Characterization of a Multiresistance Plasmid Carrying the optrA and cfr Resistance Genes From an Enterococcus faecium Clinical Isolate

Abstract

Enterococcus faecium E35048, a bloodstream isolate from Italy, was the first strain where the oxazolidinone resistance gene optrA was detected outside China. The strain was also positive for the oxazolidinone resistance gene cfr. WGS analysis revealed that the two genes were linked (23.1 kb apart), being co-carried by a 41,816-bp plasmid that was named pE35048-oc. This plasmid also carried the macrolide resistance gene erm(B) and a backbone related to that of the well-known Enterococcus faecalis plasmid pRE25 (identity 96%, coverage 65%). The optrA gene context was original, optrA being flanked by two transposase genes; this region was integrated into the gene encoding for the ζ toxin protein (orf19 of pRE25). The cfr gene was flanked by two ISEnfa5 insertion sequences and the element was inserted into an lnu(E) gene. Both optrA and cfr contexts were excisable. pE35048 oc could not be transferred to enterococcal recipients by conjugation or transformation. A plasmid-cured derivative of E. faecium E35048 was obtained following growth at 42°C, and the complete loss of pE35048-oc was confirmed by WGS. pE35048-oc exhibited some similarity but also notable differences from pEF12-0805, a recently described enterococcal plasmid from human E. faecium also co-carrying optrA and cfr; conversely it was completely unrelated to other optrA- and cfr-carrying plasmids from Staphylococcus sciuri. The optrA-cfr linkage is a matter of concern since it could herald the possibility of a co-spread of the two genes, both involved in resistance to last resort agents such as the oxazolidinones.

Full text

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ORIGINAL RESEARCH
published: 11 September 2018
doi: 10.3389/fmicb.2018.02189
Edited by:
Teresa M. Coque,
Instituto Ramón y Cajal
de Investigación Sanitaria, Spain
Reviewed by:
Yoshikazu Ishii,
Toho University, Japan
Ana R. Freitas,
Universidade do Porto, Portugal
*Correspondence:
Andrea Brenciani
a.brenciani@univpm.it;
andreabrenciani@yahoo.it
Specialty section:
This article was submitted to
Evolutionary and Genomic
Microbiology,
a section of the journal
Frontiers in Microbiology
Received: 30 April 2018
Accepted: 27 August 2018
Published: 11 September 2018
Citation:
Morroni G, Brenciani A, Antonelli A,
D’Andrea MM, Di Pilato V, Fioriti S,
Mingoia M, Vignaroli C, Cirioni O,
Biavasco F, Varaldo PE, Rossolini GM
and Giovanetti E (2018)
Characterization of a Multiresistance
Plasmid Carrying the optrA and cfr
Resistance Genes From an
Enterococcus faecium Clinical Isolate.
Front. Microbiol. 9:2189.
doi: 10.3389/fmicb.2018.02189
Characterization of a Multiresistance
Plasmid Carrying the optrA and cfr
Resistance Genes From an
Enterococcus faecium Clinical
Isolate
Gianluca Morroni1, Andrea Brenciani2*, Alberto Antonelli3, Marco Maria D’Andrea3,4,
Vincenzo Di Pilato3, Simona Fioriti2, Marina Mingoia2, Carla Vignaroli5, Oscar Cirioni1,
Francesca Biavasco5, Pietro E. Varaldo2, Gian Maria Rossolini3,6 and
Eleonora Giovanetti5
1Infectious Diseases Clinic, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical
School, Ancona, Italy, 2Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University
of Marche Medical School, Ancona, Italy, 3Department of Experimental and Clinical Medicine, University of Florence,
Florence, Italy, 4Department of Medical Biotechnologies, University of Siena, Siena, Italy, 5Unit of Microbiology, Department
of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, 6Microbiology and Virology Unit,
Florence Careggi University Hospital, Florence, Italy
Enterococcus faecium E35048, a bloodstream isolate from Italy, was the first strain
where the oxazolidinone resistance gene optrA was detected outside China. The strain
was also positive for the oxazolidinone resistance gene cfr. WGS analysis revealed that
the two genes were linked (23.1 kb apart), being co-carried by a 41,816-bp plasmid
that was named pE35048-oc. This plasmid also carried the macrolide resistance gene
erm(B) and a backbone related to that of the well-known Enterococcus faecalis plasmid
pRE25 (identity 96%, coverage 65%). The optrA gene context was original, optrA
being part of a composite transposon, named Tn6628, which was integrated into the
gene encoding for the ζtoxin protein (orf19 of pRE25). The cfr gene was flanked by
two ISEnfa5 insertion sequences and the element was inserted into an lnu(E) gene.
Both optrA and cfr contexts were excisable. pE35048-oc could not be transferred to
enterococcal recipients by conjugation or transformation. A plasmid-cured derivative of
E. faecium E35048 was obtained following growth at 42◦C, and the complete loss of
pE35048-oc was confirmed by WGS. pE35048-oc exhibited some similarity but also
notable differences from pEF12-0805, a recently described enterococcal plasmid from
human E. faecium also co-carrying optrA and cfr; conversely it was completely unrelated
to other optrA- and cfr-carrying plasmids from Staphylococcus sciuri. The optrA-cfr
linkage is a matter of concern since it could herald the possibility of a co-spread of the
two genes, both involved in resistance to last resort agents such as the oxazolidinones.
Keywords: multiresistance plasmid, optrA gene, cfr gene, oxazolidinone resistance, Enterococcus faecium
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Morroni et al. Linkage of optrA and cfr in E. faecium Plasmid
INTRODUCTION
Enterococci are members of the gut microbiota of humans and
many animals, and are widespread in the environment. They are
also major opportunistic pathogens, mostly causing healthcare-
related infections. Among the reasons of their increasing
role as nosocomial pathogens, the primary factor is their
inherent ability to express and acquire resistance to several
antimicrobial agents, with Enterococcus faecium emerging as
the most therapeutically challenging species (Arias and Murray,
2012).
Oxazolidinones are among the few agents that retain
activity against multiresistant strains of enterococci (Shaw
and Barbachyn, 2011;Patel and Gallagher, 2015), and
the emergence of resistance to these drugs is an issue of
notable clinical relevance. Particularly worrisome, due to their
potential for horizontal dissemination, are the oxazolidinone
resistances caused by cfr, encoding a ribosome-modifying
enzyme (Kehrenberg et al., 2005;Deshpande et al., 2015;
Munita et al., 2015), and optrA, encoding a ribosome
protection mechanism (Wang et al., 2015;Wilson, 2016;
Sharkey et al., 2016). Both these genes were found to
be associated with a number of different mobile genetic
elements.
The optrA gene, in particular, was discovered in China in
enterococci of human and animal origin isolated in 2005-
2014 (Wang et al., 2015) where it was detected in different
genetic contexts (He et al., 2016). Since then, optrA-positive
enterococci have been reported worldwide (Mendes et al.,
2016;Cavaco et al., 2017;Freitas et al., 2017;Pfaller et al.,
2017a,b), including Italy, where optrA was found — the
first report outside China — in two bloodstream isolates
of E. faecium which were also positive for the cfr gene,
which was not expressed (Brenciani et al., 2016b). By further
investigating one of those isolates (strain E35048), we noticed
that both optrA and cfr were capable of undergoing excision
as minicircles (Brenciani et al., 2016b). It is worth noting
that among the reported optrA protein variants (Morroni
et al., 2017), the one detected in E. faecium E35048, named
optrAE35048, is the most divergent, differing by 21 amino acid
substitutions from the firstly described optrA variant (Wang et al.,
2015).
The goal of the present work was to investigate the
locations, genetic environments, and transferability of the
optrA and cfr resistance genes detected in E. faecium E35048.
We characterized the genetic contexts and location of optrA
and cfr in E. faecium E35048, and found that both genes
were co-carried on a plasmid of original structure, named
pE35048-oc. This plasmid, which also carried the macrolide
resistance gene erm(B), shared regions of homology with
the well-characterized (Schwarz et al., 2001) and widely
distributed (Rosvoll et al., 2010;Freitas et al., 2016) conjugative
multiresistance enterococcal plasmid pRE25, but was unable
to transfer. In pE35048-oc, the genetic context of optrA
was different from those so far described in other optrA-
carrying plasmids, underscoring the plasticity of these resistance
regions.
MATERIALS AND METHODS
Bacterial Strain
optrA- and cfr-positive E. faecium E35048 (linezolid MIC,
4µg/ml; tedizolid MIC, 2 µg/ml) was isolated in Italy in 2015
from a blood culture (Brenciani et al., 2016b).
WGS and Sequence Analysis
Genomic DNA was extracted using a commercial kit (Sigma-
Aldrich, St. Louis, MO). WGS was carried out with the Illumina
MiSeq platform (Illumina Inc., San Diego, CA, United States)
by using a 2 ×300 paired end approach and a DNA library
prepared using Nextera XT DNA Sample Prep Kit (Illumina, San
Diego, CA, United States). De novo assembly was performed with
SPAdes V 3.10.0 (Bankevich et al., 2012) using default parameters.
Scaffolds characterized by a length ≤300 bp were filtered out.
Raw reads were mapped to the filtered scaffolds by using bwa (Li
and Durbin, 2009) to check the quality of the assembly. Tentative
ordering of selected scaffolds of plasmid origin was performed
by BLASTN comparisons of data from WGS to homologous
plasmids, and eventually confirmed by PCR approach followed by
Sanger sequencing. The ST was determined through the Center
for Genomic Epidemiology1. Analysis of insertion sequences
was carried out using ISFinder online database2(Siguier et al.,
2006).
PCR Mapping Experiments
PCR mapping with outward-directed primers topo-FW
(50-GAAGCGACAAGAGCAAGTAT-30) and optrA-RV (50-
TCTTGAACTACTGATTCTCGG-30), and Sanger sequencing
were used to close the pE35048-oc plasmid sequence.
To investigate the excision of the optrA and cfr
genetic contexts, PCR mapping and sequencing assays
were performed using: (i) primer pairs targeting the
regions flanking their insertion sites [orf7-FW (50-
ATTTTTCTTTTGATTTGGTA-30) and orf14up-RV
(50-AAGTAATCTTTTTTTGTTTT-30) for the cfr genetic
context; and orf33-FW (50-CTTGTTTTGGTGTTGCCCTGG-
30) and orf33-RV (50-CCACCAAGTAAAAAAGCGG-30)
for the optrA genetic context]; (ii) outward-directed
primer pairs designed from cfr and optrA genes [cfr-INV
(50-TTGATGACCTAATAAATGGAAGTA-30) and cfr-
FW (50-ACCTGAGATGTATGGAGAAG-30); optrA-INV
(50-TTTTTCCACATCCATTTCTACC-30) and optrA-FW
(50-GAAAAATAACACAGTAAAAGGC-30)] (Figure 1).
S1-PFGE, Southern Blotting and
Hybridization
Total DNA in agarose gel plugs was digested with S1 nuclease
(Thermo Fisher Scientific, Milan, Italy) and separated by PFGE
as previously described (Barton et al., 1995). After S1-PFGE,
DNA was blotted onto positively charged nylon membrane
(Ambion-Celbio, Milan, Italy) and hybridized with specific
1https://cge.cbs.dtu.dk/services/MLST/
2https://isfinder.biotoul.fr/
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FIGURE 1 | Schematic, but to scale, comparative representation of the linearized forms of plasmid pE35048-oc and plasmid pEF12-0805, both co-carrying optrA
and cfr and sharing a pRE25-related backbone. ORFs are depicted as arrows pointing to the direction of transcription; those common to pRE25 are black, with
erm(B) spotted; the erm(A) gene, not found in pRE25, is green spotted; the ORFs of the optrA and the cfr contexts are blue and red, respectively, with optrA
diagonally and cfr vertically striped. Minicircle formation by such contexts in pE35048-oc is shown above the plasmid. Other ORFs are white. The primer pairs used
are indicated by thin arrows below pE35048-oc. Gray areas between ORF maps denote >90% DNA identity.
probes (Brenciani et al., 2007). cfr and optrA probes were
obtained by PCR as described elsewhere (Wang et al., 2015;
Brenciani et al., 2016a).
Transformation and Conjugation
Experiments
Purified plasmids extracted from E. faecium E35048
were transformed into the E. faecalis JH2-2 recipient by
electrotransformation as described previously (Brenciani et al.,
2016a). The transformants were selected on plates supplemented
with florfenicol (10 µg/ml) or erythromycin (10 µg/ml).
In mating experiments, E. faecium E35048 was used as
the donor. Two florfenicol-susceptible laboratory strains were
used as recipients: E. faecium 64/3 (Werner et al., 1997), and
E. faecalis JH2-2, both resistant to fusidic acid. Conjugal transfer
was performed on a membrane filter. Transconjugants were
selected on plates supplemented with florfenicol (10 µg/ml) or
erythromycin (10 µg/ml) plus fusidic acid (25 µg/ml).
Curing Assays
Enterococcus faecium E35048 was grown overnight in brain heart
agar (BHA) at 42◦C for some passages. After each passage a
few colonies were picked up, and their DNA was extracted and
screened for the presence of the optrA and cfr genes by PCR
with specific primers (Brenciani et al., 2016b). In case of negative
testing, the strain was regarded as possibly cured and subjected to
WGS for confirmation.
Nucleotide Sequence Accession
Numbers
The complete nucleotide sequence of plasmid pE35048-oc has
been assigned to GenBank accession no. MF580438, available
under the BioProject ID PRJNA481862.
RESULTS AND DISCUSSION
Genome General Features and
Resistome of E. faecium E35048
Assembly of the raw WGS data followed by filtering of
low length contigs gave a total of 172 scaffolds (range:
310-137, 266 bp; N50: 41,930 bp; L50: 18; mean coverage:
92X). E. faecium E35048 was assigned to ST117, a globally
disseminated hospital-adapted clone (Hegstad et al.,
2014;Tedim et al., 2017). Resistome analysis revealed
the presence of six acquired resistance genes in addition
to the previously described optrA and cfr genes: erm(B)
(resistance to macrolides, lincosamides and group B
streptogramins), msr(C) (resistance to macrolides and group B
streptogramins), tet(M) (resistance to tetracycline), aphA and
aadE (resistance to aminoglycosides), and sat4 (resistance to
streptothricin).
Characterization of the optrA- and
cfr-Carrying Plasmid pE35048-oc
The optrA and cfr genes were found to be linked, 23.1 kb
apart in the linearized form, on the same contig, which also
contained regions of high similarity (96% nucleotide identity) to
the E. faecalis plasmid pRE25 (50 kb) (65% coverage) (Schwarz
et al., 2001) (GenBank accession no. NC_008445).
PCR and Sanger sequencing using outward-directed primers
targeting orf1 and optrA demonstrated that the region containing
optrA and cfr was part of a plasmid which was designated
pE35048-oc (Figure 1). The plasmid was 41,816 bp in size,
contained 42 open reading frames (ORFs), and had a G +C
content of 35%.
S1-PFGE analysis of genomic DNA extracted from E. faecium
E35048 showed four plasmids, ranging in size from ∼10 to
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∼250 kb (data not shown). Both optrA and cfr probes hybridized
with a plasmid of ∼45 kb, in agreement with sequencing data.
The characteristics of the plasmid ORFs and of their products
are detailed in Table 1. In particular, pE35048-oc carried (i) a
repS gene (orf6, corresponding to orf6 of pRE25), encoding a
theta mechanism replication protein responsible for the plasmid
replication; (ii) a putative origin of replication downstream
of orf6; and (iii) a region containing the putative minimal
conjugative unit of pRE25, consisting of 15 ORFs (orf28 to orf14,
corresponding to orf24 to orf39 of pRE25) and the origin of
transfer (oriT) found upstream of orf28 (Schwarz et al., 2001).
BLASTN analysis showed that the oriT nucleotide sequence
was shorter in pE35048-oc (only 15 bp vs. 38 bp in pRE25).
Compared to pRE25, pE35048-oc lacked (i) the region spanning
from orf41 to orf5 (two IS1216 elements probably involved in
the rearrangement occurred during plasmid evolution); (ii) orf10,
i.e., the chloramphenicol resistance cat gene; and (iii) orf11,
another replication gene encoding a rolling-circle replication
protein. In addition, compared to pRE25, pE35048-oc carried the
optrA and cfr genes and their respective genetic environments.
The optrA context (5,850 bp) consisted of the optrAE35048
gene followed by a novel insertion sequence of the IS21 family,
named ISEfa15. Consistently with other members of this family
(Berger and Haas, 2001), ISEfa15 included two CDS encoding
a transposase and a helper protein, and was bounded by 11-
bp imperfect inverted repeats (IRL 50-TGTTTATGATA-30and
IRR 50-TGTATTTGTCA-30). A truncated copy of ISEfa15, named
ISEfa15∗,was present also upstream of optrA gene. This optrA
context was flanked by 5-bp target site duplications (50-CTAAT-
30) suggesting its mobilization as a composite transposon, named
Tn6628 (Figure 1). This transposon was previously shown to
form circular intermediate (3,350 bp) including optrA and the
truncated copy of ISEfa15 (Brenciani et al., 2016b).
The proposed role of IS1216 in the dissemination of optrA
among different types of enterococcal plasmids (He et al., 2016)
is likely to be true also for other transposase genes. The optrA
context was located downstream of the erm(B) gene (orf15 of
pRE25) and was integrated into orf33 (orf19 of pRE25, which
encodes the ζtoxin protein of the ω-ε-ζtoxin/antitoxin system).
This integration inactivates ζtoxin encoded by orf33, a condition
that could prevent the correct partitioning of pE35048-oc and
lead to the appearance of plasmid-free segregants (Magnuson,
2007).
The cfr context (6,098 bp) was located between orf7 and orf14
(orf39 and orf40 of pRE25) and consisted of the cfr gene flanked
by two ISEnfa5 elements, inserted in turn into the lnu(E) gene.
The same genetic context of cfr [including the direct repeats
and the lnu(E) gene] has been reported in China in a plasmid
from a Streptococcus suis isolate from an apparently healthy pig
(Wang et al., 2013) and in Italy in an MRSA isolated from
a patient with cystic fibrosis (Antonelli et al., 2016), with cfr
being untransferable in both instances. Very recently, the cfr
gene, flanked by only one ISEnfa5, inserted upstream, has been
described in a chromosomal fragment shared by three pig isolates
of Staphylococcus sciuri (Fan et al., 2017).
PCR assays, using primer pairs targeting regions flanking
the optrA and the cfr contexts (Figure 1), and sequencing
experiments confirmed that both genes could be excised leaving
one of the two flanking genes (ISEfa15 or ISEnfa5, respectively)
at the excision sites.
Transferability of the optrA and cfr
Genes and Curing of E. faecium E35048
From pE35048-oc
Repeated attempts of conjugation and transformation
assays failed to demonstrate any optrA or cfr transfer
from E. faecium E35048 to enterococcal recipients. The
partial deletion of oriT and the lack of the rolling-circle
replication protein might be responsible for the non-conjugative
behavior of pE35048-oc compared to pRE25 (Schwarz et al.,
2001).
An optrA- and cfr-negative isogenic strain of E. faecium
E35048 was obtained after three passages on BHA at 42◦C. It
was subjected to WGS. Compared to the wild type, it disclosed
complete loss of pE35048-oc.
pE35048-oc vs. Other Plasmids Sharing
Co-carriage of optrA and cfr
Since this study was started, co-location of optrA and cfr
has been reported in a few additional plasmids, some
from pig isolates of S. sciuri (Li et al., 2016;Fan et al.,
2017) and one, pEF12-0805, from a human isolate of
E. faecium (Lazaris et al., 2017). Comparison of pE35048-
oc with the S. sciuri plasmids revealed completely unrelated
backbones and optrA and cfr contexts. On the other hand,
pE35048-oc was related with pEF12-0805 (accession no.
KY579372.1) although with significant differences (Figure 1). In
particular:
(i) pE35048-oc and pEF12-0805 share a pRE25-related
backbone (Schwarz et al., 2001), but pEF12-0805 is much larger
(72,924 bp vs. 41,816 bp) due to the presence of a larger amount
of pRE25-related regions, including the pRE25 region spanning
from orf51 to orf5 (∼12,5 kb) and a rearranged region of pRE25
containing antibiotic resistance genes aphA,aadE, and lnu(B)
(∼13 kb). (ii) A ∼4-kb remnant of the ermA-carrying transposon
Tn554 (Murphy et al., 1985) is found only in pEF12-0805. (iii)
The optrA contexts of the two plasmids are completely different,
only the optrA gene of pE35048-oc being part of a composite
transposon. The absence of insertion sequences makes it unlikely
that the optrA gene of pEF12-0805 is excisable. Moreover,
whereas in pE35048-oc the optrA context is found downstream
of erm(B), the optrA gene of pEF12-0805 is associated with
the ermA-carrying Tn554 remnant. (iv) Interestingly, the cfr
contexts of the two plasmids are the same, including some
plasmid backbone flanking regions on either side (Figure 1),
suggesting that the two plasmids might be derived from a pRE25-
related common ancestor that had initially acquired the mobile
cfr element. (v) Repeated transfer assays were unsuccessful with
both plasmids. Finally, (vi) whereas we obtained a pE35048-oc-
cured derivative of our E. faecium isolate, curing assays were
unsuccessful with E. faecium strain F120805 (Lazaris et al.,
2017).
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TABLE 1 | Amino acid sequence identities/similarities of putative proteins encoded by the pE35048-oc (GenBank accession no. MF580438).
BLASTP analysisa
ORF Start
(bp)
Stop
(bp)
Size (amino
Acid)
Predicted
function
Most significant database
match
Accession
no.
% Amino acid identity
(% aminacid similarity)
orfl 1833 1 610 DNA
Topoisomerase III
Type 1 topoisomerase (plasmid)
[Enterococcus faecium]
YP_976069.1 100 (100)
orfl 3,818 1,932 628 Group II intron Group II intron reverse
transcriptase/maturase
[Lactobacillales]
WP_010718345.1 100 (100)
b1orf3 4,917 4,555 120 DNA
Topoisomerase III
Topoisomerase [Bacilli] WP_000108744.1 100 (100)
orf4 5,534 4,917 205 Resolvase Resolvase (plasmid) [E. faecalis] YP_003864109.1 99 (100)
orf5 5,718 5,548 56 Hypothetical protein pRE25p07
(plasmid) [E. faecalis]
YP_783891.1 98 (100)
orf6 7,557 6,067 496 Replication protein Replication protein (plasmid)
[E. faecium]
NP_044463.1 100 (100)
orf7 8,213 7,941 90 Transcriptional
regulator
CopS (plasmid) [Streptococcus
pyogenes]
YP_232751.1 100 (100)
1orf8 8,901 8,446 151 Responsible for
lincomycin
resistance
Lincosamide
nucleotidyltransferase (plasmid)
[E. faecium]
ARQ19308.1 99 (100)
orf9 9,772 8,873 299 Transposase Transposase [Streptococcus
suis]
AGO02197.1 100 (100)
orf10 10,443 9,769 224 Transposase IS3 family transposase
[E. faecalis]
WP_013330754.1 100 (100)
orf11 11,867 10,809 352 23S ribosomal RNA
methyltransferase
Cfr family 23S ribosomal RNA
methyltransferase
[Staphylococcus aureus]
WP_001835153.1 100 (100)
orf12 13,177 12,278 299 Transposase Transposase [S. suis] AGO02197.1 100 (100)
orf13 13,848 13,174 224 Transposase IS3 family transposase
[E. faecalis]
WP_013330754.1 100 (100)
1orf8 13,921 14,061 47 Responsible for
lincomycin
resistance
Lincomycin resistance protein
[synthetic construct]
AGT57825.1 100 (100)
orf14 15,391 14,531 289 Hypothetical protein [S. suis] WP_079268203.1 96 (98)
orf15 15,822 15,
451
123 Hypothetical protein
[Enterococcus casseliflavus]
WP_032495652.1 99 (99)
orf16 16,546 15,809 245 Hypothetical protein [E. faecalis] WP_012858057.1 100 (100)
orf17 17,768 16,836 310 Hypothetical protein
[Enterococcus sp.
HMSC063D12]
WP_070544061.1 100 (100)
orf18 18,693 17,770 307 Membrane protein
insertase
Hypothetical protein
[Enterococcus sp.
HMSC063D12]
WP_070544063.1 99 (99)
orf19 20,366 18,711 551 Type IV secretory
pathway, VirD4
component,
TraG/TraD family
ATPase
Hypothetical protein
[Enterococcus]
WP_002325630.1 100 (100)
orf20 20,790 20,359 143 Ypsilon (plasmid) [E. faecalis] YP_003864141.1 100 (100)
orf21 21,346 20,795 183 Hypothetical protein
[E. faecium]
WP_02
9485693.1
99 (99)
orf22 22,468 21,359 369 Amidase Putative lytic transglycosylase
(plasmid) [E. faecalis]
YP_003864139.1 99 (99)
orf23 23,842 22,490 450 Conjugal transfer protein TraF
[E. faecium]
WP_085837474.1 98 (99)
orf24 25,817 23,856 653 Type IV secretory
pathway, VirB4
component
TrsE (plasmid) [E. faecalis] YP_003864137.1 100 (100)
(Continued)
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Table 1 | Continued
BLASTP analysisa
ORF Start
(bp)
Stop
(bp)
Size (amino
Acid)
Predicted
function
Most significant database
match
Accession
no.
% Amino acid identity
(% aminacid similarity)
orf25 26,457 25,828 209 Hypothetical protein
[Enterococcus]
WP_002325627.1 99 (100)
orf26 26,857 26,474 127 AM21 (plasmid) [E. faecalis] YP
003305365.1
100 (100)
orf27 27,208 26,876 110 T4SS_CagC Hypothetical protein pRE25p25
(plasmid) [E. faecalis]
YP_783909.1 100 (100)
orf28 29,217 27,232 661 Nickase Molybdopterin-guanine
dinucleotide biosynthesis
protein MobA [E. faecalis]
WP_025186512.1 99 (100)
orf29 29,509 29,808 99 Hypothetical protein pRE25p23
(plasmid) [E. faecalis]
YP_783907.1 100 (100)
orf30 29,811 30,068 85 Hypothetical protein
[Enterococcus]
WP_021109234.1 100 (100)
orf31 30,927 30,430 165 Molecular
chaperone DnaJ
Molecular chaperone DnaJ
[Enterococcus]
WP_025481726.1 97 (98)
orf32 31,353 30,946 135 Hypothetical protein pRE25p20
(plasmid) [E. faecalis]
YP_783904.1 98 (99)
1orf33 32,376 31,705 223 Zeta-toxin Toxin zeta [E. faecium] WP_002300569.1 97 (98)
orf34 33,173 32,412 253 DNA replication
protein DnaC
AAA family ATPase
[Proteiniborus ethanoligenes]
WP_091728780.1 94 (98)
orf35 34,750 33,170 526 ISEfa15
transposase
Transposase [P. ethanoligenes] WP_091728892.1 70 (84)
orf36 36,973 35,006 655 ABC-F type
ribosomal
protection protein
ABC-F type ribosomal
protection protein OptrA
[E. faecalis]
WP_078122475.1 97 (98)
orf37 38,100 37,078 340 ISEfa15
transposase
(partial)
Transposase [Clostridium
formicaceticum]
WP_070963420.1 64 (80)
1orf33 38,423 39,199 75 Zeta-toxin Zeta toxin [E. faecium] WP_080440976.1 100 (100)
orf38 38,697 38,425 90 Epsilon-antitoxin Antidote of epsilon-zeta
post-segregational killing
system (plasmid) [S. pyogenes]
YP_232758.1 100 (100)
orf39 38,929 38,714 71 Omega-repressor Transcriptional repressor
(plasmid) [S. pyogenes]
YP_232757.1 99 (100)
orf40 39,917 39,021 298 ParA putative
ATPase
Chromosome partitioning
protein ParA [S. suis]
WP_0023
87620.1
100 (100)
orf41 40,445 40,314 43 Hypothetical protein (plasmid)
[Pediococcus acidilactici]
WP_002321978.1 100 (100)
orf42 41,187 40,450 245 23S rRNA
(adenine(2058)-
N(6))
methyltransferase
23S rRNA (adenine(2058)-N(6))-
methyltransferase Erm(B)
[S. suis]
WP_024418925.1 99 (100)
aFor each ORF, only the most significant identity detected is listed. b1represents a truncated ORF.
The E. faecium hosts of the two plasmids belonged to
different sequence types and were isolated from different
sources. Strain E35048 was recovered in 2015 in Italy from
a blood culture, belonged to ST117, exhibited no mutational
mechanisms of oxazolidinone resistance, and was vancomycin
susceptible. Strain F120805, recovered in 2013 in Ireland from
feces and reported to have a linezolid MIC of 8 µg/ml,
belonged to ST80, exhibited also mutational mechanisms
of oxazolidinone resistance (involving both 23S rRNA and
ribosomal protein L3), and was vancomycin resistant (vanA
genotype). Although belonging to different sequence types,
ST80 and ST117 were part of the same clonal group,
ST78.
CONCLUSION
Distinctive findings of the optrA- and cfr-carrying
plasmid pE35048-oc are its relation to the well-known
enterococcal plasmid pRE25, shared with plasmid pEF12-0805
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fmicb-09-02189 September 11, 2018 Time: 14:14 # 7
Morroni et al. Linkage of optrA and cfr in E. faecium Plasmid
(Lazaris et al., 2017); a unique optrA context, that has never been
described before; and the fact that both the optrA and cfr contexts
are capable of excising to form minicircles. This, in addition to the
belonging of E. faecium E35048 to ST117, a globally disseminated
clone recovered in many European health institutions (Hegstad
et al., 2014;Tedim et al., 2017), might favor the spread of
optrA and cfr in the hospital setting. Under this respect, the
in vitro non-transferability of pE35048-oc is someway reassuring,
although transfer in vivo cannot be ruled out. Moreover, at the
hospital level, it cannot be excluded that co-carriage of optrA
and cfr by the same plasmid ends up turning into co-spread,
as already highlighted with pheromone-responsiveness plasmids
(Francia and Clewell, 2002), and also in consideration of the
very recent finding that, in enterococci, non-conjugative plasmids
can be mobilized by co-resident, conjugative plasmids (Di Sante
et al., 2017). Co-spread would be a cause for special concern,
considering that both optrA and cfr encode resistance, through
diverse mechanisms, to different antibiotics, including last resort
agents such as oxazolidinones.
AUTHOR CONTRIBUTIONS
AB, PV, and EG designed the study and wrote the paper. FB, OC,
and GR have contributed to critical reading of the manuscript.
GM, AA, MD, VD, SF, MM, CV, and SF did the laboratory work.
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Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
Copyright © 2018 Morroni, Brenciani, Antonelli, D’Andrea, Di Pilato, Fioriti,
Mingoia, Vignaroli, Cirioni, Biavasco, Varaldo, Rossolini and Giovanetti. This is an
open-access article distributed under the terms of the Creative Commons Attribution
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