KPC-3-Producing Klebsiella pneumoniae in Portugal Linked to Previously Circulating Non-CG258 Lineages and Uncommon Genetic Platforms (Tn4401d-IncFIA and Tn4401d-IncN)

Abstract

KPC-3-producing bacteria are endemic in many countries but only recently became apparent their wide distribution in different Portuguese hospitals. The aim of this study is to characterize genetic backgrounds associated with blaKPC−3 among Klebsiella pneumoniae isolates recently identified on non-hospitalized patients in Portugal. Twenty KPC-producing K. pneumoniae identified between October 2014 and November 2015 in three different community laboratories were characterized. Isolates were mainly from patients from long-term care facilities (n = 11) or nursing homes (n = 6), most of them (75%) previously hospitalized in different Portuguese hospitals. Standard methods were used for bacterial identification and antibiotic susceptibility testing. Carbapenemase production was assessed by the Blue-Carba test, and identification of bla genes was performed by PCR and sequencing. Epidemiological features of KPC-producing K. pneumoniae included population structure (XbaI-PFGE, MLST and wzi sequencing), genetic context (mapping of Tn4401), and plasmid (replicon typing, S1-PFGE, and hybridization) analysis. All K. pneumoniae isolates produced KPC-3, with two MDR K. pneumoniae epidemic clones representing 75% of the isolates, namely ST147 (wzi64/K14.64, February–November 2015) and ST15 (two lineages exhibiting capsular types wzi19/K19 or wzi93/K60, July-November 2015). Other sporadic clones were detected: ST231 (n = 3; wzi104), ST348 (n = 1; wzi94) and ST109 (n = 1, wzi22/K22.37). blaKPC−3 was identified within Tn4401d in all isolates, located in most cases (80%) on cointegrated plasmids (repAFIA+repAFII+oriColE1;105-250 kb) or in 50 kb IncN plasmids. In conclusion, this study highlights a polyclonal structure of KPC-3-producing K. pneumoniae and the predominance of the ST147 clone among non-hospitalized patients in Portugal, linked to platforms still unnoticed in Europe (blaKPC−3-Tn4401d-IncFIA) or firstly reported (blaKPC−3-Tn4401d-IncN). This scenario underlines the recent penetration of successful mobile genetic elements in previously circulating MDR K. pneumoniae lineages (mainly ST147 and ST15) in Portugal, rather than the importation of the global lineages from clonal group 258.

Significant temporal shifts on clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings

“…Notably, this ST11-KL105 K. pneumoniae lineage was not detected among ESBL- or carbapenemase-producers circulating in the same clinical institutions and period of time [7, 9] , indicating that the selection of ESBL or qAmpC producing K. pneumoniae occurred independently in different genetic backgrounds, or an eventual importation event of a DHA-1-producing ST11 K. pneumoniae strain. In fact, ST11-KL105 isolates producing DHA-1 have been reported in different countries, either causing infection or linked to human colonization (Table S2).…”

“…In Portugal, relevant epidemiological changes regarding resistance to extended-spectrum β-lactams in Enterobacteriaceae have been observed in the last decades, including: i) escalating resistance rates to third-generation cephalosporins, ii) long-term dissemination of qAmpC (mainly in K. pneumoniae ), iii) emergence and dispersal of plasmid-mediated carbapenemase resistance and iv) the shift from E. coli to K. pneumoniae as the main species associated with this problem (https://ecdc.europa.eu/en/antimicrobial-resistance/surveillance-and-disease-data/data-ecdc) [7–9] . ESBL-producing Enterobacteriaceae are endemic in different Portuguese clinical settings, and the widespread of main ESBL (CTX-M-15, SHV-12), and subsequently KPC-3, had been linked to the spread of particular K. pneumoniae (ST15, ST147, ST348) or E. coli clones (ST131) and plasmid types (IncR, IncF, IncHI2) [7, 9, 10] .…”

On the front line of Klebsiella pneumoniae surface structures understanding: establishment of Fourier Transform Infrared (FT-IR) spectroscopy as a capsule typing method

“…Detailed and comprehensive phylogenomics studies have shown a high specificity between certain lineages and particular K-types within CG11, CG14, CG15 or CG258 7,14,15,19,20,28 . In fact, MDR Kp expansion causing hospital or community acquired infections has been driven by clonal selection, since the population is dominated by a small number of lineages exhibiting particular K-types, where phenomes of capsular switching seem to occur sporadically at least in short time-scales (this study, Kaptive database) 6,7,38,39 . In some cases, capsular recombination events involving phenotypic changes might represent important evolutionary steps with several biological consequences, as occurred with the two different ST258 clades exhibiting KL106 or KL107 K-types, that are of interest to detect 40,41 .…”

Genetic and Biochemical Characterization of OXA-519, a Novel OXA-48-Like β-Lactamase

“…Multilocus sequence typing (MLST) of K. pneumoniae 1210, determined using MLST 1.8 software (23), revealed a novel ST, which was assigned the novel allelic profile ST2728 (1-1-211-1-1-1-1) by the K. pneumoniae MLST database (http:// bigsdb.web.pasteur.fr). This sequence type is a single-locus variant (SLV) of ST15 (1-1-1-1-1-1-1-1), a pandemic clone widely described in association with carbapenemases or ESBLs and sometimes involved in outbreaks (24)(25)(26). The acquired resistance genes were identified using ResFinder server v2.1 (http://cge.cbs.dtu.dk/services/ ResFinder-2.1) (27).…”