Genetics and regulation of outer membrane protein expression by quinolone resistance loci nfxB, nfxC, and cfxB.

Quinolone resistance mutations (cfxB1, marA1, and soxQ1) that reduce porin outer membrane protein OmpF map near 34 min on the Escherichia coli chromosome. Another such mutation, nfxC1, was found in strain KF131 (nfxB, 19 min). nfxC1 and cfxB1 mutants (selected with quinolones) differed slightly but reproducibly from marA1 (selected with tetracycline) and soxQ1 (selected with menadione) mutants in quinolone resistance and linkage to zdd2208::Tn10kan (33.7 min). For nfxB nfxC1 and cfxB1 mutants, as previously shown for marA mutants, resistance and reduced OmpF required the micF locus encoding an antisense RNA complementary to ompF mRNA and were associated with increased micF expression.     

Genetic and biochemical characterization of norfloxacin resistance in Escherichia coli.

In Escherichia coli the frequency of spontaneous single-step mutation to high levels of resistance to the newer 4-quinolone agent norfloxacin was confirmed to be over 300-fold lower than that to the older agent nalidixic acid. Serial passage on incremental concentrations of drug was necessary to produce mutants highly resistant to norfloxacin. Genetic analysis of one such highly resistant strain identified two mutations conferring drug resistance. One mutation, nfxA, mapped around 48 min on the E. coli genetic map and was shown to be an allele of gyrA by studies demonstrating an increased drug resistance of DNA gyrase reconstituted with the gyrase A subunit isolated from the mutant strain. These findings also identified the DNA gyrase A subunit as a target of norfloxacin. The second mutation, nfxB, mapped between 20 and 22 min was associated with additional resistances to tetracycline, chloramphenicol, and cefoxitin and with decreases in outer membrane porin protein OmpF. The nfxA and nfxB mutations together accounted for most, but not all, of the norfloxacin resistance phenotype of this strain.     

大肠埃希菌临床分离株对喹诺酮类抗菌药的质粒介导耐药

目的 了解近年来发现的质粒介导耐药机制在大肠埃希菌临床株对喹诺酮类耐药中所起的作用。方法 78株环丙沙星耐药菌株分离自上海5所教学医院。以克隆斑点杂交及Southern杂交方法筛选质粒介导耐药基因qnr；以接合试验了解喹诺酮耐药的可转移性；对qnr基因进行序列分析，以引物步移法对qnr周边质粒DNA进行测序、分析。结果 78株大肠埃希菌中，6株（7．7％）qnr检测阳性。在6株阳性菌中，喹诺酮耐药性均可通过质粒转移，接合子对环丙沙星的MIC较受体菌上升16～250倍。qnr基因与最早报道的序列一致，qnr位于In4族的Ⅰ类整合子上，本研究中的2个新整合子命名为In36及In37。结论 与qnr相关的质粒介导喹诺酮类耐药性在大肠埃希菌临床分离株中有一定程度流行，这可能是我国细菌对喹诺酮类耐药性上升迅速的原因之一。     

Novel quinolone resistance mutations of the Escherichia coli DNA gyrase A protein: enzymatic analysis of the mutant proteins.

Using the techniques of gap misrepair mutagenesis and site-directed mutagenesis, we have generated two novel quinolone resistance mutations of the Escherichia coli DNA gyrase A protein. DNA sequencing showed these mutations to be Ser-83----Ala and Gln-106----Arg. The mutant proteins were overproduced and purified, and their enzymatic properties were analyzed and compared with those of the wild-type enzyme. With ciprofloxacin and other quinolones, the inhibition of DNA supercoiling, relaxation, and decatenation and the induction of DNA cleavage were investigated for both wild-type and mutant enzymes. In each assay, the mutant enzymes were found to require approximately 10 times more drug to inhibit the reaction or induce cleavage than was the wild-type enzyme. However, the Ca2(+)-directed DNA cleavage reaction was indistinguishable for wild-type and mutant gyrases. We discuss models for the gyrase-mediated bactericidal effects of quinolone drugs.     

Emergence of plasmid-mediated quinolone resistance in Escherichia coli in Europe

Although quinolone resistance results mostly from chromosomal mutations, it may also be mediated by a plasmid-encoded qnr gene in members of the family Enterobacteriaceae. Thus, 297 nalidixic-acid resistant strains of 2,700 Escherichia coli strains that had been isolated at the Bicetre Hospital (Le Kremlin-Bicetre, France) in 2003 were screened for qnr by PCR. A single E. coli isolate that carried a ca. 180-kb conjugative plasmid encoding a qnr determinant was identified. It conferred low-level resistance to quinolones and was associated with a chromosomal mutation in subunit A of the topoisomerase II gene. The qnr gene was located on a sul1-type class 1 integron just downstream of a conserved region (CR) element (CR1) comprising the Orf513 recombinase. Promoter sequences for qnr expression overlapped the extremity of CR1, indicating the role of CR1 in the expression of antibiotic resistance genes. This integron was different from other qnr-positive sul1-type integrons identified in American and Chinese enterobacterial isolates. In addition, plasmid pQR1 carried another class 1 integron that was identical to In53 from E. coli. The latter integron possessed a series of gene cassettes, including those coding for the extended-spectrum beta-lactamase VEB-1, the rifampin ADP ribosyltransferase ARR-2, and several aminoglycoside resistance markers. This is the first report of plasmid-mediated quinolone resistance in Europe associated with an unknown level of plasmid-mediated multidrug resistance in Enterobacteriaceae.     

Plasmid-mediated quinolone resistance in clinical isolates of Escherichia coli from Shanghai,China

Although quinolone resistance usually results from chromosomal mutations, recent studies indicate that quinolone resistance can also be plasmid mediated. The gene responsible, qnr, is distinct from the known quinolone resistance genes and in previous studies seemed to be restricted to Klebsiella pneumoniae and Escherichia coli isolates from the University of Alabama in Birmingham, where this resistance was discovered. In Shanghai, the frequency of ciprofloxacin resistance in E. coli has exceeded 50% since 1993. Seventy-eight unique ciprofloxacin-resistant clinical isolates of E. coli from Shanghai hospitals were screened for the qnr gene by colony blotting and Southern hybridization of plasmid DNA. Conjugation experiments were done with azide-resistant E. coli J53 as a recipient with selection for plasmid-encoded antimicrobial resistance (chloramphenicol, gentamicin, or tetracycline) and azide counterselection. qnr genes were sequenced, and the structure of the plasmid DNA adjacent to qnr was analyzed by primer walking with a sequential series of outward-facing sequencing primers with plasmid DNA templates purified from transconjugants. Six (7.7%) of 78 strains gave a reproducible hybridization signal with a qnr gene probe on colony blots and yielded strong signals on plasmid DNA preparations. Quinolone resistance was transferred from all six probe-positive strains. Transconjugants had 16- to 250-fold increases in the MICs of ciprofloxacin relative to that of the recipient. All six strains contained qnr with a nucleotide sequence identical to that originally reported, except for a single nucleotide change (CTA-->CTG at position 537) encoding the same amino acid. qnr was located in complex In4 family class 1 integrons. Two completely sequenced integrons were designated In36 and In37. Transferable plasmid-mediated quinolone resistance associated with qnr is thus prevalent in quinolone-resistant clinical strains of E. coli from Shanghai and may contribute to the rapid increase in bacterial resistance to quinolones in China.     

Routes of quinolone permeation in Escherichia coli.

The uptake of quinolone antibiotics by Escherichia coli was investigated by using fleroxacin (RO 23-6240, AM 833) as a prototype compound. The uptake of fleroxacin was reduced and its MIC was increased in the presence of magnesium. Quinolones induced lipopolysaccharide release, increased cell-surface hydrophobicity and outer membrane permeability to B-lactams, and sensitized cells to lysis by detergents. These effects were also antagonized by magnesium and were very similar to those seen with EDTA and gentamicin. MICs of quinolones in portin-deficient strains were increased relative to those of the parent strain, consistent with a porin pathway of entry. However, MICs were further increased in the presence of magnesium; the size of the additional increase showed a positive correlation with quinolone hydrophobicity in an OmpF- OmpC- OmpA- strain. When quinolones were mixed with divalent cations in solution, changes in quinolone fluorescence suggestive of metal chelation were observed. The addition of fleroxacin to a cell suspension resulted in a rapid initial association of fluorescence with cells, followed by a brief decrease and a final time-dependent linear increase in cell-associated fluorescence. We interpret these results as representing chelation of outer membrane-bound magnesium by fleroxacin and other quinolones, dissociation of the quinolone-magnesium complex from the outer membrane, and diffusion of the quinolone through both porins and exposed lipid domains on the outer membrane. For a given quinolone, the contribution of the porin and nonporin pathways to total uptake is influenced by the hydrophobicity of the quinolone.     

Relationship between the expression of ompF and quinolone resistance in Escherichia coli

The outer membrane porin protein, OmpF, is widely found in gram-negative bacteria. It is known that the decreased expression of OmpF causes resistance to multiple antibiotics, including quinolones. In order to characterize the influence of decreased OmpF expression on bacterial growth, the fitness of the ompF and gyrA mutant strain of Escherichia coli selected experimentally with quinolone was compared with that of the parent strain. The expression levels of ompF in clinical isolates and the mutant selected with quinolone were determined by real-time PCR. The bacterial growth of the experimentally selected mutants was also measured both in vitro and in a urinary tract infection model in mice. Decreased ompF phenotypes were frequently found in clinical isolates that exhibited alteration of topoisomerases. The mutant experimentally obtained by the resistance selection process with quinolone showed no loss of fitness either in vitro or in vivo. These results suggest that the decreased expression of ompF and gyrA mutation do not affect the survival of the bacteria, and in fact may be responsible for the spread of high-level resistance to quinolones.     

Mechanisms of quinolone resistance in a clinical isolate of Escherichia coli highly resistant to fluoroquinolones but susceptible to nalidixic acid.

Two associated resistance mechanisms were found in a nalidixic acid-susceptible (4 micrograms/ml) but fluoroquinolone-resistant (8 to 16 micrograms/ml) strain of Escherichia coli Q2 selected under norfloxacin therapy. As compared with the susceptible E. coli Q1 isolated before treatment, changes in outer membrane proteins and lipopolysaccharides in Q2 were associated with a 1.5- to 3-fold decrease in the uptake of fluoroquinolones but not nalidixic acid. A 50% inhibition of DNA synthesis in toluene-permeabilized cells of the resistant strain E. coli Q2 required up to 500-fold increased quantities of fluoroquinolones, whereas such inhibition was obtained in both E. coli Q1 and Q2 with similar amounts of nalidixic acid. Selection from E. coli Q1 on norfloxacin of one-step resistant mutants resembling E. coli Q2 was unsuccessful. From these results we infer that a decrease in outer membrane permeability, associated with a peculiar alteration of the DNA gyrase, was responsible for the unusual quinolone resistance phenotype of E. coli Q2.     

质粒介导的大肠埃希菌和肺炎克雷伯菌耐喹诺酮类药物的研究

目的研究质粒介导的大肠埃希菌和肺炎克雷伯菌的流行情况及其对喹诺酮类药物耐药的作用。方法采用聚合酶链反应(PCR)对大肠埃希菌和肺炎克雷伯菌的qnr基因进行筛选,用实验证明qnr基因可以通过质粒介导并在细菌之间传递。结果在145株大肠埃希菌和125株肺炎克雷伯菌中共检出16株细菌携带qnr基因,其中12株为大肠埃希菌,4株肺炎克雷伯菌。16株qnr基因阳性菌株均为产超广谱内酰胺酶(ESBLs)菌株且呈多重耐药性。结论共检出16株细菌携带qnr基因,其阳性率为5.9%,大肠埃希菌阳性率高于肺炎克雷伯菌。qnr基因可以通过质粒介导,从供体菌接合转移至受体菌,且qnr在接合子中较稳定。     

Characterization of plasmid-mediated quinolone resistance determinants in Klebsiella pneumoniae and Escherichia coli from Tokai,Japan

The spread of plasmid-mediated quinolone resistance (PMQR) determinants was evaluated in 150 ceftazidime or cefotaxime-resistant clinical isolates of Klebsiella pneumoniae and Escherichia coli from Tokai, Japan between 2008 and 2011. In this study, qnrB, qnrS, and aac(6′)-Ib-cr genes were detected in 12 (50.0%), 4 (16.7%), and 1 (4.2%) of 24 K. pneumoniae isolates, respectively, while qnrA, aac(6′)-Ib-cr, and qepA genes were detected in 1 (0.8%), 11 (8.7%), and 2 (1.6%) of 126 E. coli isolates, respectively. qnr genes were mainly found in K. pneumoniae (66.7%) and to a lesser extent in E. coli (0.8%). We determined the genetic environment of the qnrB4 gene in 24.6 kb class 1 integron structure, including aar-2, cmlA, blaOXA-10, aadA1, qacEdelta1, sul1, and blaDHA-1. In a time-kill assay, introduction of the qnrB4 or qnrS1 plasmid to the recipient E. coli strain decreased the bactericidal activities of fluoroquinolones such as ciprofloxacin, levofloxacin, and pazufloxacin.     

Endogenous active efflux of norfloxacin in susceptible Escherichia coli.

Escherichia coli was shown to have an energy-dependent reduced uptake of the fluoroquinolone antimicrobial agent norfloxacin. Studies of everted inner membrane vesicles suggested that this reduced accumulation involved a carrier-mediated norfloxacin active efflux generated by proton motive force with an apparent Km of 0.2 mM and a Vmax of 3 nmol min-1 mg of protein-1. Other hydrophilic, but not hydrophobic, quinolones competed with norfloxacin for transport. Porin (OmpF)-deficient E. coli cells were twofold less susceptible to norfloxacin and showed twice as much energy-dependent reduction in drug uptake. However, active efflux assayed in everted vesicles from the OmpF strain was unchanged compared with that in the parental strain. These findings suggest that in the OmpF mutant decreased outer membrane permeability, combined with active efflux across the inner membrane, in some manner results in decreased steady-state uptake of norfloxacin and lowered drug susceptibility.     

A novel, double mutation in DNA gyrase A of Escherichia coli conferring resistance to quinolone antibiotics.

A spontaneous Escherichia coli mutant, named Q3, resistant to nalidixic acid was obtained from a previously described clinical isolate of E. coli, Q2, resistant to fluoroquinolones but susceptible to nalidixic acid (E. Cambau, F. Bordon, E. Collatz, and L. Gutmann, Antimicrob. Agents Chemother. 37:1247-1252, 1993). Q3 harbored the mutation Asp82Gly in addition to the Gly81Asp mutation of Q2. The different mutations leading to Gly81Asp, Asp82Gly, and Gly81AspAsp82Gly were introduced into the gyrA gene harbored on plasmid pJSW102, and the resulting plasmids were introduced into E. coli KNK453 (gyrAts) by transformation. The presence of Asp82Gly or Gly81Asp alone led to a low-level resistance to fluoroquinolones but not to nalidixic acid resistance. When both mutations were present, resistance to both nalidixic acid and fluoroquinolones was expressed. Purified gyrases of the different mutants showed similar rates of supercoiling. Dominance of the various gyrA mutant alleles harbored on plasmids was examined. The susceptibility to quinolones associated with wild-type gyrA was always dominant. The susceptibility to nalidixic acid expressed by the Gly81Asp mutant was dominant, while that expressed by the Asp82Gly mutant was recessive. From these results, we hypothesize that some amino acids within the quinolone resistance-determining region of gyrase A are more important for the association of subunits rather than for the activity of the holoenzyme.     

从患者胆汁分离的大肠埃希菌中质粒介导的氟喹诺酮类耐药基因的检测

目的 分析浙江省衢州市开化县第二人民医院消化内科胆汁分离的大肠埃希菌的耐药特点并调查质粒介导的喹诺酮类耐药基因的分布情况和流行特点。方法 收集该院消化内科患者2011年1月至2013年6月分离的大肠埃希菌724株,均为非重复性菌株,采用全自动微生物分析仪器VITEK 2 COMPACT进行细菌鉴定及药物敏感性分析,采用聚合酶链反应 (polymerase chain reaction,PCR)分析质粒介导的氟喹诺酮类耐药基因(plasmid-mediated quinolone resistance genes, PMQR) 如qnrA、qnrB、qnrS、aac(6')-Ib-cr和qepA 基因的流行特点。结果 胆源性大肠埃希菌的构成比达18.65%(135/724),其对环丙沙星和左氧氟沙星的耐药率高达61.5%(83/135)和55.6%(75/135),未检出碳青霉烯类抗生素耐药菌株;PCR检测PMQR基因结果显示:135株胆源性大肠埃希菌中,121株 (89.63%) qnrA1 基因阳性,45株(33.33%) qnrB4 基因阳性,32株 (23.70%) qnrB6 基因阳性,43株(31.85%) qnrS1 基因阳性,34株(25.19%) aac(6')-Ib-cr 基因阳性菌株,未检出qepA基因;其中45株(33.33%)同时携带 qnrA1、qnrB4 基因,32株(23.70%)同时携带 qnrA1、qnrB6, 25株(18.52%)同时携带 qnrA1、qnrB4、qnrS1, 21株(15.56%)同时携带 qnrA1、qnrB4、qnrS1、acc(6')-Ib-cr, 12株(100%)同时携带 qnrA1、qnrB6、qnrS1、acc(6')-Ib-cr, 且环丙沙星和左氧氟沙星的耐药率随着PMQR基因组合种类的增多而增多。结论 消化内科胆汁分离的大肠埃希菌氟喹诺酮类抗生素耐药严重,耐药基因主要以 qnrA1为主,qnrB4和qnrB6 次之,且存在多种PMQR基因组合形式,这些潜在播散的氟喹诺酮耐药基因对于临床胆道感染的治疗有很大的挑战。     

Relative contributions of the AcrAB,MdfA and NorE efflux pumps to quinolone resistance in Escherichia coli

Quinolones are widely used, broad-spectrum antimicrobial agents. In screens for genes that, when overexpressed, allow Escherichia coli to grow on otherwise lethal concentrations of the fluoroquinolone norfloxacin, the ydhE gene was identified. We have shown that ydhE encodes a multidrug efflux pump with a narrower substrate range than that of its closest homologue, encoded by norM, and named the gene norE. The relative contributions to drug resistance of NorE compared with the two other known E. coli quinolone pumps, AcrAB and MdfA, have been defined. Overexpression of each of the three pumps separately resulted in roughly similar levels of quinolone resistance, whereas simultaneous overexpression of norE or mdfA in combination with acrAB gave synergic increases in quinolone resistance. The level of quinolone resistance mediated by efflux pumps seems to be constrained to an approximately 10-fold maximum, even with increased production of the pumps. We measured the drug resistance of an isogenic set of strains containing the various permutations of single, double and triple drug efflux pump mutants. The DeltanorE and DeltamdfA mutants were somewhat more susceptible to fluoroquinolones than the parent strain, and acrAB mutants were four- to six-fold more susceptible. Mutants lacking two or all three efflux pumps were not significantly more susceptible to fluoroquinolones than those lacking only one of the three pumps.     

Plasmid-mediated quinolone resistance pump QepA2 in an Escherichia coli isolate from France

One hundred twenty-one extended-spectrum β-lactamse-producing enterobacterial clinical isolates were screened for the qepA gene. A single CTX-M-15-positive Escherichia coli isolate (0.8%) that produced the putative pump QepA2 was identified. This qepA2 gene was located onto a 90-kb mobilizable plasmid that conferred reduced susceptibility to hydrophilic fluoroquinolones.     

Mechanisms of beta-lactam and quinolone resistance in Haemophilus influenzae

Haemophilus influenzae is one of the important pathogens causing respiratory tract infections, pneumonia, and meningitis. Genotypic(g) beta-lactamase-nonproducing ampicillin resistance (gBLNAR) H. influenzae has rapidly increased since 2000 years in Japan. The resistant percentage exceeded 60% in Hib isolates from meningitis in 2009. The affinity of beta-lactam antibiotics for penicillin-binding proteins-3 (PBP3) that involved in septal peptidoglycan synthesis deceased in the resistant strains. Three amino acid substitutions, Ser385Thr, Asn526Lys and Arg517His in PBP3 encoded by ftsI gene are especially responsible for beta-lactam resistance in the gBLNAR. Susceptibilities of cephalosporin agents including cefotaxime for gBLNAR were apparently decreased than the ampicillin and carbapenem antibiotics. Though fluoroquinolone resistant isolates are rare (< 1%) in H. influenzae, strains of levofloxacin and ciprofloxacin MIC with > or = 8 microg/mL were isolated from elderly patients with CAP. These strains possessed amino acid substitutions of Ser84Phe and Asp88Asn in GyrA and Glu88Lys in ParC. It is important to practice rapidly identification of these resistant strains at routine work.     

住院患者肠道大肠埃希菌质粒介导喹诺酮类耐药基因研究

大肠埃希菌是肠道内主要定植菌,是耐药基因的重要储存库~([1]),其耐药水平直接关系到临床感染株的耐药水平,另外,肠道正常定植的大肠埃希菌还可将所携带的耐药基因传递给致病性大肠埃希菌、沙门菌及志贺菌等不同菌属~[2].     

Interaction of the plasmid-encoded quinolone resistance protein Qnr with Escherichia coli DNA gyrase

Quinolone resistance normally arises by mutations in the chromosomal genes for type II topoisomerases and by changes in the expression of proteins that control the accumulation of quinolones inside bacteria. A novel mechanism of plasmid-mediated quinolone resistance was recently reported that involves DNA gyrase protection by a pentapeptide repeat family member called Qnr. This family includes two other members, McbG and MfpA, that are also involved in resistance to gyrase inhibitors. Purified Qnr-His(6) was shown to protect Escherichia coli DNA gyrase directly from inhibition by ciprofloxacin. Here we have provided a biochemical basis for the mechanism of quinolone resistance. We have shown that Qnr can bind to the gyrase holoenzyme and its respective subunits, GyrA and GyrB. The binding of Qnr to gyrase does not require the presence of the complex of enzyme, DNA, and quinolone, since binding occurred in the absence of relaxed DNA, ciprofloxacin, or ATP. We hypothesize that the formation of Qnr-gyrase complex occurs before the formation of the cleavage complex. Furthermore, there was a decrease in DNA binding by gyrase when the enzyme interacted with Qnr. Therefore, it is possible that the reaction intermediate recognized by Qnr is one early in the gyrase catalytic cycle, in which gyrase has just begun to interact with DNA. Quinolones bind later in the catalytic cycle and stabilize a ternary complex consisting of the drug, gyrase, and DNA. By lowering gyrase binding to DNA, Qnr may reduce the amount of holoenzyme-DNA targets for quinolone inhibition.     

Mechanisms accounting for fluoroquinolone resistance in Escherichia coli clinical isolates

Fluoroquinolone MICs are increased through the acquisition of chromosomal mutations in the genes encoding gyrase (gyrA and gyrB) and topoisomerase IV (parC and parE), increased levels of the multidrug efflux pump AcrAB, and the plasmid-borne genes aac(6′)-Ib-cr and the qnr variants in Escherichia coli. In the accompanying report, we found that ciprofloxacin, gatifloxacin, levofloxacin, and norfloxacin MICs for fluoroquinolone-resistant E. coli clinical isolates were very high and widely varied (L. Becnel Boyd, M. J. Maynard, S. K. Morgan-Linnell, L. B. Horton, R. Sucgang, R. J. Hamill, J. Rojo Jimenez, J. Versalovic, D. Steffen, and L. Zechiedrich, Antimicrob. Agents Chemother. 53:229-234, 2009). Here, we sequenced gyrA, gyrB, parC, and parE; screened for aac(6′)-Ib-cr and qnrA; and quantified AcrA levels in E. coli isolates for which patient sex, age, location, and site of infection were known. We found that (i) all fluoroquinolone-resistant isolates had gyrA mutations; (ii) ~85% of gyrA mutants also had parC mutations; (iii) the ciprofloxacin and norfloxacin MICs for isolates harboring aac(6′)-Ib-cr (~23%) were significantly higher, but the gatifloxacin and levofloxacin MICs were not; (iv) no isolate had qnrA; and (v) ~33% of the fluoroquinolone-resistant isolates had increased AcrA levels. Increased AcrA correlated with nonsusceptibility to the fluoroquinolones but did not correlate with nonsusceptibility to any other antimicrobial agents reported from hospital antibiograms. Known mechanisms accounted for the fluoroquinolone MICs of 50 to 70% of the isolates; the remaining included isolates for which the MICs were up to 1,500-fold higher than expected. Thus, additional, unknown fluoroquinolone resistance mechanisms must be present in some clinical isolates.