Common Region CR1 for Expression of Antibiotic Resistance Genes

Abstract

The CR1 element defined by an orf513 gene encoding a putative recombinase and a recombination crossover site has been identified upstream of several antibiotic resistance genes in Enterobacteriaceae. This CR1 element was shown to bring promoter sequences that play a role in the expression of unrelated antibiotic resistance genes.

The role of class 1 integrons in acquisition, dissemination, and expression of antibiotic resistance genes is now well established in Enterobacteriaceae (1, 3, 8). Class 1 integrons possess two conserved features consisting of an integrase gene, intI1, in a so-called 5′ conserved sequence (5′-CS) and qacEΔ1 and sul1 genes in a so-called 3′ conserved sequence (3′-CS) (1). Promoter sequences that drive the expression of downstream-located antibiotic resistance genes have been identified in the 5′ end of the integrase gene (1). The complex class 1 integrons contain the 5′-CS and part of the 3′-CS flanking one or more gene cassettes (6). Following the 3′-CS is a region known as the common region (CR) consisting of orf513 and a recombination crossover site followed by genes that do not resemble a gene cassette and flanked by another copy of the qacEΔ1/sul1 complex (6). The encoded Orf513 may play a role in the integration of genes located nearby (mostly antibiotic resistance genes) (6). The orf513 gene and the 33-bp DNA sequence located at its right-hand boundary that may correspond to a recombination crossover site (RCS) are the common region CR1. We have recently shown that CR1 plays a role in the expression of the plasmid-mediated quinolone resistance qnrA gene by providing a promoter structure (5). The aim of the study was to analyze CR1 elements and their putative role in the expression of other antibiotic resistance determinants from nonrelated enterobacterial isolates. Six strains that encoded resistance determinants including QnrA and emerging extended-spectrum β-lactamases of the CTX-M type were included in this study (Table 1). Since the nucleotide sequence separating CR1 from the antibiotic resistance gene may vary, strains with different structures located upstream of identical qnrA and bla_CTX-M-9 genes were studied (Table 1). Primers used for PCR identification and sequencing of CR1 elements and associated resistance genes are shown in Table 2.

TABLE 1.

Characteristics of the clinical strains included in this study

Strain	Geographical origin	Gene	Distance separating CR1 from the resistance gene (bp)	Antibiotic resistancea	Source or reference
E. coli Lo	Bicêtre, France	qnrA	98	Quinolone	5
K. pneumoniae K149	Melbourne, Australia	qnrA	31	Quinolone	This study
E. coli B36	Madrid, Spain	blaCTX-M-9	94	ESBL	This study
K. pneumoniae KP40C	Madrid, Spain	blaCTX-M-9	94	ESBL	2
E. coli JAB	Bicêtre, France	blaCTX-M-2	266	ESBL	4
A. baumannii AYE	Bicêtre, France	dfrA10	149	TMP	7

^aESBL, extended-spectrum β-lactamase; TMP, trimethoprim.

TABLE 2.

Primers used in this study

Primer	Expt	Nucleotide sequence (5′-3′)	Location	Source or reference
ORF513D3	PCR	CTCACGCCCTGGCAAGGTTT	orf513	5
ORF513D5	PCR	CTTTTGCCCTAGCTGCGGT	orf513	5
QnrA	PCR	GGGTATGGATATTATTGATAAAG	qnrA	9
QnrB	PCR	CTAATCCGGCAGCACTATTA	qnrA	9
Pre-qnrA1	PCR	CGGCAGTTAAAATTGGGGCT	Upstream of qnrA	This study
Pre-qnrA2	PCR	GAGGGAATTTCAGGTAAGATAC	Upstream of qnrA	This study
CTX-MA1	PCR	SCSATGTGCAGYACCAGTAA	blaCTX-M	4
CTX-MA2	PCR	CCGCRATATGRTTGGTGGTG	blaCTX-M	4
dfrB	PCR	ATGCGCAGCATTTGGGTGTC	dfr	This study
dfrF	PCR	GTTATGGAGCAGCAACGATG	dfr	This study
GSP1-qnrA	5′-RACE	AAGTACATCTTATGGCTGACTTGA	qnrA	5
GSP2-qnrA	5′-RACE	ATGAAACTGCAATCCTCGAAACTG	qnrA	5
GSP3-qnrA	5′-RACE	TGGCTGAAGTCACACTGATAAAAG	qnrA	5
GSP1-blaCTX-M-9	5′-RACE	CCAGCGCATGACCCAGCGTAAC	blaCTX-M-9	This study
GSP2-blaCTX-M-9	5′-RACE	GCGTCATTGTGCCGTTGACGTGT	blaCTX-M-9	This study
GSP3-blaCTX-M-9	5′-RACE	GCACCGCACTCGTCTGCGCATA	blaCTX-M-9	This study
GSP1-blaCTX-M-2	5′-RACE	CGCGAGCGGCGTGGTGGTAT	blaCTX-M-2	This study
GSP2-blaCTX-M-2	5′-RACE	CGTTCATCGGCACGGTAGAGAA	blaCTX-M-2	This study
GSP3-blaCTX-M-2	5′-RACE	CCAAGCCGACCTCCCGAACTT	blaCTX-M-2	This study
GSP1-dfrA10	5′-RACE	GCACCCCAACCAGCGAAGCT	dfrA10	This study
GSP2-dfrA10	5′-RACE	GCACTTCGTGCTCTGTGATAGTT	dfrA10	This study
GSP3-dfrA10	5′-RACE	GCCTTGATTACCGAATGCTCT	dfrA10	This study

Mapping of the transcription start sites was performed by 5′ rapid amplification of cDNA ends (5′-RACE). Total RNA was isolated from the different strains studied using the RNeasy Midi kit (QIAGEN, Courtaboeuf, France). 5′-RACE reactions were performed using 5 μg of total RNA of each strain and the 5′-RACE System kit (version 2.0; Invitrogen Life Technologies, Cergy Pontoise, France) according the manufacturer's recommendations. After a reverse transcription step with gene-specific primer GSP1 and reverse transcriptase, the cDNA was tailed with terminal deoxynucleotidyl transferase and was subsequently amplified with another gene-specific primer, GSP2, combined with an oligo(dT) adapter primer provided with the kit (Table 2). This PCR product was used as a template for a nested PCR with another adapter primer and primer GSP3. The PCR product obtained was cloned into pCR-BluntII-Topo (Invitrogen), and the corresponding clones possessing the larger insert were sequenced. Analysis of the cloned sequence allowed the determination of the transcription initiation site(s), defined as the first nucleotide following the sequence of the adapter primer. Promoter sequences were determined subsequently. For each transcription assay, at least 10 clones were analyzed, and the entire experiment was repeated twice for all strains.

Identical CR1 elements were identified in all cases, and their 3′ ends are shown in Fig. 1. The CR1 element was associated with the qnrA gene in two cases, with bla_CTX-M-9 in two cases, with bla_CTX-M-2 in one case, and with the dfrA10 gene encoding trimethoprim resistance in one case (Table 1 and Fig. 1). The distance separating the RCS of CR1 from the start codon of the antibiotic resistance genes varied. This distance upstream of the qnrA gene was 98 and 31 bp for Escherichia coli Lo and Klebsiella pneumoniae K149, respectively (Table 1). An identical 94-bp region was identified between the RCS of CR1 and the start codon of the bla_CTX-M-9 gene in E. coli B36 and K. pneumoniae KP40. However, a 95-bp duplication was identified at the right-hand boundary of CR1 in E. coli B36 (Fig. 1). A 149-bp sequence was identified between CR1 and the dfrA10 gene in Acinetobacter baumannii AYE, whereas a 266-bp region was identified upstream of the bla_CTX-M-2 gene in E. coli JAB.

FIG. 1.

Promoter structures for the expression of antibiotic resistance genes as determined by 5′-RACE experiments for the qnrA gene from E. coli Lo and K. pneumoniae K149 (A), bla _CTX-M-9 from E. coli B36 and K. pneumoniae KP40C (B), dfrA10 from A. baumannii AYE (C), and bla_CTX-M-2 from E. coli JAB (D). The +1 initiation sites of transcription and the active promoter sequences are in boldface type. The −35 and −10 motifs of other promoters are boxed. Promoter P_CR1-2, which was identified previously for the qnrA gene in E. coli Lo, is indicated for the sake of consistency (5). The ATG start codons are capitalized. The right-hand boundary of the CR1 element is shaded in gray.

Analysis of the 5′-RACE PCR products obtained from QnrA-positive E. coli Lo revealed a single type of transcription product that was different from that previously reported (5). Although promoter P_CR1-2 has been identified previously (5), a +1 transcription site located 136 bp upstream of the qnrA gene led to the identification of another promoter, termed P_CR1-1 (Fig. 1). In the previous study, identification of the P_CR1-2 promoter was likely the result of selection of truncated transcripts during the 5′-RACE experiment. The same promoter, P_CR1-1, controlled the expression of the qnrA gene in K. pneumoniae K149, the bla_CTX-M-9 gene in E. coli strain B36 and in K. pneumoniae KP40C, and the dfr10 gene in A. baumannii AYE (Fig. 1). These results also indicated that promoter P_CR1-1, provided by the CR1 element, was active in Enterobacteriaceae and A. baumannii. The expression of the bla_CTX-M-2 gene in E. coli JAB depended on another promoter, P_ORI, located outside the CR1 element between the CR1 and the initiation codon of the resistance gene (Fig. 1).

Our results showed that CR1-mediated promoter sequences were involved in the expression of the qnrA, dfrA10, and bla_CTX-M-9 genes (Fig. 1) and that P_CR1-1 plays a major role in antibiotic resistance gene expression when CR1 is present. This study emphasizes that CR1 plays a significant role by providing promoter sequences for the expression of unrelated antibiotic resistance genes.