluations from numerous sources, including: Accelerate Diagnostics, Achaogen Inc., Allecra Therapeutics, Amplex, AstraZeneca UK Ltd, Basilea Pharmaceutica, Becton Dickinson Diagnostics, bioMérieux, Bio-Rad Laboratories, BSAC, Cepheid, Check-Points B.V., Cubist Pharmaceuticals, Department of Health, Enigma Diagnostics, Food Standards Agency, GlaxoSmithKline Services Ltd, Henry Stewart Talks, IHMA Ltd, Kalidex Pharmaceuticals, Melinta Therapeutics, Merck Sharpe & Dohme Corp., Meiji Seika Pharmo Co., Ltd, Mobidiag, Momentum Biosciences Ltd, Nordic Pharma Ltd, Norgine Pharmaceuticals, Rempex Pharmaceuticals Ltd, Roche, Rokitan Ltd, Smith & Nephew UK Ltd, Trius Therapeutics, VenatoRx Pharmaceuticals and Wockhardt Ltd. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Introduction

Carbapenemase-producing Enterobacteriaceae (CPE) have emerged as a global public health concern during the last two decades [1, 2]. CPE isolates are usually multidrug-resistant (MDR) or even extensively- or pandrug-resistant (XDR/PDR), resulting in limited antibiotic treatment options [1, 3, 4]. Due to the lack of effective therapy, CPE infections have been associated with high mortality rates [5, 6]. Currently, colistin and various combination regimens are generally used for treatment of CPE infections. However, the clinical evidence is mainly based on case reports and observational retrospective studies [1, 4]. Worryingly, high rates of colistin resistance among CPE have been observed in certain regions [7, 8]. Although colistin resistance is often mutation-based, plasmid-mediated colistin resistance has now also been described [9–14], and observed in CPE isolates [11, 15–17].

The main carbapenemases among Enterobacteriaceae include KPC (Ambler class A), the metallo-β-lactamases NDM, VIM and IMP (Ambler class B), and OXA-48-like enzymes (Ambler class D) [1]. Certain carbapenemases dominate in specific regions and countries, i.e. NDM in the Indian subcontinent, KPC in Italy, Portugal, Israel, Greece and the US, and OXA-48-like in many Mediterranean (e.g. Turkey and Malta) and North African countries as well as some other European countries (e.g. Belgium, France, Germany and Spain) [7, 18–20]. Specific clones or clonal groups (CG) are often associated with specific carbapenemases, while other carbapenemases show a more broad diversity with respect to host genetic backgrounds [2, 21]. The global spread of KPC has mainly been associated with Klebsiella pneumoniae sequence type (ST) 258 or CG 258 [2, 21, 22]. In contrast, NDM and OXA-48-like enzymes are broadly distributed in various genetic backgrounds of K. pneumoniae and Escherichia coli and for blaNDM there is no clear link to a specific plasmid backbone [2, 21]. For blaOXA-48-like there is molecular evidence supporting an association with a specific internationally epidemic IncL plasmid backbone [23–25].

The emergence of CPE in the Nordic countries has mainly been associated with single sporadic cases associated with import [26–36], and the prevalence is low compared with other European countries [7, 19]. However, there are indications of local dissemination unrelated to travel in Denmark [37, 38].

The aim of this study was to analyse the epidemiological, phenotypic and molecular characteristics of CPE isolated in Norway from 2007 to 2014 to understand the molecular epidemiology associated with the emergence of CPE in Norway.

Materials and methods

Bacterial strains and demographic data

The study collection consisted of 59 CPE isolates genetically-verified at the Norwegian National Advisory Unit on Detection of Antimicrobial Resistance from 2007–2014. The criteria for submitting isolates to the Unit included reduced susceptibility to carbapenems according to the Norwegian Working Group for Antibiotics (AFA, https://unn.no/fag-og-forskning/arbeidsgruppen-for-antibiotikasporsmal-og-metoder-for-resistensbestemmelse-afa)/Nordic Committee on Antimicrobial Susceptibility Testing (NordicAST) guidelines (www.nordicast.org). In 2012 mandatory reporting of confirmed CPE cases to the Norwegian Surveillance System for Communicable Diseases (MSIS) was established. After confirmation at the Advisory Unit, MSIS and the primary lab are notified. The primary laboratory subsequently notifies the responsible clinician, who also reports data to MSIS. Clinical data were collected from the laboratory requisition. Multiple isolates from the same patient were included in the analysis if they were (i) of different species, (ii) the same species, but harboured a different carbapenemase gene or (iii) if the isolates were of the same species and harboured the same carbapenemase gene, but were identified >1 year apart.

Phenotypic analysis

Species identification was performed using MALDI-TOF MS (Bruker Daltonik GmbH, Bremen, Germany). MIC profiling was performed using gradient strips (Liofilchem, Roseto degli Abruzzi, Italy/bioMérieux, Marcy-l’Étolie, France) and broth microdilution for colistin using in-house designed premade Sensititre microtiter plates (TREK Diagnostic Systems/Thermo Fisher Scientific, East Grinstead, UK). Interpretation was according to EUCAST clinical breakpoints version 6.0 (www.eucast.org). Non-susceptibility included both the intermediate and resistant categories. The AmpC Confirm kit (ROSCO Diagnostica, Taastrup, Denmark), ESBL combination discs (Becton-Dickinson, Franklin Lakes, NJ, USA), KPC, MBL and OXA-48 Confirm kit (ROSCO Diagnostica) and the in-house version of Carba NP test were used for phenotypic typing of β-lactamases [39, 40].

Molecular analysis

The presence of carbapenemase genes was initially determined by various PCRs for blaKPC, blaIMI, blaVIM, blaNDM, blaIMP, blaGIM, blaSPM, blaSIM and blaOXA-48-like [41–44]. WGS was performed on all isolates using the MiSeq platform (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, genomic DNA was purified using the GenElute bacterial genomic DNA kit (Sigma-Aldrich, St. Louis, MO, USA). DNA libraries were prepared using Nextera/Nextera XT kits (Illumina) followed by paired-end sequencing. Contigs were assembled using SPAdes [45] through the iMetAMOS extension [46] of the MetAMOS package [47]. The presence of resistance genes/mutations, carbapenemase genes and single nucleotide polymorphisms (SNP) variations were determined using a customised algorithm that uses Bowtie 2 to map reads against a locally curated reference database and assembled from publically accessible databases. The database comprised sequences for all reported carbapenemase variants. Samtools was used to generate an mpileup file [48] which was then parsed based on read depth (> 10 reads per base) and base-call agreement (> 90%) to determine the base type at each nucleotide position relative to the closest reference sequence. Presence of reported carbapenemase variants were defined based on 100% identity across the whole length of the corresponding reference gene.

STs of Klebsiella spp., E. coli and Enterobacter cloacae complex were determined from WGS data using the Klebsiella MLST database (http://bigsdb.pasteur.fr/klebsiella/klebsiella.html), EnteroBase (http://enterobase.warwick.ac.uk/species/index/ecoli) for E. coli, and the E. cloacae MLST database (http://pubmlst.org/ecloacae). Core genome MLST (cgMLST) was performed on K. pneumoniae isolates using 694 loci as previously described [22]. A phylogenetic tree was constructed based on the concatenated sequence alignments using RAxML [49] and FigTree (http://tree.bio.ed.ac.uk/software/figtree/).

Genbank accession numbers

WGS data have been deposited at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA295003.

Ethical considerations

The study was reviewed and approved by the Regional Committee for Medical and Health Research Ethics North (reference no. 2016/2122/REK Nord and 2017/146/REK Nord) and the Data Protection Officer at the University Hospital of North Norway (reference no. 2017/1562). The need for patient consent was waived by the Regional Committee for Medical and Health Research Ethics North (reference no. 2017/146/REK nord)

Results

Bacterial isolates

In total 59 CPE were identified from 53 patients of which 44 were hospitalized patients. Samples from eight patients were taken at general practitioners or in other health care institutions (e.g. elderly care homes). For one patient no information was obtained. Of the 53 patients, four had multiple CPE isolates belonging to different species or different STs. One patient had four blaNDM-1-positive strains of different species (Proteus mirabilis, Providencia stuartii, Citrobacter sp. and K. pneumoniae) isolated within a four-month period. Another had blaKPC-2-positive K. pneumoniae and Enterobacter cloacae complex isolates in the same faecal screening sample. A third had blaNDM-1-positive E. coli and E. cloacae complex isolates identified in two different specimens (wound secretion and urine, respectively) within a one-month period. The fourth patient yielded two blaNDM-1-positive K. pneumoniae strains with unrelated STs from specimens taken 21 months apart.

Increasing number of CPE identified during the study period from a high proportion of clinical isolates

CPE isolates were identified in 14 of 22 clinical microbiology laboratories representing all health regions in Norway. The number of CPE cases per year, diversity of carbapenemase variants and species increased during the study period (Table 1), but with a trend towards dominance of NDM and OXA-48-like carbapenemase variants and increasing number of carbapenemase-producing E. coli. Fifty-six percent of the patients were male. The patient age ranged from 3–96 years (mean 63 and median 66 years). The majority of CPE were isolated from urine (n = 22, 37%), blood culture (n = 9, 15%) and faecal screening (n = 9, 15%).

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Table 1. Time-line and distribution of identified CPEs and carbapenemase variants.

No. of isolates in parenthesis.

https://doi.org/10.1371/journal.pone.0187832.t001

Association with travel or hospitalization abroad

Thirty-three patients (62%) had a known history of travel and/or hospitalization abroad (Table 2). Sixteen patients (30%) reported no travel or hospitalization abroad and for four patients (8%), no information was obtained. With respect to the non-direct import cases, eight cases were associated with secondary spread from imported cases. This included six cases associated with a previously described, small but long-term outbreak of blaKPC-2-positive K. pneumoniae/E. cloacae complex in 2007–2010 [50]. In addition, two other intra-hospital transmissions of blaKPC-2-positive K. pneumoniae [28] and blaVIM-27-positive K. pneumoniae were observed involving one additional patient in each case.

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Table 2. Distribution of isolates according to association with importation.

https://doi.org/10.1371/journal.pone.0187832.t002

Bacterial species and carbapenemase diversity

Overall Klebsiella spp. (K. pneumoniae, n = 36; Klebsiella variicola n = 1; Klebsiella quasipneumoniae n = 1) were dominant, followed by E. coli (n = 14), E. cloacae complex (n = 4) and single isolates of P. stuartii, P. mirabilis and Citrobacter sp. (Table 1 and S1 Table). The most dominant carbapenemase gene family was blaKPC, found in K. pneumoniae (n = 18) and E. cloacae complex (n = 2), followed by blaNDM identified in K. pneumoniae (n = 8), E. coli (n = 6), E. cloacae complex (n = 1), P. stuartii (n = 1), P. mirabilis (n = 1) and Citrobacter sp. (n = 1). blaVIM was identified in K. pneumoniae (n = 4), E. coli (n = 2) and K. quasipneumoniae (n = 1) while blaOXA-48-like was identified in K. pneumoniae (n = 5), E. coli (n = 5) and K. variicola (n = 1). In addition, we identified one K. pneumoniae isolate harbouring both blaNDM and blaOXA-48-like and single isolates with blaIMI (E. cloacae complex) and blaIMP (E. coli). With respect to KPC, KPC-2 (n = 18) was the most predominant allele with the closest KPC-3 (n = 2) variant detected in only two isolates. The remaining carbapenemase genes encoded three different variants of NDM (NDM-1, n = 16; NDM-7, n = 2; and NDM-5, n = 1), four OXA-48-like (OXA-48, n = 7; OXA-181, n = 2; OXA-245, n = 2 and OXA-162, n = 1) and four VIM (VIM-1, n = 3; VIM-27, n = 2; VIM-4, n = 1; and VIM-29, n = 1). The single isolates with blaIMI and blaIMP encoded IMI-9 and IMP-26, respectively.

Bacterial population structure and linkage to specific carbapenemase alleles

MLST and cgMLST (Fig 1) showed that K. pneumoniae was dominated by KPC-producing clonal group (CG) 258, more specifically ST258 (n = 15) and its single locus variants (SLV) ST855 (n = 1) and ST340 (n = 1). The CG258 cluster comprised 21 isolates and included nearly all KPC-producers (n = 17) in addition to four ST11 isolates carrying blaNDM-1 (n = 2) or blaOXA-245 (n = 2) genes. Outside CG258, blaKPC was only identified in one isolate belonging to ST461. Among the K. pneumoniae isolates cgMLST identified two other clusters represented by more than one isolate: one representing CG147 and including ST147 with blaVIM-27 (n = 2) or blaNDM-1 (n = 1) and ST273 with blaVIM-1 (n = 1), and one representing CG17 including ST17 with blaNDM-1 (n = 2) and ST336 with blaNDM-7 (n = 1). The remaining K. pneumoniae isolates represented genetically diverse single strains harbouring blaNDM-1 (ST37 and ST101), blaNDM-1 + blaOXA-181 (ST525), blaOXA-48 (ST187 and ST405), blaOXA-162 (ST14) and blaVIM-1 (ST2134). The K. quasipneumoniae isolate carrying blaVIM-1 belonged to ST1466 and the K. variicola with blaOXA-48 belonged to ST981.

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Fig 1. Phylogenetic tree of K. pneumoniae isolates based on alignment of concatenated sequences of the 694 cgMLST scheme of K. pneumoniae [22].

The tree was constructed in RAxML [49] and visualized using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Clonal groups with >1 isolates are boxed. Sequence type (ST), carbapenemase gene and year of isolation is indicated for each isolate. Isolates associated with the long-term outbreak [50] and the two occurrences of intra-hospital transmission are labelled *, # and ¤, respectively.

https://doi.org/10.1371/journal.pone.0187832.g001

Ten diverse genetic backgrounds were identified among the E. coli isolates (n = 14). None of the STs were SLVs or double locus variants (DLVs) of any other. Only ST38 (n = 3) and ST410 (n = 3) were represented by >1 isolate. All three ST38 isolates carried blaOXA-48, while the three ST410 strains harboured each a different carbapenemase gene (blaNDM-1, blaVIM-4 or blaOXA-181). The remaining strains were genetically diverse and carried various carbapenemase genes/variants: blaNDM-1 (ST131, ST617 and ST681), blaNDM-5 (ST636), blaNDM-7 (ST101), blaOXA-48 (ST405), blaVIM-29 (ST6355) and blaIMP-26 (ST95).

The four carbapenemase-producing E. cloacae complex isolates were all of different STs: ST456 and ST484 both with blaKPC-2, ST92 with blaNDM-1 and ST635 with blaIMI-9. All STs were defined as singletons (no SLVs) by BURST analysis of the E. cloacae MLST database (http://pubmlst.org/ecloacae/, last accessed 24.06.2016).

Antimicrobial susceptibility profile and performance of phenotypic methods for detection of CPE

All isolates were multidrug-resistant (MDR) according to the definitions by Magiorakos et al. [51]. (Table 3 and S1 Table). One isolate, a blaNDM-1-positive P. stuartii was non-susceptible to all relevant antimicrobial agents tested. Overall fosfomycin and colistin were the most active antimicrobial agents with 85% and 79% of the isolates being susceptible when excluding P. mirabilis and P. stuartii isolates which are intrinsically resistant to colistin [52] (Table 3). Seven of the twelve colistin-resistant isolates were K. pneumoniae ST258 with blaKPC-2 (n = 6) or blaKPC-3 (n = 1). The other colistin-resistant isolates included K. pneumoniae ST525 with blaNDM-1 + blaOXA-181, K. pneumoniae ST147 with blaNDM-1, K. pneumoniae ST336 with blaNDM-7, E. cloacae complex ST635 with blaIMI-9 and E. cloacae complex ST456 with blaKPC-2.

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Table 3. Antimicrobial resistance profiles of CPE isolates according to species and carbapenemase variant.

https://doi.org/10.1371/journal.pone.0187832.t003

High levels of non-susceptibility were observed to aminoglycosides (gentamicin, 51%; amikacin, 63%; and tobramycin, 83%), tigecycline (58%) and ciprofloxacin (83%).

With respect to the carbapenems, 41% were susceptible to meropenem, 39% to imipenem and 3% to ertapenem. All isolates had meropenem and ertapenem MIC values above the EUCAST screening breakpoint for carbapenemase detection (http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Resistance_mechanisms/EUCAST_detection_of_resistance_mechanisms_v1.0_20131211.pdf) (S1 Table). For imipenem nine isolates had MIC values below the screening breakpoint. There was no clear correlation between carbapenemase variant and susceptibility to meropenem and imipenem with the exception that among the isolates harbouring blaOXA-48-like (excluding the strain with both blaNDM-1 and blaOXA-181) 9/11 and 8/11 were susceptible to meropenem and imipenem, respectively. As expected, a high level of resistance was observed against other β-lactams (Table 3 and S1 Table). Three isolates: one K. pneumoniae (blaOXA-48), one K. variicola (blaOXA-48) and the blaIMI-9-positive E. cloacae complex isolate were susceptible to extended-spectrum cephalosporins (cefotaxime, ceftazidime and cefuroxime) and aztreonam. Interestingly, all OXA-48-like-positive E. coli and Klebsiella spp. as well as 83% and 89% of NDM-positive E. coli and Klebsiella spp. isolates, respectively were susceptible to mecillinam. Nine (15%) of the isolates tested negative for carbapenemase-production with the in-house Carba NP test (S1 Table), including six blaNDM-1-positive isolates (E. coli n = 2, P. stuartii, P. mirabilis, Citrobacter sp. and K. pneumoniae), two blaOXA-48-like-positive isolates (E. coli and K. pneumoniae) and one E. cloacae complex isolate (blaIMI-9). The KPC, MBL and OXA-48 confirm kit correctly identified the presence of either an MBL or KPC in all relevant isolates except for one blaNDM-1-positive P. mirabilis strain (S1 Table). The single blaIMI-9-positive E. cloacae complex isolate also showed significant synergy with boronic acid only. With the exception of the isolate harbouring both blaNDM-1 and blaOXA-181, where synergy was observed between meropenem and dipicolinic acid, no synergy was observed with the β-lactamase inhibitors for all blaOXA-48-like-positive isolates. Moreover, with the exception of two isolates, all blaOXA-48–like-positive isolates showed no zones of inhibition around the temocillin tablet, which may indicate the presence of OXA-48-like carbapenemases according to the manufacturer’s guidelines. The meropenem-meropenem/EDTA gradient strip correctly identified all MBL-positive isolates, with the exception of the K. pneumoniae strain positive for both blaNDM-1 and blaOXA-181 where the test was inconclusive (S1 Table).

Association with other antibiotic resistance determinants

BlaCTX-M and specifically blaCTX-M-15 were the most common ESBL variants identified and were mainly associated with K. pneumoniae and E. coli isolates with blaNDM (10/15 isolates) or blaOXA-48-like (8/11 isolates) and E. coli isolates with blaVIM (2/2 isolates) (S1 Table). BlaCTX-M were not identified in blaKPC-positive K. pneumoniae isolates. One E. coli isolate with blaOXA-48 harboured both blaCTX-M-14 and blaCTX-M-15. blaCTX-M-15 was also identified in one blaKPC-2- and one blaNDM-1-positive E. cloacae complex. BlaCMY (n = 12) were the most common plasmid-mediated AmpC variants identified with blaCMY-6 particularly associated with blaNDM (n = 9). The two blaOXA-48-like-positive Klebsiella spp. isolates that were susceptible to extended-spectrum cephalosporins and aztreonam were negative for ESBL and plasmid-mediated AmpC genes.

In addition to various genes encoding aminoglycoside-modifying enzymes, the 16S rRNA methylase genes rmtC and armA, were identified in eight and five isolates, respectively (S1 Table). With the exception of the single isolate of E. coli with blaIMP-26, armA and rmtC were only associated with isolates harbouring blaNDM-1. In Klebsiella spp. insertional disruption of mgrB [53] associated with colistin resistance was identified in seven K. pneumoniae isolates (S1 Table). Insertional disruption of mgrB was also observed in two clinically colistin susceptible (MIC = 1 mg/L) K. pneumoniae isolates. One K. pneumoniae isolate with a disrupted mgrB also carried a nonsense mutation in pmrB leading to a truncated PmrB. Two colistin-resistant K. pneumoniae isolates had mutations in pmrA resulting in amino acid substitutions of G53C and D86E in one, and G53C in the other. In one colistin-resistant Klebsiella spp. isolate (MIC >8 mg/L) no previously described colistin resistance determinants were identified. The strain had mutations in pmrA (PmrA E57G) and pmrB (PmrB T246A) compared with the colistin-susceptible K. pneumoniae strain MGH 78578 [54], but neither mutation has been linked with colistin resistance and PmrB T246A is commonly found in K. pneumoniae [54]. No mutations were identified in phoP, phoQ or the mgrB promoter for this isolate. The plasmid-mediated colistin resistance genes mcr-1 [9], mcr-2 [10], mcr-3 [12], mcr-4 [13] and mcr-5 [14] were not detected.

All E. coli, K. pneumoniae and E. cloacae complex isolates with high-level ciprofloxacin resistance (MIC ≥32 mg/L) harboured mutations in both gyrA and parC (S1 Table). In addition, various plasmid-mediated quinolone resistance determinants were identified, including aac(6’)-Ib-cr (n = 24), qnrB1 (n = 8), qnrB4 (n = 1), qnrB19 (n = 2), qnrD (n = 1) and qnrS1 (n = 8).

Discussion

The main objective of this study was to gain a better understanding of the molecular epidemiology associated with the emergence of CPE in Norway. As observed in other Nordic countries [26, 27, 32–36] the emergence of CPE in Norway is also mainly associated with importation, highlighting the importance of targeted screening of patients hospitalized abroad and patients with a recent travel history to a country with a high prevalence of CPE. A relatively low number of cases (15%) were identified through faecal screening in contrast to Sweden (74,5%) and France (59.8%) [26, 55]. This difference is most likely due to dissimilarities in the use of targeted screening and that CPE screening in Norway was not fully implemented in the study period. This could also explain why a higher proportion of CPE cases in Sweden (81%) were associated with import [26]. Revised recommendations for infection prevention and control, including indications for screening for CPE, were introduced in Norway in August 2015 and in the first six months of 2016, 63% of CPE cases were identified through faecal screening. The occurrence of one long-term outbreak and two separate incidences of secondary transmission further highlights the importance of rapid implementation of infection prevention and control measures before confirmation of CPE if patients have risk factors (e.g. hospitalization abroad) or when an MDR isolate is identified.

The diversity of species and genetic backgrounds observed is probably due to the high degree of importation from a variety of countries (Table 2). Several studies have shown that the dissemination of resistance genes among clinical strains of Enterobacteriaceae is often associated with high-risk clones and the linkage between specific genetic backgrounds and resistance genes [2, 21, 56]. The cgMLST analysis of K. pneumoniae isolates showed that the observed epidemiology reflects the current global epidemiology (Fig 1), where blaKPC-2/-3 spread is primarily driven by strains associated with CG258 (and more specifically, ST258). In contrast, ST11 (a member of CG258, and a single locus variant of ST258) has been shown to be associated with a diversity of carbapenemase genes including blaKPC, blaNDM, blaVIM and blaOXA-48-like in different geographical regions [2, 57, 58]. Accordingly, the four ST11 strains in this study harboured either blaNDM-1 (n = 2) or blaOXA-245 (n = 2). Notably, cgMLST has shown that ST11 and ST340 represent a genetic sublineage within CG258 [22]. Isolates with blaNDM and blaVIM belonging to two other globally dispersed high-risk CGs like CG17 and CG147 [2] were also identified. The identification of blaVIM-1 and blaOXA-48 in K. quasipneumoniae and K. variicola, respectively shows that these Klebsiella species also contribute to the dissemination of carbapenemase genes and infections as both isolates were associated with infection. K. variicola have been shown to be frequently associated with bloodstream infections and associated with higher mortality than K. pneumoniae [59].

All three E. coli ST38 isolates harboured blaOXA-48, which is consistent with previous observations showing a prevalent linkage of ST38 to blaOXA-48 in a large collection of clinical isolates from European and North-African countries [23]. In contrast, the three E. coli isolates belonging to ST410 were associated with different carbapenemase genes (blaNDM-1, blaVIM-4 or blaOXA-181) indicating the ability of this genetic background to maintain different plasmids and resistance genes. ST410 E. coli isolates have also previously been identified harbouring blaKPC-2 [60]. The global dissemination of blaNDM has so far not been linked to specific high-risk clones or epidemic plasmids [21] and this is also reflected among the five blaNDM-positive E. coli isolates, which belonged to five different genetic backgrounds. However, one strain belonged to the international high-risk clone ST131 [21] and another to ST101, which has previously been found to be associated with blaNDM and other carbapenemases in several countries (e.g. Bangladesh [61], USA [62], Canada [63, 64] and Bulgaria [65]).

CPE frequently exhibit MDR or XDR phenotypes, limiting treatment options [1, 4]. This was also observed in our strain collection (Table 2 and S1 Table) due to the association with a wide variety of other acquired resistance genes, including 16S rRNA methylase genes conferring high-level broad-spectrum aminoglycoside resistance [66] and chromosomal mutations/insertions resulting in ciprofloxacin and colistin resistance (S1 Table). The mechanism(s) behind colistin resistance in one K. pneumoniae strain and the colistin-resistant E. cloacae isolates remains to be determined. Interestingly, a high prevalence of susceptibility to mecillinam among OXA-48- and NDM-producing E. coli and K. pneumoniae isolates was observed. Marrs et al. also showed high levels of in vitro susceptibility to mecillinam among NDM-producing E. coli and K. pneumoniae isolates from Pakistan [67], suggesting that mecillinam could have a role in the treatment of uncomplicated urinary tract infections caused by OXA-48- or NDM-producing E. coli or K. pneumoniae [68].

Rapid identification of CPE is essential for timely implementation of enhanced infection control measures to reduce transmission of CPE and prevent infections [3]. As observed in previous studies [69, 70] false-negative results (15%) for carbapenemase production were observed with the in-house version of the Carba NP test, particularly with NDM- and OXA-48-like-producing isolates. Identification of OXA-48-like-producers can be particularly challenging due to their relatively low level of activity against carbapenems and the lack of specific inhibitors [71]. The relatively high number of false-negative Carba NP results could also be due to the media used. In our study, colonies for the Carba NP test were harvested from MH agar and Literacka et al have recently reported that MH agar from different companies were associated with false-negative results for MBL-producers [72]. High-level resistance to temocillin is a sensitive and specific indicator for the presence of OXA-48-like enzymes [73]. All blaOXA-48-like–positive isolates in our collection showed high-level resistance (MIC>128 mg/L) to temocillin, but several isolates harboring blaVIM and blaNDM also had temocillin MIC >128mg/L showing that testing for synergy with metal chelators (e.g. EDTA or dipicolinic acid) is necessary to discriminate between isolates with OXA-48 and MBLs.

Conclusions

The low prevalence of clinical CPE in Norway is consistent with the general low level of antimicrobial resistance compared with other countries. The relatively low level of antibiotic consumption and the use of narrow spectrum antibiotics [74] have probably contributed to this situation. The low prevalence is also reflected in the epidemiology of Norwegian CPE; mainly associated with importation, exhibiting a broad diversity of genetic backgrounds and carbapenemase variants that mirror the global epidemiology. Only a few cases of secondary spread also support this notion. In order to limit the infection pressure brought by increasing travel and globalization, continued emphasis must be put on diagnostic capabilities, surveillance and infection control.

Supporting information

S1 Table. Strain collection and associated phenotypic and molecular data.

https://doi.org/10.1371/journal.pone.0187832.s001

(XLSX)

Acknowledgments

Center for Bioinformatics at UiT The Arctic University of Norway is acknowledged for genome sequencing of part of the strain collection and initial bioinformatic analysis. We are grateful for assistance on the phylogenetic analysis of Klebsiella spp. by Jessin Janice and Ellen H. Josefsen for technical assistance. Tohru Miyoshi-Akiyama and colleagues are acknowledged for curating the Enterobacter cloacae MLST database and for providing novel STs.

This work was performed through a collaborative project with the diagnostic microbiology laboratories in Norway forming the Norwegian Study Group on CPE. We acknowledge the contributions of the representatives in the study group including: Trond E. Ranheim (Akershus University Hospital), Karianne Wiger Gammelsrud (Oslo University Hospital Rikshospitalet, Oslo University Hospital Aker and Oslo University Hospital Radiumhospitalet), Annette Onken (Vestre Viken Bærum Hospital), Kristina Papp (Vestre Viken Drammen Hospital), Liv Jorunn Sønsteby (Haugesund Hospital), Haima Mylvaganam (Haukeland University Hospital), Angela Kümmel (Levanger Hospital), Einar Nilsen (Molde Hospital), Hege Elisabeth Larsen (Nordland Hospital), Hans-Johnny Schjelderup Nilsen (St. Olavs University Hospital), Iren H. Löhr and Anita Brekken (Stavanger University Hospital), Anita Kanestrøm (Østfold Hospital), Guro Furset Jensen (Sørlandet Hospital), Nils Olav Hermansen (Oslo University Hospital Ullevål), Gunnar Skov Simonsen (University Hospital of North Norway), Dagfinn Skaare (Vestfold Hospital) and Reidar Hide (Ålesund Hospital).

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