Co-integrate Col3m
bla
NDM-1
-harboring plasmids in clinical
Providencia rettgeri
isolates from Argentina
Authors: De Belder Denise , Martino Florencia , Tijet Nathalie , Melano Roberto G. , Faccone Diego , De Mendieta Juan Manuel , Rapoport Melina , Albornoz Ezequiel , Petroni Alejandro , Tuduri Ezequiel , Derdoy Laura , Cogut Sandra , Errecalde Laura , Pasteran Fernando , Corso Alejandra , Gomez Sonia A. 
Published: September 2023

ABSTRACT

The first cases of
bla
NDM
in Argentina were detected in three
Providencia rettgeri
(Pre) recovered from two hospitals in Buenos Aires city in 2013. The isolates were genetically related, but the plasmid profile was different. Here, we characterized the
bla
NDM-1
-harboring plasmids of the first three cases detected in Argentina. Hybrid assembly obtained from short- and long-read sequencing rendered
bla
NDM-1
in Col3M plasmids of
ca
. 320 kb (p15268A_320) in isolate PreM15268, 210 kb (p15758B_210) in PreM15758, and 225 kb (p15973A_225) in PreM15973. In addition, PreM15758 harbored a 98-kb circular plasmid (p15758C_98) flanked by a putative recombination site (
hin
-Tn
As2
), with 100% nucleotide ID and coverage with p15628A_320. Analysis of PFGE/S1-nuclease gel, Southern hybridization with
bla
NDM-1
probe, hybrid assembly of short and long reads suggests that pM15758C_98 can integrate by homologous recombination. The three
bla
NDM-1
-plasmids were non-conjugative
in vitro
. Moreover,
tra
genes were incomplete, and oriT was not found in the three
bla
NDM-1
-plasmids. In two isolates, bla
NDM-1
was embedded in a partially conserved structure flanked by two IS
Kox2
. In addition, all plasmids harbored
aph(3')-Ia
,
aph(3')-VI
, and
qnr
D1 genes and
aac(6´)Ib-cr
,
bla
OXA-1
,
cat
B3, and
arr3
as part of a class 1 integron. Also, p15268A_320 and p15973A_225 harbored
bla
PER-2
. To the best of our knowledge, this is the first report of clinical
P. rettgeri
harboring bla
NDM-1
in an atypical genetic environment and located in unusual chimeric Col3M plasmids. The study and continuous surveillance of these pathogens are crucial to tracking the evolution of these resistant plasmids and finding solutions to tackle their dissemination.

IMPORTANCE

Infections caused by carbapenem hydrolyzing enzymes like NDM (New Delhi metallo-beta-lactamase) represent a serious problem worldwide because they restrict available treatment options and increase morbidity and mortality, and treatment failure prolongs hospital stays. The first three cases of NDM in Argentina were caused by genetically related
P. rettgeri
recovered in two hospitals. In this work, we studied the genetic structure of the plasmids encoding
bla
NDM
in those index cases and revealed the enormous plasticity of these genetic elements. In particular, we found a small plasmid that was also found inserted in the larger plasmids by homologous recombination as a co-integrate element. We also found that the
bla
NDM
plasmids were not able to transfer or move to other hosts, suggesting their role as reservoir elements for the acquisition of resistance genes. It is necessary to unravel the dissemination strategies and the evolution of these resistant plasmids to find solutions to tackle their spread.