A multispecies outbreak of carbapenem-resistant bacteria harboring the blaKPC gene in a non-classical transposon element

Abstract

Background Klebsiella pneumoniae is the most frequent KPC-producing bacteria. The blaKPC gene is frequently embedded in Tn4401 transposon, and less frequently in non-Tn4401 elements (NTEKPC) variants I-III. The first case of KPC in the UC-CHRISTUS Clinical Hospital was detected in Pseudomonas aeruginosa. Soon after this event, KPC was detected in 2 additional Pseudomonas aeruginosa, 3 Escherichia coli, 3 Enterobacter cloacae, 3 Klebsiella pneumoniae, and 1 Citrobacter freundii, isolated from 6 different patients. We aimed to elucidate the possible mechanisms of genetic transfer and dissemination of the blaKPC gene among isolates of this multispecies outbreak. A molecular epidemiology analysis of the above mentioned clinical isolates (n = 13) through Multi-Locus Sequence Typing, plasmid analysis, Pulsed-Field Gel-Electrophoresis, and Whole-genome sequencing (WGS) was performed. Results High-risk sequence types were found: K. pneumoniae ST11, P. aeruginosa ST654, and E. cloacae ST114. All enterobacterial isolates were not clonal except for 3 E. coli isolated from the same patient. WGS analysis in 6 enterobacterial isolates showed that 4 of them had blaKPC embedded in a novel variant of NTEKPC designated NTEKPC-IIe. Upstream of blaKPC gene there was a 570 pb truncated blaTEM-1 gene followed by an insertion sequence that was 84% similar to ISEc63, a 4473 bp element of the Tn3 family. Downstream the blaKPC gene there was a truncated ISKpn6 gene, and the inverted repeat right sequence of Tn4401. The ISec63-like element together with the blaKPC gene plus Tn4401 remnants were inserted in the Tra operon involved in conjugative transfer of the plasmid. This NTE was carried in a broad host-range IncN plasmid. P. aeruginosa isolates carried blaKPC gene embedded in a typical Tn4401b transposon in a different plasmid, suggesting that there was no plasmid transfer between Enterobacteriaceae and P. aeruginosa as initially hypothesized. Conclusions Most enterobacterial isolates had blaKPC embedded in the same NTEKPC-IIe element, suggesting that this multispecies KPC outbreak was due to horizontal gene transfer rather than clonal spread. This poses a greater challenge to infection control measures often directed against containment of clonal spread.

Acquisition of resistance to ceftazidime-avibactam during infection treatment in Pseudomonas aeruginosa through D179Y mutation in one of two blaKPC-2 gene copies without losing carbapenem resistance

“…The plasmids described in this work, pPA-1 and pPA-2, were similar to pPA2047 a 43,660 bp plasmid from P. aeruginosa recently reported in Argentina (>65% identity) (Cejas et al, 2022), and to pPae-13, a plasmid that was recently reported in a KPC-PA clinical isolate in the same Institutional Hospital as the present work (>60% identity) (Wozniak et al, 2021). It is possible that replicative transposition of bla KPC -containing Tn4401b transposon in pPae-13 plasmid had produced pPA-1, and pPA-2 subsequently evolved through point mutation.…”

Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche

“…It cannot be ruled out that pDCCK1-KPC might have been transferred from E. hormaechei HA2pEho to K. pneumoniae HA7pKpn within the patient, although it is not possible to confirm it. Putative HGT of bla KPC-2 has been previously reported to have taken place intrapatient (Anchordoqui et al, 2015;Wozniak et al, 2021). The study by Anchordoqui et al (2015) was also carried out in Argentina, and HGT was reported to have taken place between E. coli and K. pneumoniae, E. cloacae and K. pneumoniae, and Citrobacter freundii and Klebsiella oxytoca.…”

“…On the other hand, E. hormaechei ST78 was identified as a high-risk clone among both extended-spectrum β-lactamase-producing ECC and CRECC ( Gomez-Simmonds et al., 2018 ; Emeraud et al., 2022 ). E. hormaechei ST45 is recognized as a high-risk clone ( Izdebski et al., 2015 ) reported in Australia ( Sidjabat et al., 2015 ), Colombia ( Falco et al., 2021 ), Chile ( Wozniak et al., 2021 ), Germany ( Heiden et al., 2020 ), Spain ( Fernández et al., 2015 ), and other countries in Europe ( Izdebski et al., 2015 ). As a whole, these results suggest that the establishment of successful high-risk clones of E. hormaechei in the nosocomial niche provides the opportunity to evolve to MDR phenotypes mediated by the acquisition and maintenance of diverse plasmids, which may have been substantial contributors to the continuous rise of CRECC.…”

Ecological dynamics of plasmid transfer and persistence in microbial communities

“…The presence of plasmids can dramatically alter the ecology of natural communities, for example, by providing resistance to heavy metals [15] , encoding genes essential for virulence [16] , or facilitating the spread of antibiotic resistance 17 , 18•• . Conjugative plasmids, for example, are instrumental in shuttling transposons harbouring carbapenem resistance genes between Enterobacterales , causing multispecies outbreaks of carbapenem-resistant infections 19 , 20 , 21 , 22 . A retrospective analysis of within-patient dynamics of carbapenemase-encoding pOXA-48 plasmids showed that transfer among members of the gut microbiota is rife, and is likely responsible for the long-term establishment of antibiotic resistance within patients [18] .…”