https://orcid.org/0000-0003-1195-9471
Abstract
To characterize genomes of Klebsiella pneumoniae ST11 NDM-1 responsible for a countrywide outbreak in Poland and compare them phylogenetically with other Polish and international ST11 strains.
Seventy-one carbapenemase-producing K. pneumoniae ST11 isolates from Poland, including 66 representatives of the NDM-1 epidemic from 2012–18, were sequenced using Illumina MiSeq. Additionally, three outbreak isolates were also sequenced using MinION. The clonality and phylogenetic analysis was done by core-genome MLST and SNP approaches. Resistomes, virulomes, K/O antigens and plasmid replicons were screened for. The detailed plasmid analysis was based on full assemblies using Oxford Nanopore Technologies data.
Chromosomes of the outbreak isolates formed an essentially homogeneous cluster (though accumulating SNPs gradually with time), differing remarkably from other Polish NDM-1/-5-, KPC-2- or OXA-48-producing K. pneumoniae ST11 strains. The cluster belonged to a clade with 72 additional isolates identified worldwide, including closely related NDM-1 producers from several countries, including organisms from Bulgaria and Greece. All these had KL24 and O2v1 antigens and the chromosomal yersiniabactin locus YbST230 residing in the ICEKp11 element. The specific blaNDM-1-carrying Tn125 transposon derivative, named Tn125A, was located in IncFII/pKPX-1- and/or IncR-like plasmids; however, the IncRs rearranged extensively during the outbreak, contributing to highly dynamic plasmid profiles and resistomes.
The K. pneumoniae ST11 NDM-1 genotype that has been expanding in Poland since 2012 is largely monoclonal and represents a novel international high-risk lineage that is also spreading in other countries.
Introduction
Infections caused by carbapenemase-producing Enterobacterales (CPE), including those with New Delhi MBLs (NDMs), are among the leading global threats to public health. NDM CPE have spread worldwide from major reservoirs in South Asia and some other regions.1–3 Their blaNDM genes locate within randomly truncated Tn125 transposons,1,4 carried by plasmids of various replicon types and subtypes, including FII, A/C, X or R.1,2 Plasmid mobility contributes to the high taxonomic and clonal diversity of NDM CPE; however, clonal spread has been reported too.2
Since 2012, Poland has been experiencing massive expansion of Klebsiella pneumoniae ST11 producing NDM-1. Two previous studies analysed isolates from the period 2012–16 with ∼2600 unique infection or colonization cases5,6 and, in 2017–18, this more than doubled, so that the national CPE surveillance system5,6 stopped confirming carriage cases in the endemic Warsaw region due to logistic problems. The studies mentioned utilized standard methods and, for dealing with large isolate numbers, the Tn125 remnant specific for the outbreak strain, Tn125A, was used as a screening marker.5,6 The ST11 NDM-1 Tn125A isolates had two blaNDM-1 plasmids of the IncFII/pKPX-1 and/or IncR types, found first in a single isolate in Czechia,7 with IncR tending to rearrange.5,6 Here we present the evolution, phylogenetic relationships and genomic characteristics of the outbreak isolates.
Materials and methods
Clinical isolates
Sixty-seven K. pneumoniae ST11 NDM-1 Tn125A isolates, from the first outbreak case in 2012 to the end of 2018, were included (Table 1). Strains from 2012–16 were from previous study samples,5,6 whereas those from 2017–18 were qualified recently by Tn125 PCR mapping6 and MLST. Altogether, the isolates originated from 64 hospitals in 42 cities of 14/16 administrative regions. Additionally, four other known Polish carbapenemase-positive K. pneumoniae ST11 were included as controls, being non-outbreak isolates with NDM-1 or NDM-5 from 2015–16,6 KPC-2 from 20098 or OXA-48 from 2016.9
K. pneumoniae ST11 isolates included in the study: basic epidemiological data and resistomesa
| Isolate no. | Year | City and hospital symbol | Plasmid replicon profiles | Type of Tn125b | Acquired antimicrobial resistance genes | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β-lactams | aminoglycosidesc | fluoro quinolonesc | macrolide, lincosamide and streptogramin antibiotics | phenicols | sulphona mides | tetra cycline | trimetho prim | |||||
| 6713/12d | 2012 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3243/13e | 2013 | Poznań HP9 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3810/13 | 2013 | Poznań HP2 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaOXA-1 | — | — | mph(A) | — | — | tet(A) | dfrA14 |
| 3846/13f | 2013 | Warsaw HW9 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aac(3)-IIa | aac(6′)-Ib-cr | – | — | — | — | dfrA14 |
| 5264/13 | 2013 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 1272/14 | 2014 | Poznań HP1 | FII/pKPX-1, R, FIA, ColRNAI | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | — | — | dfrA14 |
| 2894/14 | 2014 | Kielce HT6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3108/14 | 2014 | Poznań HP11 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3301/14 | 2014 | Gorzów HF3 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4699/14 | 2014 | Warsaw HW18 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4854/14 | 2014 | Warsaw HW19 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 5254/14 | 2014 | Kraków HK6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 1982/15 | 2015 | Warsaw HW21 | FII/pKPX-1, R, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2044/15 | 2015 | Warsaw HW5 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2653/15 | 2015 | Warsaw HW6 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2887/15 | 2015 | Pruszków HWA7 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 3028/15 | 2015 | Warsaw HW24 | FII/pKPX-1, R | A | blaNDM-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 3688/15 | 2015 | Ostróda HN4 | R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4784/15 | 2015 | Białystok HB1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4841/15 | 2015 | Białystok HB2 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5085/15 | 2015 | Wrocław HD7 | FII/pKPX-1, R, FIBK, FIIK, L/M | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 175/16 | 2016 | Warsaw HW1 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 459/16 | 2016 | Białystok HB3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 722/16 | 2016 | Warsaw HW12 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1182/16 | 2016 | Radom HM11 | FII/pKPX-1, FIBK, FIIK | Ag | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1187/16 | 2016 | Warsaw HW13 | FII/pKPX-1, R, FIBK, L/M | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1204/16 | 2016 | Warsaw HW15 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1361/16 | 2016 | Biała HL3 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1463/16 | 2016 | Kutno HE1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 2012/16 | 2016 | Katowice HS3 | FII/pKPX-1, R, FIA, HI2 | A | blaNDM-1, blaCTX-M-9, blaTEM-1, blaOXA-1 | aadA2, ant(2'')-Ia, aph(3′′)-Ib, aph(6)-Id | qnrA1 | — | sul1, sul2 | tet(R) | dfrA14, dfrA16 | |
| 2155/16 | 2016 | Choszczno HZ6 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2569/16 | 2016 | Siedlce HM10 | FII/pKPX-1, R, FIB, HI1B | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1 | — | — | catA2 | — | — | dfrA14 |
| 3030/16 | 2016 | Inowrocław HC3 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3071/16 | 2016 | Gdańsk HG1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3199/16 | 2016 | Hajnówka HB4 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 3312/16 | 2016 | Augustów HB7 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4054/16 | 2016 | Kielce HT6 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 4268/16 | 2016 | Łódź HE9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 5356/16 | 2016 | Suwałki HB10 | FII/pKPX-1, FIB, FII, Col156 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5773/16 | 2016 | Olsztyn HN10 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 140/17 | 2017 | Łomża HB8 | FII/pKPX-1, L/M, ColRNAI | A | blaNDM-1, blaCTX-M-3, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aac(3)-IId, aadA2, armA | — | mph(E), msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 206/17 | 2017 | Wrocław HD9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | sul1 | — | dfrA14 |
| 344/17 | 2017 | Sokółka HB16 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 346/17 | 2017 | Warsaw HW11 | R | A | blaNDM-1, blaCTX-M-15 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 420/17 | 2017 | Płońsk HM4 | R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 427/17 | 2017 | Ciechanów HM9 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 759/17 | 2017 | Włoszczowa HT12 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 792/17 | 2017 | Warsaw HW3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1122/17 | 2017 | Warsaw HW22 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2612/17 | 2017 | Białogard HZ9 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 2768/17 | 2017 | Ełk HN7 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 3072/17 | 2017 | Grudziądz HC12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 3172/17 | 2017 | Gliwice HS14 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 3382/17 | 2017 | Bełchatów HE14 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 4141/17 | 2017 | Radzyń HL7 | FII/pKPX-1, R, FIBK, FIIK, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | qnrB19 | — | — | sul2 | — | dfrA14 |
| 4367/17 | 2017 | Białystok HB15 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 4819/17 | 2017 | Pisz HN22 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 8334/17 | 2017 | Kraków HK5 | FII/pKPX-1, R, HI2 | A | blaNDM-1, blaCTX-M-9, blaOXA-1 | aadA2, ant(2′′)-Ia | — | — | — | sul1 | — | dfrA14 |
| 8692/17 | 2017 | Jarocin HP6 | FII/pKPX-1, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 611/18 | 2018 | Kozienice HM23 | FII/pKPX-1, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib, aph(3′)-Ia | — | mph(A) | — | — | — | dfrA14 |
| 1047/18 | 2018 | Malbork HG11 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 1286/18 | 2018 | Przasnysz HM12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2137/18 | 2018 | Koszalin HZ3 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aadA1, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul1, sul2 | — | dfrA12, dfrA14 |
| 2201/18 | 2018 | Sieradz HE24 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 3364/18 | 2018 | Brodnica HC8 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 4041/18 | 2018 | Mońki HB19 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aadA1 | aac(6′)-Ib-cr | — | catA1 | sul1 | tet(D) | dfrA12, dfrA14 |
| 1659/18 | 2018 | Grajewo HB21 | R, FIA, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | catA1 | sul1 | — | dfrA12 |
| 3954/16 | 2016 | Kalisz HP10 | R, FIBK, FIIK, ColRNAI, Col(BS512) | K | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1, aadA2, aph(3′)-Ia, aph(3′)-VI | qnrS1 | mph(A) | — | sul1 | tet(A) | dfrA12 |
| 2839/15 | 2015 | Siedlce HM10 | R, FIBK, FIIK, X3, FIA(HI1) | P | blaNDM-5, blaCTX-M-15, blaDHA-1, blaTEM-1,-9 | aac(6′)-Ib, aadA1, aadA2 | qnrB4 | — | catA1 | sul1 | — | dfrA12 |
| 4286/09 | 2009 | Warsaw HW6 | FIB(pQil), FIIK, M2, Q1, Col440l | — | blaKPC-2, blaCTX-M-3 | aadA2, armA | qnrA1 | msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 4396/16 | 2016 | Białystok HB1 | R, FIBK, FIIK, | — | blaOXA-48, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aadA1, aadA2, armA | — | msr(E) | — | sul1 | — | — |
| Isolate no. | Year | City and hospital symbol | Plasmid replicon profiles | Type of Tn125b | Acquired antimicrobial resistance genes | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β-lactams | aminoglycosidesc | fluoro quinolonesc | macrolide, lincosamide and streptogramin antibiotics | phenicols | sulphona mides | tetra cycline | trimetho prim | |||||
| 6713/12d | 2012 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3243/13e | 2013 | Poznań HP9 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3810/13 | 2013 | Poznań HP2 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaOXA-1 | — | — | mph(A) | — | — | tet(A) | dfrA14 |
| 3846/13f | 2013 | Warsaw HW9 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aac(3)-IIa | aac(6′)-Ib-cr | – | — | — | — | dfrA14 |
| 5264/13 | 2013 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 1272/14 | 2014 | Poznań HP1 | FII/pKPX-1, R, FIA, ColRNAI | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | — | — | dfrA14 |
| 2894/14 | 2014 | Kielce HT6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3108/14 | 2014 | Poznań HP11 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3301/14 | 2014 | Gorzów HF3 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4699/14 | 2014 | Warsaw HW18 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4854/14 | 2014 | Warsaw HW19 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 5254/14 | 2014 | Kraków HK6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 1982/15 | 2015 | Warsaw HW21 | FII/pKPX-1, R, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2044/15 | 2015 | Warsaw HW5 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2653/15 | 2015 | Warsaw HW6 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2887/15 | 2015 | Pruszków HWA7 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 3028/15 | 2015 | Warsaw HW24 | FII/pKPX-1, R | A | blaNDM-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 3688/15 | 2015 | Ostróda HN4 | R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4784/15 | 2015 | Białystok HB1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4841/15 | 2015 | Białystok HB2 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5085/15 | 2015 | Wrocław HD7 | FII/pKPX-1, R, FIBK, FIIK, L/M | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 175/16 | 2016 | Warsaw HW1 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 459/16 | 2016 | Białystok HB3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 722/16 | 2016 | Warsaw HW12 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1182/16 | 2016 | Radom HM11 | FII/pKPX-1, FIBK, FIIK | Ag | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1187/16 | 2016 | Warsaw HW13 | FII/pKPX-1, R, FIBK, L/M | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1204/16 | 2016 | Warsaw HW15 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1361/16 | 2016 | Biała HL3 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1463/16 | 2016 | Kutno HE1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 2012/16 | 2016 | Katowice HS3 | FII/pKPX-1, R, FIA, HI2 | A | blaNDM-1, blaCTX-M-9, blaTEM-1, blaOXA-1 | aadA2, ant(2'')-Ia, aph(3′′)-Ib, aph(6)-Id | qnrA1 | — | sul1, sul2 | tet(R) | dfrA14, dfrA16 | |
| 2155/16 | 2016 | Choszczno HZ6 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2569/16 | 2016 | Siedlce HM10 | FII/pKPX-1, R, FIB, HI1B | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1 | — | — | catA2 | — | — | dfrA14 |
| 3030/16 | 2016 | Inowrocław HC3 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3071/16 | 2016 | Gdańsk HG1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3199/16 | 2016 | Hajnówka HB4 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 3312/16 | 2016 | Augustów HB7 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4054/16 | 2016 | Kielce HT6 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 4268/16 | 2016 | Łódź HE9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 5356/16 | 2016 | Suwałki HB10 | FII/pKPX-1, FIB, FII, Col156 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5773/16 | 2016 | Olsztyn HN10 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 140/17 | 2017 | Łomża HB8 | FII/pKPX-1, L/M, ColRNAI | A | blaNDM-1, blaCTX-M-3, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aac(3)-IId, aadA2, armA | — | mph(E), msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 206/17 | 2017 | Wrocław HD9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | sul1 | — | dfrA14 |
| 344/17 | 2017 | Sokółka HB16 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 346/17 | 2017 | Warsaw HW11 | R | A | blaNDM-1, blaCTX-M-15 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 420/17 | 2017 | Płońsk HM4 | R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 427/17 | 2017 | Ciechanów HM9 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 759/17 | 2017 | Włoszczowa HT12 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 792/17 | 2017 | Warsaw HW3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1122/17 | 2017 | Warsaw HW22 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2612/17 | 2017 | Białogard HZ9 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 2768/17 | 2017 | Ełk HN7 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 3072/17 | 2017 | Grudziądz HC12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 3172/17 | 2017 | Gliwice HS14 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 3382/17 | 2017 | Bełchatów HE14 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 4141/17 | 2017 | Radzyń HL7 | FII/pKPX-1, R, FIBK, FIIK, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | qnrB19 | — | — | sul2 | — | dfrA14 |
| 4367/17 | 2017 | Białystok HB15 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 4819/17 | 2017 | Pisz HN22 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 8334/17 | 2017 | Kraków HK5 | FII/pKPX-1, R, HI2 | A | blaNDM-1, blaCTX-M-9, blaOXA-1 | aadA2, ant(2′′)-Ia | — | — | — | sul1 | — | dfrA14 |
| 8692/17 | 2017 | Jarocin HP6 | FII/pKPX-1, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 611/18 | 2018 | Kozienice HM23 | FII/pKPX-1, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib, aph(3′)-Ia | — | mph(A) | — | — | — | dfrA14 |
| 1047/18 | 2018 | Malbork HG11 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 1286/18 | 2018 | Przasnysz HM12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2137/18 | 2018 | Koszalin HZ3 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aadA1, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul1, sul2 | — | dfrA12, dfrA14 |
| 2201/18 | 2018 | Sieradz HE24 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 3364/18 | 2018 | Brodnica HC8 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 4041/18 | 2018 | Mońki HB19 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aadA1 | aac(6′)-Ib-cr | — | catA1 | sul1 | tet(D) | dfrA12, dfrA14 |
| 1659/18 | 2018 | Grajewo HB21 | R, FIA, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | catA1 | sul1 | — | dfrA12 |
| 3954/16 | 2016 | Kalisz HP10 | R, FIBK, FIIK, ColRNAI, Col(BS512) | K | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1, aadA2, aph(3′)-Ia, aph(3′)-VI | qnrS1 | mph(A) | — | sul1 | tet(A) | dfrA12 |
| 2839/15 | 2015 | Siedlce HM10 | R, FIBK, FIIK, X3, FIA(HI1) | P | blaNDM-5, blaCTX-M-15, blaDHA-1, blaTEM-1,-9 | aac(6′)-Ib, aadA1, aadA2 | qnrB4 | — | catA1 | sul1 | — | dfrA12 |
| 4286/09 | 2009 | Warsaw HW6 | FIB(pQil), FIIK, M2, Q1, Col440l | — | blaKPC-2, blaCTX-M-3 | aadA2, armA | qnrA1 | msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 4396/16 | 2016 | Białystok HB1 | R, FIBK, FIIK, | — | blaOXA-48, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aadA1, aadA2, armA | — | msr(E) | — | sul1 | — | — |
Only acquired resistance genes are shown, as identified by ResFinder 3.2.13
Nomenclature of the Tn125 derivatives is according to the previous report.6
The aac(6′)-Ib-cr gene shown in the ‘aminoglycosides’ and ‘fluoroquinolones’ columns is the same gene, conferring resistance to both classes of antimicrobials.
The following resistance genes were located on the individual plasmids in this isolate: IncFII/pKPX-1, blaNDM-1 and aac(6′)-Ib; IncR, blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1, aph(3′′)-Ib, aph(6)-Id, aac(6′)-Ib-cr, dfrA14 and sul2; and IncFIBK, mph(A) and tet(A).
The following resistance genes were located on the individual plasmids in this isolate: IncFII/pKPX-1, blaNDM-1 and aac(6′)-Ib; IncR, blaTEM-1, blaOXA-1, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id, aac(6′)-Ib-cr, dfrA14 and sul2; and IncFIBK, mph(A) and tet(A).
The following resistance genes were located on the individual plasmids in this isolate: IncFII/pKPX-1, blaNDM-1 and aac(6′)-Ib; and IncR, blaCTX-M-15, blaOXA-1, aac(3)-IIa, aac(6′)-Ib-cr and dfrA14.
The Tn125 remnant in this isolate was truncated further by an IS26 insertion, retaining only 271 bp of the tat gene.
K. pneumoniae ST11 isolates included in the study: basic epidemiological data and resistomesa
| Isolate no. | Year | City and hospital symbol | Plasmid replicon profiles | Type of Tn125b | Acquired antimicrobial resistance genes | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β-lactams | aminoglycosidesc | fluoro quinolonesc | macrolide, lincosamide and streptogramin antibiotics | phenicols | sulphona mides | tetra cycline | trimetho prim | |||||
| 6713/12d | 2012 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3243/13e | 2013 | Poznań HP9 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3810/13 | 2013 | Poznań HP2 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaOXA-1 | — | — | mph(A) | — | — | tet(A) | dfrA14 |
| 3846/13f | 2013 | Warsaw HW9 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aac(3)-IIa | aac(6′)-Ib-cr | – | — | — | — | dfrA14 |
| 5264/13 | 2013 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 1272/14 | 2014 | Poznań HP1 | FII/pKPX-1, R, FIA, ColRNAI | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | — | — | dfrA14 |
| 2894/14 | 2014 | Kielce HT6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3108/14 | 2014 | Poznań HP11 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3301/14 | 2014 | Gorzów HF3 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4699/14 | 2014 | Warsaw HW18 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4854/14 | 2014 | Warsaw HW19 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 5254/14 | 2014 | Kraków HK6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 1982/15 | 2015 | Warsaw HW21 | FII/pKPX-1, R, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2044/15 | 2015 | Warsaw HW5 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2653/15 | 2015 | Warsaw HW6 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2887/15 | 2015 | Pruszków HWA7 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 3028/15 | 2015 | Warsaw HW24 | FII/pKPX-1, R | A | blaNDM-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 3688/15 | 2015 | Ostróda HN4 | R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4784/15 | 2015 | Białystok HB1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4841/15 | 2015 | Białystok HB2 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5085/15 | 2015 | Wrocław HD7 | FII/pKPX-1, R, FIBK, FIIK, L/M | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 175/16 | 2016 | Warsaw HW1 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 459/16 | 2016 | Białystok HB3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 722/16 | 2016 | Warsaw HW12 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1182/16 | 2016 | Radom HM11 | FII/pKPX-1, FIBK, FIIK | Ag | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1187/16 | 2016 | Warsaw HW13 | FII/pKPX-1, R, FIBK, L/M | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1204/16 | 2016 | Warsaw HW15 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1361/16 | 2016 | Biała HL3 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1463/16 | 2016 | Kutno HE1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 2012/16 | 2016 | Katowice HS3 | FII/pKPX-1, R, FIA, HI2 | A | blaNDM-1, blaCTX-M-9, blaTEM-1, blaOXA-1 | aadA2, ant(2'')-Ia, aph(3′′)-Ib, aph(6)-Id | qnrA1 | — | sul1, sul2 | tet(R) | dfrA14, dfrA16 | |
| 2155/16 | 2016 | Choszczno HZ6 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2569/16 | 2016 | Siedlce HM10 | FII/pKPX-1, R, FIB, HI1B | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1 | — | — | catA2 | — | — | dfrA14 |
| 3030/16 | 2016 | Inowrocław HC3 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3071/16 | 2016 | Gdańsk HG1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3199/16 | 2016 | Hajnówka HB4 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 3312/16 | 2016 | Augustów HB7 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4054/16 | 2016 | Kielce HT6 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 4268/16 | 2016 | Łódź HE9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 5356/16 | 2016 | Suwałki HB10 | FII/pKPX-1, FIB, FII, Col156 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5773/16 | 2016 | Olsztyn HN10 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 140/17 | 2017 | Łomża HB8 | FII/pKPX-1, L/M, ColRNAI | A | blaNDM-1, blaCTX-M-3, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aac(3)-IId, aadA2, armA | — | mph(E), msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 206/17 | 2017 | Wrocław HD9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | sul1 | — | dfrA14 |
| 344/17 | 2017 | Sokółka HB16 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 346/17 | 2017 | Warsaw HW11 | R | A | blaNDM-1, blaCTX-M-15 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 420/17 | 2017 | Płońsk HM4 | R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 427/17 | 2017 | Ciechanów HM9 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 759/17 | 2017 | Włoszczowa HT12 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 792/17 | 2017 | Warsaw HW3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1122/17 | 2017 | Warsaw HW22 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2612/17 | 2017 | Białogard HZ9 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 2768/17 | 2017 | Ełk HN7 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 3072/17 | 2017 | Grudziądz HC12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 3172/17 | 2017 | Gliwice HS14 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 3382/17 | 2017 | Bełchatów HE14 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 4141/17 | 2017 | Radzyń HL7 | FII/pKPX-1, R, FIBK, FIIK, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | qnrB19 | — | — | sul2 | — | dfrA14 |
| 4367/17 | 2017 | Białystok HB15 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 4819/17 | 2017 | Pisz HN22 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 8334/17 | 2017 | Kraków HK5 | FII/pKPX-1, R, HI2 | A | blaNDM-1, blaCTX-M-9, blaOXA-1 | aadA2, ant(2′′)-Ia | — | — | — | sul1 | — | dfrA14 |
| 8692/17 | 2017 | Jarocin HP6 | FII/pKPX-1, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 611/18 | 2018 | Kozienice HM23 | FII/pKPX-1, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib, aph(3′)-Ia | — | mph(A) | — | — | — | dfrA14 |
| 1047/18 | 2018 | Malbork HG11 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 1286/18 | 2018 | Przasnysz HM12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2137/18 | 2018 | Koszalin HZ3 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aadA1, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul1, sul2 | — | dfrA12, dfrA14 |
| 2201/18 | 2018 | Sieradz HE24 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 3364/18 | 2018 | Brodnica HC8 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 4041/18 | 2018 | Mońki HB19 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aadA1 | aac(6′)-Ib-cr | — | catA1 | sul1 | tet(D) | dfrA12, dfrA14 |
| 1659/18 | 2018 | Grajewo HB21 | R, FIA, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | catA1 | sul1 | — | dfrA12 |
| 3954/16 | 2016 | Kalisz HP10 | R, FIBK, FIIK, ColRNAI, Col(BS512) | K | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1, aadA2, aph(3′)-Ia, aph(3′)-VI | qnrS1 | mph(A) | — | sul1 | tet(A) | dfrA12 |
| 2839/15 | 2015 | Siedlce HM10 | R, FIBK, FIIK, X3, FIA(HI1) | P | blaNDM-5, blaCTX-M-15, blaDHA-1, blaTEM-1,-9 | aac(6′)-Ib, aadA1, aadA2 | qnrB4 | — | catA1 | sul1 | — | dfrA12 |
| 4286/09 | 2009 | Warsaw HW6 | FIB(pQil), FIIK, M2, Q1, Col440l | — | blaKPC-2, blaCTX-M-3 | aadA2, armA | qnrA1 | msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 4396/16 | 2016 | Białystok HB1 | R, FIBK, FIIK, | — | blaOXA-48, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aadA1, aadA2, armA | — | msr(E) | — | sul1 | — | — |
| Isolate no. | Year | City and hospital symbol | Plasmid replicon profiles | Type of Tn125b | Acquired antimicrobial resistance genes | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β-lactams | aminoglycosidesc | fluoro quinolonesc | macrolide, lincosamide and streptogramin antibiotics | phenicols | sulphona mides | tetra cycline | trimetho prim | |||||
| 6713/12d | 2012 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3243/13e | 2013 | Poznań HP9 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | aac(6′)-Ib-cr | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3810/13 | 2013 | Poznań HP2 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaOXA-1 | — | — | mph(A) | — | — | tet(A) | dfrA14 |
| 3846/13f | 2013 | Warsaw HW9 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(6′)-Ib, aac(3)-IIa | aac(6′)-Ib-cr | – | — | — | — | dfrA14 |
| 5264/13 | 2013 | Poznań HP5 | FII/pKPX-1, R, FIA, FIBK, FIIK | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 1272/14 | 2014 | Poznań HP1 | FII/pKPX-1, R, FIA, ColRNAI | A | blaNDM-1, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | — | — | — | — | dfrA14 |
| 2894/14 | 2014 | Kielce HT6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3108/14 | 2014 | Poznań HP11 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 3301/14 | 2014 | Gorzów HF3 | R, FIA, FIBK, FIIK, L/M | A | blaNDM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4699/14 | 2014 | Warsaw HW18 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4854/14 | 2014 | Warsaw HW19 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1 | aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 5254/14 | 2014 | Kraków HK6 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 1982/15 | 2015 | Warsaw HW21 | FII/pKPX-1, R, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2044/15 | 2015 | Warsaw HW5 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2653/15 | 2015 | Warsaw HW6 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 2887/15 | 2015 | Pruszków HWA7 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 3028/15 | 2015 | Warsaw HW24 | FII/pKPX-1, R | A | blaNDM-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 3688/15 | 2015 | Ostróda HN4 | R, FIA, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | mph(A) | — | sul2 | tet(A) | dfrA14 |
| 4784/15 | 2015 | Białystok HB1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4841/15 | 2015 | Białystok HB2 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5085/15 | 2015 | Wrocław HD7 | FII/pKPX-1, R, FIBK, FIIK, L/M | A | blaNDM-1, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 175/16 | 2016 | Warsaw HW1 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 459/16 | 2016 | Białystok HB3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 722/16 | 2016 | Warsaw HW12 | FII/pKPX-1, R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1182/16 | 2016 | Radom HM11 | FII/pKPX-1, FIBK, FIIK | Ag | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 1187/16 | 2016 | Warsaw HW13 | FII/pKPX-1, R, FIBK, L/M | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1204/16 | 2016 | Warsaw HW15 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1361/16 | 2016 | Biała HL3 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | sul2 | — | dfrA14 |
| 1463/16 | 2016 | Kutno HE1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aph(3′′)-Ib, aph(6)-Id | — | — | — | sul2 | tet(A) | dfrA14 |
| 2012/16 | 2016 | Katowice HS3 | FII/pKPX-1, R, FIA, HI2 | A | blaNDM-1, blaCTX-M-9, blaTEM-1, blaOXA-1 | aadA2, ant(2'')-Ia, aph(3′′)-Ib, aph(6)-Id | qnrA1 | — | sul1, sul2 | tet(R) | dfrA14, dfrA16 | |
| 2155/16 | 2016 | Choszczno HZ6 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2569/16 | 2016 | Siedlce HM10 | FII/pKPX-1, R, FIB, HI1B | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1 | — | — | catA2 | — | — | dfrA14 |
| 3030/16 | 2016 | Inowrocław HC3 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3071/16 | 2016 | Gdańsk HG1 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 3199/16 | 2016 | Hajnówka HB4 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 3312/16 | 2016 | Augustów HB7 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 4054/16 | 2016 | Kielce HT6 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 4268/16 | 2016 | Łódź HE9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 5356/16 | 2016 | Suwałki HB10 | FII/pKPX-1, FIB, FII, Col156 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 5773/16 | 2016 | Olsztyn HN10 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 140/17 | 2017 | Łomża HB8 | FII/pKPX-1, L/M, ColRNAI | A | blaNDM-1, blaCTX-M-3, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aac(3)-IId, aadA2, armA | — | mph(E), msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 206/17 | 2017 | Wrocław HD9 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | sul1 | — | dfrA14 |
| 344/17 | 2017 | Sokółka HB16 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 346/17 | 2017 | Warsaw HW11 | R | A | blaNDM-1, blaCTX-M-15 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 420/17 | 2017 | Płońsk HM4 | R | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | sul2 | — | dfrA14 |
| 427/17 | 2017 | Ciechanów HM9 | FII/pKPX-1, R, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 759/17 | 2017 | Włoszczowa HT12 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 792/17 | 2017 | Warsaw HW3 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 1122/17 | 2017 | Warsaw HW22 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 2612/17 | 2017 | Białogard HZ9 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 2768/17 | 2017 | Ełk HN7 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 3072/17 | 2017 | Grudziądz HC12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 3172/17 | 2017 | Gliwice HS14 | FII/pKPX-1, R | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | — |
| 3382/17 | 2017 | Bełchatów HE14 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(3)-IIa | — | — | — | — | — | — |
| 4141/17 | 2017 | Radzyń HL7 | FII/pKPX-1, R, FIBK, FIIK, N | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib | qnrB19 | — | — | sul2 | — | dfrA14 |
| 4367/17 | 2017 | Białystok HB15 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aadA1 | — | — | catA1 | sul1 | tet(D) | dfrA1, dfrA14 |
| 4819/17 | 2017 | Pisz HN22 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 8334/17 | 2017 | Kraków HK5 | FII/pKPX-1, R, HI2 | A | blaNDM-1, blaCTX-M-9, blaOXA-1 | aadA2, ant(2′′)-Ia | — | — | — | sul1 | — | dfrA14 |
| 8692/17 | 2017 | Jarocin HP6 | FII/pKPX-1, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 611/18 | 2018 | Kozienice HM23 | FII/pKPX-1, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib, aph(3′)-Ia | — | mph(A) | — | — | — | dfrA14 |
| 1047/18 | 2018 | Malbork HG11 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaOXA-1 | — | — | — | — | — | — | dfrA14 |
| 1286/18 | 2018 | Przasnysz HM12 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib, aac(3)-IIa | — | — | — | — | — | dfrA14 |
| 2137/18 | 2018 | Koszalin HZ3 | FII/pKPX-1, R, FIBK | A | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1 | aac(6′)-Ib, aadA1, aph(3′′)-Ib, aph(6)-Id | — | — | — | sul1, sul2 | — | dfrA12, dfrA14 |
| 2201/18 | 2018 | Sieradz HE24 | FII/pKPX-1 | A | blaNDM-1, blaOXA-1 | aac(6′)-Ib | — | — | — | — | — | dfrA14 |
| 3364/18 | 2018 | Brodnica HC8 | FII/pKPX-1 | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | — | — | — | dfrA14 |
| 4041/18 | 2018 | Mońki HB19 | FII/pKPX-1, FIBK, FIIK | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aadA1 | aac(6′)-Ib-cr | — | catA1 | sul1 | tet(D) | dfrA12, dfrA14 |
| 1659/18 | 2018 | Grajewo HB21 | R, FIA, FIBK, FIIK, ColRNAI | A | blaNDM-1, blaCTX-M-15, blaOXA-1 | aac(6′)-Ib-cr, aac(3)-IIa | aac(6′)-Ib-cr | — | catA1 | sul1 | — | dfrA12 |
| 3954/16 | 2016 | Kalisz HP10 | R, FIBK, FIIK, ColRNAI, Col(BS512) | K | blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aac(3)-IIa, aadA1, aadA2, aph(3′)-Ia, aph(3′)-VI | qnrS1 | mph(A) | — | sul1 | tet(A) | dfrA12 |
| 2839/15 | 2015 | Siedlce HM10 | R, FIBK, FIIK, X3, FIA(HI1) | P | blaNDM-5, blaCTX-M-15, blaDHA-1, blaTEM-1,-9 | aac(6′)-Ib, aadA1, aadA2 | qnrB4 | — | catA1 | sul1 | — | dfrA12 |
| 4286/09 | 2009 | Warsaw HW6 | FIB(pQil), FIIK, M2, Q1, Col440l | — | blaKPC-2, blaCTX-M-3 | aadA2, armA | qnrA1 | msr(E) | — | sul1 | — | dfrA12, dfrA14 |
| 4396/16 | 2016 | Białystok HB1 | R, FIBK, FIIK, | — | blaOXA-48, blaCTX-M-15, blaTEM-1, blaOXA-1,-9 | aadA1, aadA2, armA | — | msr(E) | — | sul1 | — | — |
Only acquired resistance genes are shown, as identified by ResFinder 3.2.13
Nomenclature of the Tn125 derivatives is according to the previous report.6
The aac(6′)-Ib-cr gene shown in the ‘aminoglycosides’ and ‘fluoroquinolones’ columns is the same gene, conferring resistance to both classes of antimicrobials.
The following resistance genes were located on the individual plasmids in this isolate: IncFII/pKPX-1, blaNDM-1 and aac(6′)-Ib; IncR, blaNDM-1, blaCTX-M-15, blaTEM-1, blaOXA-1, aph(3′′)-Ib, aph(6)-Id, aac(6′)-Ib-cr, dfrA14 and sul2; and IncFIBK, mph(A) and tet(A).
The following resistance genes were located on the individual plasmids in this isolate: IncFII/pKPX-1, blaNDM-1 and aac(6′)-Ib; IncR, blaTEM-1, blaOXA-1, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id, aac(6′)-Ib-cr, dfrA14 and sul2; and IncFIBK, mph(A) and tet(A).
The following resistance genes were located on the individual plasmids in this isolate: IncFII/pKPX-1, blaNDM-1 and aac(6′)-Ib; and IncR, blaCTX-M-15, blaOXA-1, aac(3)-IIa, aac(6′)-Ib-cr and dfrA14.
The Tn125 remnant in this isolate was truncated further by an IS26 insertion, retaining only 271 bp of the tat gene.
WGS
Genomes of all isolates were sequenced with the Illumina MiSeq platform (Illumina, San Diego, CA, USA); reads were assembled with SPAdes 3.10.1.10 Three isolates were also subjected to long-read sequencing using MinION (Oxford Nanopore Technologies, Oxford, UK). The MiSeq and MinION hybrid read assemblies were done with MaSuRCA 3.2.2.11
Clonality analysis
Core-genome MLST (cgMLST) profiles were defined using the BIGSdb software12 and compared using BioNumerics 7.6.3 (Applied Maths, Sint-Martens-Latem, Belgium). The SNP analysis of the sample was done using BioNumerics, using the first outbreak isolate 6713/12 as a reference. The SNP-based phylogenetic analysis of the isolates against all K. pneumoniae ST11 genomes available in GenBank was performed using Parsnp, with and without the recombination filtration option (https://github.com/marbl/parsnp), and using BioNumerics. The ST11 sequences were downloaded using the NCBI Genome Downloading Scripts (https://github.com/kblin/ncbi-genome-download). The phylogenetic tree was depicted using iTOL (https://itol.embl.de).
Resistomes, Tn125 and plasmid analyses
Antimicrobial resistance genes were detected using ResFinder 3.1, applying a criterion of 100% sequence identity.13 Tn125-like structures were analysed using Lasergene (DNASTAR, Madison, WI, USA). Plasmid replicon types were identified using PlasmidFinder 2.1.14 Comparisons of plasmids were done using BLASTn and the results were visualized using BRIG (http://brig.sourceforge.net/).
K/O serotypes and virulomes
Capsule (K) and LPS (O) antigen types of the isolates were determined using Kaptive (https://github.com/katholt/Kaptive). Virulomes were defined using BIGSdb, with 90% identity threshold, and the Institut Pasteur MLST databases (https://bigsdb.web.pasteur.fr/klebsiella/klebsiella.html).
Nucleotide sequence accession numbers
Genomic sequences have been deposited in the NCBI under the Bio-Project and Bio-Samples numbers PRJNA610720 and SAMN14314560–14314631, respectively. Sequences of plasmids of the NMI6713/12, NMI3243/13 and NMI3846/13 isolates are available under the following GenBank accession numbers: (i) IncFII/pKPX-1 types: pIncFII_6713, MT415054; pIncFII_3846, MT415055; and pIncFII_3243, MT415056; (ii) IncR types: pIncR_6713, MT415057; pIncR_3846, MT415058; and pIncR_3243, MT415059; and (iii) IncFIBK types: pIncFIBK_6713, MT439327; and pIncFIBK_3243, MT439326.
Results and discussion
Clonality and phylogenetic analysis
This genomic analysis followed two previous studies on the expansion of the particular K. pneumoniae ST11 NDM-1 genotype in Poland since 2012.5,6 Three early isolates, including the first one identified (6713/12), were long-read sequenced, revealing chromosomes of ∼5.46–5.52 Mb and two to three plasmids of various types and size (described below). The specific Tn125A element of the epidemic organism5,6 encompassed 2994 bp of Tn125, from a 253 bp part of the upstream ISAba125 tnpA gene to 806 bp of tat.4
The cgMLST analysis showed high homogeneity of all but one of the ST11 NDM-1 Tn125A isolates, differing in only zero to six loci in pairs of closest relatives and a maximum distance of 14, comprising two subclusters of 18 and 9 isolates identical in all 689 loci (Figure S1, available as Supplementary data at JAC Online). Otherwise, one isolate (1659/18) and the four control ST11 strains varied at 71–95 loci from the most similar outbreak profiles. The in-sample SNP analysis revealed 564 chromosomal polymorphic positions in total among 66/67 ST11 NDM-1 Tn125A isolates, with 10–70 SNPs between any individual isolate and the reference index isolate (Table S1 and Figure S2). The temporal distribution of the SNPs with respect to the reference isolate reflected their gradual accumulation during the outbreak, from 12 SNPs on average in 2013 to 38 in 2018, showing the population diversification process (Figure S3). Like in cgMLST, one isolate (1659/18) fell outside of the cluster, differing by 2480 SNPs from the reference and locating closer to the controls, namely the OXA-48 or NDM-5 producers (Table S1 and Figure S2). Most of the SNPs (∼92%–94%) between these and the outbreak cluster accumulated within a ∼0.76 Mb chromosome segment, suggesting extensive recombination with a more distant clone during ST11 evolution, as proposed previously.15,16 The analysis showed that not all ST11 NDM-1 Tn125A isolates must be of the outbreak; the ‘orphan’ isolate (1659/18) might arise by import or acquisition of a Tn125A-carrying plasmid from the epidemic genotype (discussed below), as proposed for other organisms.6
The 66 outbreak isolates were subjected to phylogenetic analysis against all 934 ST11 strains identified among 8130 K. pneumoniae genomes available in GenBank (as of 3 December 2019). The sample clustered in a clade with 72 isolates recovered worldwide, 34 of which had NDM-1, including 20 closest relatives with the Tn125A element (Figure 1). These were collected during 2013–16 in Greece (n = 14), Bulgaria, Poland, Italy and the UK (mainly by the EuSCAPE CPE survey17,18) and in Tunisia and the USA. The European isolates formed a uniform cluster, in which the non-Polish strains differed by only 25–87 SNPs from the Polish index isolate (Table S2). However, the SNP distribution split precisely the Polish and Greek subclusters and the isolates from other countries (Figure S4). In summary, even though related ST11 K. pneumoniae strains of the basal clade occurred globally (Figure 1), the analysed genotype has emerged mainly in Europe, especially its mid-southern part.5–7,19 This study has demonstrated the international character of the sublineage, with epidemic potential documented at least in Poland and Greece.5,6,19
SNP-based phylogenetic tree of all study Polish K. pneumoniae ST11 isolates compared with the international ST11 genomes available in GenBank. The 66 Polish outbreak and 72 related international isolates forming a single clade are marked in blue, as are representatives of other clades, manually selected, and Polish non-outbreak or control ST11 strains are marked in grey. Numbers in the inner circle correspond to original numbers of the study isolates or GenBank assembly numbers. The presence of the blaNDM-1 gene is indicated by green or brown: the green circle corresponds to the Tn125A element and the brown circle corresponds to other Tn125 derivatives. The presence of IncFII/pKPX-1 and IncR replicons is indicated in the outer circles using black and purple, respectively. The tree was constructed using Parsnp and visualized with iTOL. BG, Bulgaria; CA, Canada; CZ, Czechia; DE, Germany; ES, Spain; GR, Greece; HU, Hungary; IN, India; MY, Malaysia; IT, Italy; NO, Norway; PK, Pakistan; PL, Poland; RU, Russia; SK, Slovakia; TH, Thailand, TN, Tunisia; UK, United Kingdom; US, USA; VN, Vietnam. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.
Plasmid analysis and resistomes
Perhaps the earliest single isolate of the ST11 NDM-1 Tn125A sublineage was found in 2012 in Czechia, with two plasmids of the IncFII/pKPX-1 (pB-3002cz) and IncR (pS-3002cz) types, sharing a ∼40 kb region comprising Tn125A.7 The previous Polish outbreak studies revealed the common presence of the IncFII/pKPX-1-like plasmids and the high prevalence but also frequent rearrangements of the IncRs.5,6 The analysis reported here has provided the most comprehensive data on the plasmid content of the epidemic genotype. Thirteen replicons in total were detected in the 66 isolates, split into 21 profiles of one to five replicons each (Table 1), showing again the differentiation of the organism. The prevailing replicons were IncFII/pKPX-1 and IncR, present in 61 and 33 isolates, respectively, with each isolate having at least one of these and 28 isolates having both (as did the international closest relatives; Figure 1).
The long-read sequencing of three early isolates (6713/12, 3243/13 and 3846/13) revealed their complete plasmid assemblies, with whole IncFII/pKPX-1 and IncR molecules, plus IncFIBK in two isolates. Tn125A-carrying pIncFII_6713 and pIncFII_3846 (both ∼97.7 kb) showed 100% coverage and almost 100% identity with the Czech prototype pB-3002cz (Figure S5). pIncFII_3243 (∼76.8 kb) had an ∼20 kb deletion, retaining Tn125A. In accordance with a previous observation,5 the IncRs were less stable (Figure S6). pIncR_6713 (∼74 kb) had two separate blocks (∼34.5 and ∼23.6 kb) of >99% identity with pS-3002cz, including a 1686 bp Tn125 remnant. Modifications of pIncR_3243 (∼69.6 kb) and pIncR_3846 (∼47.3 kb) resulted in ∼16 and ∼40 kb deletions, respectively, including whole Tn125s. Therefore, co-detection of IncFII/pKPX-1 and IncR replicons in outbreak isolates needn’t imply the presence of two blaNDM-1 copies, as in the very first Czech and Polish isolates. Fragments of extensive homology in two coexisting plasmids likely recombine yielding multiple rearrangements. Interestingly, the single non-epidemic, ‘orphan’ ST11 NDM-1 Tn125A isolate (1659/18) had a sole IncR plasmid of 100% coverage and ∼100% identity with pS-3002cz, suggesting acquisition from the outbreak organism.
With around 40 different gene profiles, resistomes of the 66 outbreak isolates were the main aspect of their in-sample diversity, largely due to multiple combinations of seven β-lactamase and 10 aminoglycoside-modifying enzyme (AME) genes (Table 1). The resistomes comprised 3–15 acquired genes and an average isolate had 7.3 of these. Most of the genes were plasmidic; however, only for the three long-read sequenced isolates could the genes be unambiguously assigned to individual plasmids. IncFII/pKPX-1 carried blaNDM-1 and aac(6′)-Ib. The IncRs varied with blaNDM-1, blaCTX-M-15, blaTEM-1 and blaOXA-1 β-lactamase genes, aac(6′)-Ib, aph(3′′)-Ib, aph(6)-Id and aac(3)-IIa AME genes [the aac(6′)-Ib-cr variant also compromising fluoroquinolones] and dfrA14 and sul2 genes (affecting trimethoprim and sulphonamides, respectively). With time, correlations between resistance genes and, for example, IncR-like plasmids have loosened, likely due to their rearrangements or loss, and acquisition of multiple others, resulting in ∼20 newer plasmid profiles.
Serotypes and virulomes
The K and O antigens of the outbreak isolates were identified as KL24 and O2 variant 1 (O2v1), respectively, differing from the ‘orphan’ and control strains (Table S3). The serotype diversity of all the ST11 isolates used was remarkable, corresponding to earlier reports; however, knowledge on the K/O antigen distribution in ST11 remains scarce.16,20,21 Virulence-associated genes (Table S3) included chromosomal mrkABCDF and mrkHIJ operons, responsible for type 3 fimbriae, involved in adhesion and biofilm formation.22,23 The second group comprised the fyuA, irp1/2 and ybtAEPQSTUX genes specifying synthesis and secretion of yersiniabactin, a siderophore overrepresented in hypervirulent and invasive K. pneumoniae strains.22,24,25 The ybt cluster represented the YbST230 type and resided in a 92 344 bp ICEKp element (six SNPs with the ICEKp11 variant), the major ybt platform in K. pneumoniae, inserted into the tRNA-Asn locus.24 The identical arrangement was found in the close relatives of the outbreak isolates from Greece, Bulgaria and other countries, whereas the Polish ‘orphan’ ST11 NDM-1 Tn125A and three control ST11 strains had different ybt loci.
Conclusions
This study revealed the evolution and genomic characteristics of the K. pneumoniae ST11 NDM-1 lineage, the expansion of which in Poland has been one of the most spectacular recent phenomena in CPE epidemiology in Europe. The strictly clonal type of the outbreak has been confirmed, though one isolate with the same ST and Tn125 variant was shown to be non-related. The epidemic organism had few but important virulence factors, and various resistance mechanisms, the diversity of which was driven by changes of the plasmid content and rearrangements. Phylogenetically the isolates were virtually identical to strains that caused the outbreak in Greece19 and spread to other countries. Therefore, we suggest the sublineage ST11 NDM-1 Tn125A represents a novel high-risk K. pneumoniae genotype and provide baseline data for its future identification and tracking.
Acknowledgements
A part of the data described in the paper was presented at the Twenty-Eighth European Congress of Clinical Microbiology and Infectious Diseases, Madrid, Spain, 2018 (Poster P2339) and the Twelfth International Meeting on Microbial Epidemiological Markers, Dubrovnik, Croatia, 2019 (Poster P250).
We are very thankful to: (i) Elżbieta Literacka and Dorota Żabicka from the National Reference Centre for Susceptibility Testing in Warsaw for the study material; (ii) Marta Biedrzycka, Małgorzata Herda and Katarzyna Malinowska for their excellent experimental support; and (iii) all of the clinical microbiologists who provided the study material.
Funding
This work was partially financed by: (i) grants 2017/01/X/NZ7/00220 and 2018/31/B/NZ7/04002 from the Polish National Science Centre; and (ii) SPUB MIKROBANK from the Polish Ministry of Science and Higher Education. In addition, a 2017 French Government Scholarship from the French Embassy in Poland was given to R.I. to visit the Brisse lab.
Transparency declarations
None to declare.
Supplementary data
Figures S1 to S6 and Tables S1 to S3 are available as Supplementary data at JAC Online.
