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Antimicrobial Agents and Chemotherapy logoLink to Antimicrobial Agents and Chemotherapy
. 2010 Oct 18;55(1):376–381. doi: 10.1128/AAC.00875-10

Sequence of pR3521, an IncB Plasmid from Escherichia coli Encoding ACC-4, SCO-1, and TEM-1 β-Lactamases

C C Papagiannitsis 1, L S Tzouvelekis 1,2, S D Kotsakis 1, E Tzelepi 1, V Miriagou 1,*
PMCID: PMC3019680  PMID: 20956594

Abstract

The sequence of pR3521, a self-transmissible plasmid from Escherichia coli, was determined. pR3521 (110,416 bp) comprised a contiguous IncB sequence (84,034 bp) sharing extensive similarities with IncI replicons and an acquired region (26,382 bp) carrying sequences of diverse origin, containing blaACC-4, blaSCO-1, blaTEM-1b (two copies), strA, strB, sul2, and aacC2.


Multidrug resistance among enterobacteria is commonly due to acquisition of plasmids carrying various resistance determinants (4). We have previously identified pR3521, a self-transferable and multiresistant plasmid from an Escherichia coli isolate from a hospitalized patient in Greece (18). Work had been largely focused on the characterization of loci containing blaACC-4, an ampC gene encoding ACC-4, an extended-spectrum variant of the ACC-1 cephalosporinase (19), and blaSCO-1, a novel gene of unknown origin coding for an RTG-type carbenicillinase (18, 21). blaACC-4 was included in a sequence derived from the chromosome of Hafnia alvei and linked with ISEcp1. blaSCO-1 was included in a segment of likely chromosomal origin that was associated with IS26 (18, 19). Plasmid-mediated production of SCO-1 and ACC-1 has also been described for Klebsiella pneumoniae, Proteus mirabilis, and Salmonella enterica serovar Livingstone in Europe and North Africa, but detailed characteristics of the respective plasmids were not reported (6, 13).

In this study, the complete nucleotide sequence of pR3521 is presented. pR3521 belonged to incompatibility (Inc) group B, which is closely related to the IncI family of replicons (5, 17). A hypothesis as to the mechanisms of accumulation of diverse resistance genes in pR3521 is also discussed.

General features of pR3521.

An E. coli K-12 transconjugant clone was used as a source of pR3521 (18). Plasmid pR3521, purified by CsCl gradient ultracentrifugation, was partially digested with Sau3A, and the fragments were ligated into the chloramphenicol-resistant vector pBCSK(+) (Stratagene, La Jolla, CA). The recombinant plasmids were used to transform E. coli DH5α. Transformants were selected with chloramphenicol (20 μg/ml). Recombinant plasmids were purified with a Qiagen plasmid midi kit (Qiagen, Hilden, Germany), and the nucleotide sequences of the inserts were determined using an ABI 377 sequencer (Applied Biosystems, Foster City, CA). Sequence gaps were filled by primer walking and sequencing of PCR products using primers hybridizing to known regions (18, 19). Contigs were assembled using the Laser Gene software program (DNASTAR, Madison, WI). For sequence analysis and annotation, the BLAST algorithm (www.ncbi.nlm.nih.gov/BLAST/), an insertion sequence (IS) finder (www-is.biotoul.fr/), an open reading frame (ORF) finder (www.bioinformatics.org/sms/), and the Artemis software program (www.sanger.ac.uk/) were utilized.

The sequence of pR3521 comprised 110,416 bp (G+C content, 52.6%) and included 124 coding sequences (119 complete and 5 truncated). The ORFs and their characteristics are presented in Table 1. A circular map of pR3521 is shown in Fig. 1. The plasmid was composed of two distinct parts: a contiguous plasmidic segment of 84,034 kb (G+C content, 53%), sharing similarities with replicons of complex I, and an acquired sequence of 26,382 bp (G+C content, 51.3%), containing eight antibiotic resistance genes (blaACC-4, blaSCO-1, blaTEM-1b [two copies], strA, ΔstrB, aacC2, and sul2), intact (n = 7) and defective (n = 1) mobile elements (including four IS26 elements, IS26-1 to IS26-4), single copies of ISKpn11 and ISKpn12, a ΔISEcpI element, and one Tn2 transposon as well as sequences of diverse chromosomal origins.

TABLE 1.

Names, coordinates, and putative functions of ORFs identified in the IncB plasmid pR3521a

Gene name Coordinatesb Putative function(s)
yagA Compl. 533-1627 Hypothetical protein
yafB 1981-2583 Hypothetical protein
orf1 Compl. 3279-3560 Hypothetical protein
orf2 Compl. 3666-3941 Plasmid stabilization protein (RelE/ParE family)
orf3 Compl. 3941-4219 CopG family protein
repA Compl. 5133-6209 Replication initiation protein
traB 6866-7507 F pilus assembly
traC 7648-8310 F pilus assembly
yqiJ 8577-9197 Putative adhesin
yqiK 9224-10918 Putative adhesin
pilI 10999-11241 Type IV prepilin cluster
pilL 11942-13012 Type IV prepilin cluster; lipoprotein
pilM 13016-13453 Type IV prepilin cluster
pilN 13485-15104 Type IV prepilin cluster; secretin protein
pilO 15125-16420 Type IV prepilin cluster
pilP 16410-16868 Type IV prepilin cluster
pilQ 16971-18479 Type IV prepilin cluster; ATP-binding protein
pilR 18481-19575 Type IV prepilin cluster; membrane protein
pilS 19703-20173 Type IV prepilin cluster; prepilin
pilT 20220-20705 Type IV prepilin cluster
pilU 20721-21347 Type IV prepilin cluster; prepilin peptidase
pilV 21364-22725 Type IV prepilin cluster
orf4 23183-23473 Hypothetical protein
orf5 Compl. 23565-23885 Hypothetical protein
traE 24147-24968 F pilus assembly
traF 25070-26272 F pilus assembly
traH 26376-26834 F pilus assembly
traI 26831-27667 DNA helicase
traJ 27651-28799 ATP-binding protein
traK 28796-29086 F pilus assembly
sogL 29150-33211 DNA primase
sogS 29339-33211 Regulator of SogL
traL 33228-33578 F pilus assembly
traM 33590-34285 Mating signal
traN 34296-35255 Aggregate stability
traO 35259-36590 Hypothetical protein
traP 36587-37300 Conjugal transfer protein
traQ 37297-37827 Conjugal transfer protein
traR 37874-38272 Hypothetical protein
traS 38329-38580 Surface exclusion
traT 38687-39313 Surface exclusion
traU 39608-42652 F pilus assembly
traV 42652-43272 F pilus assembly
traW 43395-44435 F pilus assembly
traX 44432-45001 F pilin acetylation
traY 45076-47247 Integral membrane protein
excA 47545-47982 Surface exclusion
orf6 48256-49842 Hypothetical protein
pndA Compl. 49980-50132 Postsegregation killing
pndC Compl. 49987-50280 Counter protein for PndA
orf7 50384-50704 Hypothetical protein
orf8 Compl. 50749-51066 Hypothetical protein
orf9 51035-51361 Hypothetical protein
orf10 51365-51580 Hypothetical protein
orf11 Compl. 51778-52332 Hypothetical protein
yeaH 52712-53029 Putative nuclease
orf12 Compl. 53419-53715 Hypothetical protein
orf13 Compl. 54250-54357 Hypothetical protein
trbA 54734-56050 Conjugal transfer protein
trbB 56047-57171 Conjugal transfer protein
trbC 57152-59455 Conjugal transfer protein
orfA*1 59569-59735 Hypothetical protein
sul2 60319-61134 Dihydropteroate synthase
strA 61195-61998 Streptomycin phosphotransferase
strB*1 61998-62106 Streptomycin phosphotransferase (nonfunctional)
blaTEM-1 Compl. 62254-63114 TEM-1 β-lactamase precursor
tnpA Compl. 63253-63957 TnpA transposase of IS26-1
orfA*2 Compl. 64047-64182 Hypothetical protein
tnpB*1 (rcr2) 64299-64771 Putative transposase (nonfunctional)
tnpA Compl. 64824-65528 TnpA transposase of IS26-2
ΔtnpR 65642-66003 Resolvase (nonfunctional)
blaSCO-1 Compl. 66139-67005 SCO-1 carbenicillinase precursor
Glycosidase-like gene 67167-68366 Cellulase-like protein
umuC Compl. 69483-70760 UV protection
umuD Compl. 70766-71194 UV protection
dbp Compl. 71290-71562 Putative DNA-binding protein
tnpA 71687-72037 Putative transposase of ISKpn12
tnpA 72058-72447 Putative transposase of ISKpn12
σ′70 gene 72515-73066 σ′70 factor-like protein
tnpA Compl. 73591-74421 Putative transposase of ISKpn11
tnpA Compl. 74418-74750 Putative transposase of ISKpn11
aacC2 Compl. 75088-75948 Gentamicin-(3)-N-acetyl-transferase
blaTEM-1 Compl. 76090-76950 TEM-1 β-lactamase precursor
tnpR Compl. 77133-77726 TnpR resolvase of Tn2
tnpA 77695-80859 TnpA transposase of Tn2
strB*2 80893-81625 Streptomycin phosphotransferase (nonfunctional)
tnpB*2 Compl. 81597-81668 Putative transposase (nonfunctional)
tnpA 81732-82436 TnpA transposase of IS26-3
ΔtnpA 82489-82669 TnpA transposase of ISEcp1 (nonfunctional)
blaACC-4 82963-84123 ACC-4 cephalosporinase precursor
gdhA Compl. 84186-85100 Glutamate dehydrogenase
ΔtnpA Compl. 85123-85297 TnpA transposase of Tn2 (nonfunctional)
tnpA 85361-86065 TnpA transposase of IS26-4
orfB Compl. 86177-86626 Hypothetical protein
nikB Compl. 86694-89405 Relaxase
nikA Compl. 89417-89836 Relaxosome component protein
yggA 89976-90317 Hypothetical protein
ydiA Compl. 90403-91254 Hypothetical protein
ydhA Compl. 91376-91747 Hypothetical protein
ygeA 91831-92082 Hypothetical protein
orf14 Compl. 92113-92295 Hypothetical protein
ydgA Compl. 92358-93272 Hypothetical protein
ccgAII Compl. 93269-93658 Prevention of RecA overproduction
ygdA Compl. 93835-94197 Hypothetical protein
ygcA Compl. 94194-94628 Hypothetical protein
orf15 94747-95244 Hypothetical protein
ardA Compl. 95360-95860 Anti-restriction protein
ygaA Compl. 96330-96926 Hypothetical protein
psiA Compl. 96923-97642 Plasmid SOS inhibition protein A
psiB Compl. 97639-98073 Plasmid SOS inhibition protein B
yfhA Compl. 98128-100086 Hypothetical protein
orf16 100145-100378 Hypothetical protein
ssb Compl. 100436-100963 Single-stranded DNA-binding protein
orf17 101084-101557 Hypothetical protein
yffA Compl. 101735-101926 Hypothetical protein
yfeC Compl. 101926-102345 Hypothetical protein
yfeB Compl. 102392-102817 Hypothetical protein
yfdA Compl. 103234-104004 Hypothetical protein
yfcB Compl. 103961-104482 Hypothetical protein
yfcA Compl. 104496-104717 Hypothetical protein
yfbB Compl. 104714-105400 Hypothetical protein
yfbA Compl. 105474-105779 Hypothetical protein
yfaB Compl. 105783-106709 Hypothetical protein
yfaA Compl. 106723-106992 Hypothetical protein
impC 107104-107352 UV protection
impA 107349-107786 UV protection
impB 107786-109057 UV protection
parA-like gene 109258-110184 ParA-like partitioning protein
a

GenBank accession no. GU256641.

b

“Compl.” indicates that the gene is the reverse complement of the positions shown.

FIG. 1.

FIG. 1.

Overview of the IncB plasmid pR3521. The main regions as well as the indicative genes are shown in the outer circle (a complete list of genes can be found in Table 1). The next circle shows ORFs in the plus orientation and the 3rd-circle ORFs in the minus orientation. The innermost circle shows the G+C content plotted against the average G+C content of the entire plasmid sequence (52.6%). The inner circle plots the G+C skew. MDR, multidrug resistant.

Plasmid scaffold.

pR3521 possessed a single replication region of 1,368 bp (positions 5133 to 6500) identical to that of the IncB plasmid pMU707 (GenBank accession no. M93062) (23). It also exhibited significant similarities, ranging from 92 to 99%, with the replication regions of the IncI1 plasmids R64, pO113, pSERB1, and pEK204 (GenBank accession no. AP005147, AY258503, AY686591, and EU935740, respectively). The replication region of pR3521 included, apart from repA, two segments, RNAI and RNAII, that control copy number by inhibiting RepA translation through an antisense-RNA-mediated mechanism (27). The origin of replication (ori) located downstream of repA and the cis regulatory region between repA and ori were identical to those of pMU707 (22).

The relatively large transfer region of pR3521 (>50 kb; positions 6866 to 59455) was upstream of the RepA-encoding sequence and shared extensive structural as well as sequence similarities (71 to 98%) with the transfer regions of the IncI1 plasmids pO113, pSERB1, and pEK204 (7, 14, 28). The transfer region was organized in two blocks, tra and trb. tra (positions 6866 to 47247) included 12 pil genes (pilI and pilL to pilV), encoding thin pili required for liquid matings (11), as well as 22 additional genes, namely, traB, traC, traE, traF, traH to traK, and traL to traY, implicated in conjugal transfer (12). Between traC and pilI, the adhesin-encoding yqiJ and yqiK genes were identified (2). The transfer region also contained a sog gene upstream of traL. SogL is a SogS-regulated DNA primase suppressing dnaG mutations (16). trb (positions 54734 to 59455) comprised the trbABC operon, whose products are also involved in conjugation (9). In the region intervening between tra and trb, a segment including excA, analogous to the exc gene of IncI1 plasmids required for surface exclusion (8), along with pndA and pndC was identified. The products of the pnd genes contribute to plasmid maintenance (9). Also, 10 ORFs of unknown function were scattered throughout tra. The oriT operon, which included the origin of transfer and the nikA and nikB genes (whose products form a relaxation complex at the oriT site [10]), was distantly located from the trbABC operon due to insertion of a 26.4-kb acquired region in the sequence intervening between trbC and nikB. However, the oriT operon was apparently functional, as indicated by the self-transfer capability of pR3521 (18).

The plasmidic backbone also included the following: an ardA gene (positions 95367 to 95867), encoding an antirestriction protein; a psiBA operon (positions 96930 to 98080), whose products, PsiB and PsiA, inhibit the SOS response (1); and an ssb locus (positions 100443 to 100970), encoding Ssb, a single-stranded DNA protein (25). At positions 107104 to 109057, an impCAB operon, implicated in survival and induction of mutagenesis under UV irradiation, was found (24). pR3521 also possessed a parA-like gene, involved in segregational stability.

The close relationship of the rep regions of the complex I plasmids (IncI, -B, -K, and -Z) has been established in earlier studies (5, 17). The structure of the backbone of pR3521, being the first fully characterized IncB plasmid, extends this similarity to additional regions, such as tra, further supporting the common origin of these replicons.

Multidrug resistance region.

A 26.4-kb mosaic region was inserted into an ORF (here designated orfA) of the plasmidic backbone that corresponded to the LH0063 ORF of p0113 (GenBank accession no. AY258503) (Fig. 2). A remnant of the first 167 bp of orfA (orfA*1) was found at the boundary of the acquired region. A segment of 281 bp, exhibiting no significant homology with any known sequence, was adjacent to the remnant of orfA. This segment was followed by a noncoding sequence (302 bp), sul2, strA, and an strB gene with a truncation of the 3′ end (strB*1) similar to that described for plasmid RSF1010 (GenBank accession no. M28829). strAB could be a remnant of Tn5393, as suggested by the presence of an inverted repeat (IR) characteristic of this transposon (positions 64704 to 64758). The module comprising trbC, orfA*1, sul2, strA, and strB*1 has also been described to occur in other partially characterized IncB plasmids from E. coli (3).

FIG. 2.

FIG. 2.

Schematic diagram of the hypothetical successive steps (I to VI) leading to the evolution of the multiresistant acquired region of pR3521 (top of the figure). Sequences are drawn to scale. ORFs are shown by arrows indicating direction of transcription. The sequence depicted at the bottom of the figure is from the IncB-related pO113/IncI plasmid. Target site duplications (TSD) generated by transposition are indicated as DR1, DR2, and DR3. The complement and reverse sequences of DR1, DR2, and DR3 are indicated as DR1′, DR2′, and DR3′, respectively.

A fragment of a Tn2-like transposon including a 38-bp inverted repeat (IRbla) and blaTEM-1 was adjacent to strB*1. IS26-1, along with the remaining part of orfA (orfA*2), was located upstream of blaTEM-1. However, orfA*2 was in an orientation opposite to that expected, indicating an inversion event. The bounding sequence contained ΔtnpB (also designated rcr2 in the IncB plasmid p838B-R; GenBank accession no. HM749967), IS26, ΔtnpR, blaSCO-1, and a glycosidase-like gene (18). Downstream (1,118 bp) of the glycosidase gene, two probably chromosomal genes, umuC and umuD (needed for maximal SOS mutagenesis [26]), as well as dbp, encoding a putative DNA-binding protein (15), were identified. A mosaic sequence comprising ISKpn12, ISKpn11, aacC2, and a Tn2 transposon was located upstream of dbp. This region was highly homologous to a sequence carried by K. pneumoniae 12836 (15). The IRtnp repeat of Tn2 was adjacent to the remaining part of strB (strB*2). Direct repeats (DRs) of 5 bp (GACTC) (DR2 in Fig. 2) were found within the coding sequences of strB*1 and strB*2 at the boundaries of IRs of Tn2. Downstream of strB*2, there was the remaining part of tnpB (tnpB*2) adjoining IS26-3. Notably, 8-bp reverse and complement sequences were located at the boundaries of tnpB*1 (tnpB with a truncation of the 3′ end) and IS26-2 (GGAGATGA) (DR1′ in Fig. 2) and tnpB*2 (tnpB with a truncation of the 5′ end) and IS26-3 (TCATCTCC) (DR1 in Fig. 2) as well as orfA*2 and IS26-1 (CTTTGCCT) (DR3′ in Fig. 2) and orfB and IS26-4 (AGGCAAAG) (DR3 in Fig. 2). The reverse and complement orientation of these 8-bp sequences suggested IS26-mediated inversions. Upstream of the IS26-4 sequence was an ACC-4-encoding segment that has been described previously (19). This segment comprised an ISEcp1 element that was truncated (due to insertion of IS26-3), a fragment that originated from the chromosome of H. alvei (blaACC-4 and gdhA), and an IS26-4 sequence in parallel orientation with IS26-3, therefore forming a class I composite transposon.

Hypotheses on the formation of the acquired region.

The multiresistant region apparently arose from multiple insertions and DNA rearrangements (Fig. 2). A possible initial event could be the insertion of the RSF1010-originated module comprising sul2, strA, strB, and tnpB within orfA of pR3521 (possible step I). This hypothesis is corroborated by sequencing data from other IncB plasmids, such as p99309, p99051, and p99171, showing insertion of similar modules in orfA-like genes (3). A subsequent event could be the insertion of two IS26 elements, one disrupting the 3′ end of the tnpB gene and another inserted into the IncB scaffold in the sequence intervening between orfA*2 and orfB, thus creating 8-bp DRs at the boundaries of the elements (DR1 and DR3, respectively) (possible step II). Truncation of strB was likely due to transposition of a Tn2-like element, as indicated by the target site duplications (TSD) (DR2) flanking the IRs of the transposon (possible step III). Of note, the structure resulting from steps I, II, and III was similar to a sequence identified in the IncB plasmid p838B-R. A SCO-1-encoding segment (comprising blaSCO-1, the glycosidase gene, umuC, and umuD) and a module comprising ISEcp1, blaACC-4, and gdhA, both associated with IS26 elements, could then have been inserted within Tn2 (possible step IV). It was not clear whether ISKpn11 and ISKpn12 had been inserted independently or recruited in a single event along with Tn2. However, the latter notion is supported by the existence of a similar sequence (comprising umuD, dbp, ISKpn12, the σ′70 gene, ISKpn11, Tn1000, and the Tn2* hybrid) in K. pneumoniae 12836 (15). Homologous recombination between IS26-2 and IS26-3 and then recombination between IS26-1 and IS26-3 could be proposed as the final events in the evolution of the acquired region (possible steps V and VI). This assumption is in line with the reverse and complement orientation of the 8-bp sequences found within tnpB*1 (DR1′) and orfA*2 (DR3′). The related sequences discussed by Doloy et al. (6) and Partridge (20) underscore the central role of IS26 in the formation of this structure type.

Nucleotide sequence accession number.

The complete nucleotide sequence of plasmid pR3521 has been assigned GenBank accession no. GU256641.

Footnotes

Published ahead of print on 18 October 2010.

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